PMC_ID PMC_Year Journal IF Article Title Type of paper Secondary analysis Data availability statement (yes/no) Data availability with explaination(yes/no) Data availability (yes/no) "If Data availability = yes, where do they share data? (SRA/GEO/other)" "If other database, specifiy which one" Code availability statement (Yes/No) Code availability (Yes/No (reason)) Code availability (Yes/No) Reproducibility "If Code availability = yes, What kind of code do they share?" "If Code availability = yes, where do they share code (supplementary/ GitHub/ other)" "If Code availability = yes, do they share the code as notebook or R markdown file (.Rmd)? (yes/no)" "If yes, notebook/Rmd" "If yes, single/ multiple" Summary data (yes/ no/ partial) Number of citations Gender of the PI "Experience of PI/ Last author (Check their profile or webpage to see whether they are an associate/ assistant/ professor/ professor emiretus, etc)" PI/ last author's training background - CS/ Bioinformatics/ Other PI (last author's) education level - PhD/PostDoc/ Master's etc First author's education level First author's training background (CS/ Bioinformatics/ Other) PMC6686906 2019 Nat_Genet 28 Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture Research article hybrid yes yes for secondary/ no for primary no yes yes yes Package GitHub no yes 47 Male Associate Professor "CS, Bioinformatics" Postdoc MS Bioinformatics PMC7610512 2020 Nat_Genet 38.3 Regulation of single-cell genome organization into TADs and chromatin nanodomains Research article Hybrid yes yes for secondary/Available upon request for primary no yes yes yes Matlab scripts GitHub no yes 39 Male Research Director Other Postdoc Postdoc "Other, Genetics" PMC7343611 2020 Nat_Genet 38.3 Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases Research article Hybrid yes yes yes Other datadryad yes yes yes Analytical GitHub yes notebook multiple yes 31 Female Assistant Professor Other Phd Postdoc CS PMC6767648 2019 Genome_Med 11 Identifying Crohn’s disease signal from variome analysis Research article hybrid yes yes for secondary/ Available upon request for primary no no yes yes software Other (Website) no yes 58 Female Associate Professor Bioinformatics Phd Phd Bioinformatics PMC6862797 2019 Genome_Biol 9.5 Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize Research article no yes yes yes SRA no no no no no no no 74 Male Professor Other Phd Masters Other PMC6554452 2019 Nat_Biotechnol 37 Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts Research article no yes no no no no no no 59 Male Professor Other "MD,Phd" Phd Other PMC6894935 2019 Nat_Biotechnol 37 A highly soluble Sleeping Beauty transposase improves control of gene insertion Research article no yes Available upon request upon request no no no no 75 Female Professor Other Phd Phd Other PMC7145761 2019 Nat_Biotechnol 37 An electroencephalographic signature predicts antidepressant response in major depression Research article no yes yes yes other NIMH yes no (Cannot find the code) no no 70 Male Professor Other "MD,Phd" Postdoc Other PMC6858544 2019 Nat_Biotechnol 37 Targeted isolation and cultivation of uncultivated bacteria by reverse genomics Research article no yes yes yes SRA no no no no 94 Male Group Leader "Other,Genetics" Phd Phd Other PMC6730565 2019 Nat_Biotechnol 37 CRISPR DNA base editors with reduced RNA off-target and self-editing activities Research article no yes yes yes "SRA,GSE" yes no (available upon request) no no 24 Male Professor "Other,Genetics" "MD,Phd" MD Other PMC7065968 2019 Nat_Biotechnol 37 Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs Research article no yes yes yes GSE yes no (available upon request) no no 53 Male Professor Other Phd Phd Other PMC6974401 2019 Nat_Genet 28 Identifying cross-disease components of genetic risk across hospital data in the UK Biobank Research article no yes yes yes other treewas.org no no no no 45 Male Professor Other BA Postdoc Bioinformatics PMC6443099 2019 Nat_Genet 28 Transposable elements drive widespread expression of oncogenes in human cancers Research article no yes yes yes GSE yes no no yes 58 Male Professor Computational Biology Phd PMC6441365 2019 Nat_Genet 28 Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration Research article no yes yes yes GSE no no no no 52 Male Professor Other Phd Postdoc "Other, Genetics" PMC6546603 2019 Nat_Methods 31 Bioluminescent-based imaging and quantification of glucose uptake in vivo Research article no yes Available upon request upon request no no no no 46 Female Associate Professor Other Postdoc Postdoc Other PMC6549241 2019 Nat_Methods 31 "Aromatic 19F-13C TROSY: A background-free approach to probe biomolecular structure, function and dynamics" Research article no yes yes yes other https://artlab.dana-farber.org/19f_13c_aromatictrosy.html no no no no 53 Male Associate Professor Other Phd Postdoc Other PMC6532422 2019 Nat_Methods 31 A photo-cleavable surfactant for top-down proteomics Research article no yes yes yes other PRIDE no no no no 33 Female Professor Other Phd Postdoc Other PMC6599567 2019 Nat_Methods 31 LADL: Light-activated dynamic looping for endogenous gene expression control Research article no no no no yes no (available upon request) no no 28 Female Assistant Professor Other Phd Postdoc "Other, Genomics" PMC6885017 2019 Nat_Methods 31 Real-time volumetric microscopy of in-vivo dynamics and large-scale samples with SCAPE 2.0 Research article no yes Available upon request upon request yes no (available upon request) no no 51 Female Professor Other Postdoc Phd Other PMC6519746 2019 Nat_Methods 31 One-step generation of modular CAR-T with AAV-Cpf1 Research article no yes yes yes SRA yes no (available upon request) no no 37 Male Associate Professor "Other, Genetics" Postdoc Postdoc Other PMC6451109 2019 Nucleic_Acids_Res 11.5 SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite Research article no no no no no no no no no no no 58 Female Team Leader "Other, Genetics" Phd Postdoc "Other, Genetics" PMC6943129 2019 Nucleic_Acids_Res 11.5 A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming Research article no no no no no no no no no no no 99 Male Professor Other Phd PMC6468246 2019 Nucleic_Acids_Res 11.5 TRF2 positively regulates SULF2 expression increasing VEGF-A release and activity in tumor microenvironment Research article no no no no no no no no no no no 56 PMC6868433 2019 Nucleic_Acids_Res 11.5 Characterization of the Type III restriction endonuclease PstII from Providencia stuartii Research article no no no no no no no no no no no 68 Male Professor Other Phd PMC6895259 2019 Nucleic_Acids_Res 11.5 Citrus exocortis viroid causes ribosomal stress in tomato plants Research article no no no no no no no no no no no 70 Female Professor Other Phd MS Other PMC6736032 2019 Nucleic_Acids_Res 11.5 Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence Research article no yes yes yes GEO PDB no no no no 82 Male Associate Professor Other Postdoc Postdoc Other PMC7083059 2020 BMC_Bioinformatics 3.5 2D electrophoresis image brightness correction based on gradient interval histogram Research article no yes yes yes other supplementary files no no no no 18 Male Professor Other Phd PMC7310558 2020 Genome_Med 11.1 Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort Research article no yes Partial data available no other http://snd.gu.se/ no no no no 46 Male Professor Other Posddoc Postdoc Other PMC7315544 2020 Genome_Med 11.1 Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis Research article no yes yes yes GEO no no no no 59 Male Senior Research Associate "Other, Genetics" Postdoc PMC7031924 2020 Genome_Med 11.1 A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons Research article no yes yes yes Other Synapse and ucsc.edu no no no no 114 Male Professor Other "MD,Phd" Postdoc Bioinformatics PMC7008032 2020 Nat_Biotechnol 55 An integrated perfusion machine preserves injured human livers for 1 week Research article no yes Available upon request upon request no no no no 94 Male Professor Other MD MD Other PMC7854778 2020 Nat_Biotechnol 55 CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells Research article no yes yes yes SRA yes no (available upon request) no no 93 Male Professor "Other, Genetics" "MD, Phd" Phd Other PMC7878201 2020 Nat_Biotechnol 55 Single-cell metabolic profiling of human cytotoxic T cells Research article no yes yes yes Other Zenodo yes no (available upon request) no no 47 Male Professor Other Phd Postdoc Other PMC7610413 2020 Nat_Methods 28.6 Up to 100-fold speedup and multiplexing in optimized DNA-PAINT Research article no yes Available upon request upon request no no no no 33 Male Professor Other Postdoc Postdoc Other PMC7799389 2020 Nat_Methods 28.6 Time-resolved cryoEM using Spotiton Research article no yes Available upon request upon request no no no no 34 Female Adjunct Professor Other Phd Postdoc Other PMC7199528 2020 Nat_Methods 28.6 Kilohertz two-photon fluorescence microscopy imaging of neural activity in vivo Research article no yes Partial availability no no no no no 68 Female Associate Professor Other Postdoc Postdoc Other PMC7359951 2020 Nat_Methods 28.6 Deep three-photon imaging of the brain in intact adult zebrafish Research article no yes Available upon request upon request yes no (available upon request) no no 67 Male Professor Other Phd Postdoc "Other, Biostatistics" PMC7192605 2020 Nucleic_Acids_Res 17 A novel NGS library preparation method to characterize native termini of fragmented DNA Research article no yes yes yes SRA no no no no 45 Male Assistant Professor Other Phd Postdoc Other PMC7641733 2020 Nucleic_Acids_Res 17 HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA Research article no no no no no no no no 79 Male Professor Other Postdoc Postdoc Other PMC7797046 2020 Nucleic_Acids_Res 17 The nature of the modification at position 37 of tRNAPhe correlates with acquired taxol resistance Research article no no no no no no no no 77 Male Professor Other BSc Phd Other PMC7797069 2020 Nucleic_Acids_Res 17 The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis Research article no yes yes yes GEO no no no no 68 Male Professor Other Phd Phd Other PMC7826286 2020 Nucleic_Acids_Res 17 Chromatin structure restricts origin utilization when quiescent cells re-enter the cell cycle Research article no yes yes yes GEO no no no no 70 Female Professor "Other,Genetics" Phd Postdoc Other PMC7641319 2020 Nucleic_Acids_Res 17 Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT Research article no no no no no no no no 92 Male PostDoc Other Postdoc PMC8419911 2021 Genome_Biol 15.1 "Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection" Research article no yes yes yes SRA no no no no 0 Male Associate Professor CS Phd Postdoc Other PMC8082814 2021 Genome_Biol 15.1 The impact of cell type and context-dependent regulatory variants on human immune traits Research article no yes yes (Restricted) yes other EGA no no no no 4 Male Assistant Professor CS Postdoc B.S Other PMC7784034 2021 Genome_Biol 15.1 Histone modifications during the life cycle of the brown alga Ectocarpus Research article no yes yes yes GEO no no no no 7 Male Senior Researcher Other Phd Postdoc Other PMC8118107 2021 Genome_Biol 15.1 Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways Research article no yes yes yes GEO no no no no 0 Female Associate Professor Other Phd MD Other PMC7836461 2021 Genome_Med 12 Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trial Research article no yes Available upon request upon request yes no no no 2 Female Professor Other MD MD Other PMC8008663 2021 Genome_Med 12 Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae Research article no yes yes yes SRA no no no no 6 Male Professor Other "MD,Phd" MD Other PMC7610786 2021 Nat_Biotechnol 55 ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin Research article no yes yes yes Other EGA no no no no 12 Male Professor CS Postdoc Phd Other PMC7946812 2021 Nat_Genet 41.3 VisuaLife: library for interactive visualization in rich web applications Research article no yes yes yes other "dbgap,GWAS" no no no no 16 Female Professor Other "MD, Phd" Phd "Other, Genetics" PMC7954958 2021 Nat_Methods 48 Decoding the protein composition of whole nucleosomes with Nuc-MS Research article no yes yes yes other MassIVE no no no no 9 Male Professor Other Phd Phd Other PMC7968994 2021 Nucleic_Acids_Res 19.3 DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context Research article no no no no no no no no 15 PMC8421218 2021 Nucleic_Acids_Res 19.3 c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry Research article no yes yes yes other PDB no no no no 0 Male Researcher Other Postdoc Phd Other PMC8053121 2021 Nucleic_Acids_Res 19.3 A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis Research article no yes yes yes GEO no no no no 2 Male Professor PMC7897508 2021 Nucleic_Acids_Res 19.3 Crystal structure of a tick-borne flavivirus RNA-dependent RNA polymerase suggests a host adaptation hotspot in RNA viruses Research article no yes yes yes other Protein Data Bank no no no no 1 Male Professor Other Phd Phd CS PMC8216272 2021 Nucleic_Acids_Res 19.3 G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol Research article no yes yes yes other Protein Data Bank no no no no 1 Male Professor Other Phd Phd Other PMC7897473 2021 Nucleic_Acids_Res 19.3 Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism Research article no yes yes yes other Protein Data Bank no no no no 3 Male Professor Other Phd Phd Other PMC8136789 2021 Nucleic_Acids_Res 19.3 Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL Research article no yes yes yes GEO no no no no 2 Male Postdoc Researcher Other Phd Postdoc Other PMC5073995 2016 BMC_Bioinformatics 2.5 Successful classification of cocaine dependence using brain imaging: a generalizable machine learning approach Research article no yes no no no no no 27 Male Emeritus Professor Other MD Doctor CS PMC5123308 2016 BMC_Bioinformatics 2.5 An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees Research article no yes no no no no no 3 Male Professor Other Computational Biology PostDoc Phd Bioinformatics PMC4831157 2016 Genome_Biol 11.2 Single-cell analysis of long non-coding RNAs in the developing human neocortex Research article no yes yes yes GEO no no no 300 Male Professor Other Medicine MD MD Medicine PMC5131449 2016 Genome_Biol 11.2 Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease Research article no yes yes yes GEO no no no 35 Male Associate Professor Other Medicine MD PMC5048656 2016 Genome_Med 7.1 Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Research article no yes yes yes other ENA no no no 35 Female Professor Other Phd Phd Genomics PMC4752745 2016 Genome_Med 7.1 Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus Research article no yes yes yes other ENA no no no 24 Male Professor Other Phd Phd Other PMC5015242 2016 Genome_Med 7.1 Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring Research article no yes yes yes SRA no no no 14 Male Professor Other Phd PMC5180407 2016 Genome_Med 7.1 Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations Research article no yes yes yes other cBioPortal no no no 123 Male Other MD EdD Other PMC4942401 2016 Nat_Biotechnol 42 A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo Research article no no no no no no no 177 Male Associate Professor Other MD PMC4786489 2016 Nat_Biotechnol 42 A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice Research article no no no no no no no 484 Male Professor Other MD PMC5225075 2016 Nat_Biotechnol 42 Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array Research article no no no no no no no 572 Male Associate Professor Other Phd Phd Other PMC4980997 2016 Nat_Biotechnol 42 A recellularized human colon model identifies cancer driver genes Research article no no yes yes SRA no no no 80 Male Professor Other Phd Phd Other PMC4963286 2016 Nat_Genet 28 "Genome-wide association study of behavioral, physiological and gene expression traits in commercially available outbred CFW mice" Research article no no yes yes other Excel Sheets no no no 103 Male Professor Other Phd Phd Other PMC5289555 2016 Nat_Methods 25 Multi-domain structure and correlated dynamics determined by self-consistent FRET networks Research article no no yes yes other supplementary file no no no 109 Male Professor Other PostDoc PostDoc Other PMC5210665 2016 Nucleic_Acids_Res 10.2 DrugCentral: online drug compendium Research article no yes yes yes other Drug Center no no no 208 Male Professor Other MD-Phd Phd Other Computational Chemistry PMC5001587 2016 Nucleic_Acids_Res 10.2 Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression Research article no no yes yes other supplementary file no no no 18 Male Professor Other Phd PMC5333178 2017 BMC_Bioinformatics 2.6 Interactive exploration of ligand transportation through protein tunnels Research article no no no (Available upon request) upon request no no no 20 Female Associate Professor CS Phd Phd Bioinformatics PMC5599895 2017 Genome_Biol 11.6 Dynamic DNA methylation reconfiguration during seed development and germination Research article no yes yes yes GEO no no no 167 Male Professor Other Postdoc Phd Other PMC5604343 2017 Genome_Biol 11.6 DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A Research article no yes yes yes GEO no no no 150 Female Chair and Professor Other Postdoc Phd Other PMC5517843 2017 Genome_Biol 11.6 Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice Research article no yes yes yes other ENA no no no 181 Male Professor Postdoc Phd PMC5372248 2017 Genome_Med 9 Ethnic and diet-related differences in the healthy infant microbiome Research article no yes no no no no no 76 Female Professor Other "MD,Phd" Postdoc Other PMC5394620 2017 Genome_Med 9 Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers Research article no yes yes yes other precisionFDA no no no 45 Male Professor Other Postdoc Phd Bioinformatics PMC5693798 2017 Genome_Med 9 Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese Research article no yes yes yes other Project Mine web browser no no no 26 Male Head of Department Other "MD,Phd" Postdoc Other PMC5340623 2017 Nat_Biotechnol 36 Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit Research article no no no no no no no 349 Female Professor Other Phd Other PMC5462862 2017 Nat_Biotechnol 36 Generation of inner ear organoids with functional hair cells from human pluripotent stem cells Research article no no no no no no no 191 Female Professor Other Phd Phd Other PMC5340646 2017 Nat_Biotechnol 36 A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear Research article no no no no no no no 225 Male Associate Professor Other Phd "MD, Phd" Other PMC5462860 2017 Nat_Biotechnol 36 CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome Research article no yes yes yes GEO no no no 342 Male Professor Other Phd Phd Other PMC5722674 2017 Nat_Biotechnol 36 Generation of TCRs of higher affinity by antigen-driven differentiation of progenitor T cells in vitro Research article no yes yes yes other ImmuneACCESS no no no 28 Male Professor Other "MD,Postdoc" PMC5557292 2017 Nat_Biotechnol 36 Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions Research article no yes yes yes SRA no no (Available upon request) no 369 Male Associate Professor Other Postdoc Phd Other PMC5664152 2017 Nat_Genet 27.2 Germline hypomorphic CARD11 mutations in severe atopic disease Research article no yes no (Available upon request) upon request no no no 144 Male Professor Other MD PMC5803080 2017 Nat_Genet 27.2 SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters Research article no yes yes yes GEO no no no 168 Female Associate Professor Other Phd PMC5560095 2017 Nat_Genet 27.2 Kmt1e regulates a large neuron-specific topological chromatin domain Research article no yes yes yes GEO no no no 107 Male Professor Other "MD,Phd" Postdoc Other PMC5675000 2017 Nat_Genet 27.2 "Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands" Research article no yes yes yes other dbGaP no no no 498 Female Professor Other MD Phd Other Statistical Genetics PMC5490654 2017 Nat_Genet 27.2 Meta-analysis of five genome-wide association studies identifies multiple new loci associated with testicular germ cell tumor Research article no yes yes yes other EGA no no no 103 Female Professor Other MD Phd Other PMC5326681 2017 Nat_Genet 27.2 Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets Research article no yes yes yes other Biobank no no no 246 Male Professor PMC5709169 2017 Nat_Genet 27.2 Ancient hybridization and strong adaptation to viruses across African vervet monkey populations Research article no yes yes yes other NCBI SRA no no no 71 Male Associate Professor Other Postdoc Postdoc Computational Genomics PMC5659388 2017 Nat_Genet 27.2 Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma Research article no yes yes yes other IGCG no no (Available upon request) no 50 Male Professor Other "MD,Phd" Phd Other PMC5909187 2017 Nat_Methods 27 Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors Research article no yes no (Available upon request) upon request no no no 166 Male Professor Other Genetics "MD,Phd" Phd Epigenetics PMC5426913 2017 Nat_Methods 27 Generation of mature T cells from human hematopoietic stem/progenitor cells in artificial thymic organoids Research article no yes no (Available upon request) upon request no no no 117 Female Associate Project Scientist Other Phd "MD,Phd" Other PMC5636219 2017 Nat_Methods 27 Internally ratiometric fluorescent sensors for evaluation of intracellular GTP levels and distribution Research article no yes no (Available upon request) upon request no no no 43 Male Professor Other Genetics Phd Phd Other PMC5482233 2017 Nat_Methods 27 Large-field-of-view imaging by Multi-Pupil Adaptive Optics Research article no yes no (Available upon request) upon request yes no no 88 Male Assistant Professor Other Phd Postdoc Other PMC5730411 2017 Nat_Methods 27 Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics Research article no yes yes yes other NCBI no no no 73 Male Associate Professor Other Phd PMC5777571 2017 Nat_Methods 27 One-step generation of conditional and reversible gene knockouts Research article no yes yes yes other Addgene no no no 56 Male Group Leader Other Phd Phd Other PMC5678970 2017 Nat_Methods 27 Red-shifted luciferase-luciferin pairs for enhanced bioluminescence imaging Research article no yes yes yes other GenBank no no no 118 Male Associate Professor Other Postdoc Phd Other PMC5389697 2017 Nucleic_Acids_Res 11.6 Alternative lengthening of telomeres can be maintained by preferential elongation of lagging strands Research article no no no no no no no 51 Male Professor Other Phd Phd Other PMC5814900 2017 Nucleic_Acids_Res 11.6 Triggering nucleic acid nanostructure assembly by conditional kissing interactions Research article no no no no no no no 10 Male CSO Other Phd Postdoc Other PMC5570051 2017 Nucleic_Acids_Res 11.6 Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression Research article no no no no no no no 19 Male Associate Professor Other Phd PMC5861427 2017 Nucleic_Acids_Res 11.6 ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes Research article no no no no no no no 94 PMC5737895 2017 Nucleic_Acids_Res 11.6 ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes Research article no no no no no no no 13 Male Assistant Professor Other Postdoc Phd Other PMC5737570 2017 Nucleic_Acids_Res 11.6 The yeast 2-μm plasmid Raf protein contributes to plasmid inheritance by stabilizing the Rep1 and Rep2 partitioning proteins Research article no no yes yes other Genbank no no no 10 Female Professor Other Postdoc Postdoc PMC5870398 2018 Genome_Biol 12 Correction to: Redefining mouse transgenesis with CRISPR/Cas9 genome editing technology Research article no no no no no no no 38 Male Group Leader Other "MD, Phd" PMC6299574 2018 Genome_Biol 12 Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation Research article no yes yes yes GEO no no no 68 Male Head Other Genetics Phd PMC6305572 2018 Genome_Biol 12 SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing Research article no yes yes yes GEO no no no 32 Male Associate Professor Other Postdoc Postdoc Other PMC5830331 2018 Genome_Med 11 NSAID use and somatic exomic mutations in Barrett’s esophagus Research article no yes no (Available upon request) upon request no no no 18 BS Other PMC6286558 2018 Genome_Med 11 Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing Research article no yes yes yes other EGP no no no 97 Female Director "Other, Genetics" Postdoc Postdoc Other PMC6329375 2018 Nat_Biotechnol 32 Human ESC-Derived Cardiomyocytes Restore Function in Infarcted Hearts of Non-Human Primates Research article no no no no no no no 395 Male Professor Other "MD,Postdoc" Phd Other PMC6072461 2018 Nat_Biotechnol 32 Dual gene activation and knockout screen reveals directional dependencies in genetic networks Research article no yes yes yes SRA no no no 104 Male Professor "Other, Genetics" Postdoc Postdoc Other PMC6093211 2018 Nat_Biotechnol 32 ED SUM: Signaling by the neurotransmitter acetylcholine is monitored in cells and animals with a sensitive reporter. Research article no yes yes yes other Addgene no no no 0 Male Professor Other Phd Phd Other PMC6126964 2018 Nat_Biotechnol 32 Diseases caused by different mutations in the two alleles of a gene are treated in mice by Cas-9-induced allelic exchange. Research article no yes yes yes SRA no no no 0 Male Professor Other Postdoc Phd "Other, Genetics" PMC5990468 2018 Nat_Biotechnol 32 High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR/Cas9 in yeast Research article no yes yes yes SRA yes no (Available upon request) no 63 Male Professor Other Phd Phd PMC5942543 2018 Nat_Biotechnol 32 Simultaneous lineage tracing and cell-type identification using CRISPR/Cas9-induced genetic scars Research article no yes yes yes GEO yes no (Link expired) no 335 Male Group Leader Other Postdoc Phd Bioinformatics PMC6168378 2018 Nat_Genet 25.5 Genome-wide association analyses identify 39 new susceptibility loci for diverticular disease Research article no yes yes yes other UK Biobank no no no 74 Female Professor Other "MD,Phd" MD Other PMC5984618 2018 Nat_Genet 25.5 The Rosa genome provides new insights into the domestication of modern roses Research article no yes yes yes other DDBJ/ENA/GenBank no no no 256 Male Research Director Other Postdoc PMC5934307 2018 Nat_Genet 25.5 Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma Research article no yes yes yes other EGA no no no 170 Male Professor Other Postdoc Postdoc Other PMC6521726 2018 Nat_Genet 25.5 "Genetics of Blood Lipids Among ~300,000 Multi-Ethnic Participants of the Million Veteran Program" Research article no yes yes yes other dbGaP no no no 394 Male Associate Professor "Other, Biostatistics" "MD, Phd" MD Other PMC6677388 2018 Nat_Methods 28.5 Reliability of human 3D cortical organoid generation Research article no yes yes yes GEO no no no 230 Male Associate Professor Other Postdoc Postdoc "Other, Genetics" PMC6009585 2018 Nucleic_Acids_Res 11.2 The longevity SNP rs2802292 uncovered: HSF1 activates stress-dependent expression of FOXO3 through an intronic enhancer Research article no no no no no no no 53 Male Associate Professor Other "MD, Phd" Phd Other PMC5861426 2018 Nucleic_Acids_Res 11.2 Characterization of DNA ADP-ribosyltransferase activities of PARP2 and PARP3: new insights into DNA ADP-ribosylation Research article no no yes yes no no no 81 Phd Other PMC6182162 2018 Nucleic_Acids_Res 11.2 NAD+-dependent synthesis of a 5′-phospho-ADP-ribosylated RNA/DNA cap by RNA 2′-phosphotransferase Tpt1 Research article no no no no no no no 25 Male Professor Other "MD, Phd" Phd Other PMC5961129 2018 Nucleic_Acids_Res 11.2 Expanding RNA binding specificity and affinity of engineered PUF domains Research article no yes yes yes other Protein Data Bank no no no 33 Male Professor Other Postdoc PMC6212713 2018 Nucleic_Acids_Res 11.2 Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex Research article no yes yes yes GEO no no no 6 Female Professor Other Postdoc Postdoc Other PMC6379650 2018 Nucleic_Acids_Res 11.2 NMR solution structure of an asymmetric intermolecular leaped V-shape G-quadruplex: selective recognition of the d(G2NG3NG4) sequence motif by a short linear G-rich DNA probe Research article no yes yes yes other Protein Data Bank no no no 15 Male Professor Other Phd PMC6125643 2018 Nucleic_Acids_Res 11.2 "Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins" Research article no yes no no other Korea National Institute of Health yes no (Link expired) no 6 Male CEO Bioinformatics Phd MD Other PMC5048069 2016 Bioinformatics 7.3 PEP_scaffolder: using (homologous) proteins to scaffold genomes Research article no no no no yes no (Link Expired) no no 11 Assistant Professor PMC6660700 2019 Genome_Med 11 A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing Research article no yes no (Patient family consent) no no no no no 35 Male Professor "Other,Genetics" "MD,Postdoc" Phd Other PMC6489363 2019 Genome_Biol 9.5 Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification Research article no yes yes yes SRA yes yes yes Package Zenodo no yes 56 Male Director of Reseach Other Phd Phd Other PMC6816165 2019 Genome_Biol 9.5 RaGOO: fast and accurate reference-guided scaffolding of draft genomes Research article no yes yes yes SRA yes yes yes Package GitHub no yes 59 Male Professor CS Phd Phd CS PMC6954335 2019 Nat_Biotechnol 37 In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription Research article no yes yes yes other caltech.edu yes yes yes software no no 70 Male Professor Other Phd Postdoc Other PMC6587591 2019 Nat_Biotechnol 37 Capturing sequence diversity in metagenomes with comprehensive and scalable probe design Research article no yes yes yes SRA yes yes yes Package GitHub no yes 75 Male Director Other Postdoc Phd CS PMC6956735 2019 Nat_Biotechnol 37 A community effort to create standards for evaluating tumor subclonal reconstruction Research article no yes yes yes other EGA yes yes yes Package GitHub no yes 53 Male Professor Other Phd Phd Other PMC6893138 2019 Nat_Biotechnol 37 High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell Research article no yes yes yes GSE yes yes yes Package GitHub no yes 19 Male Professor Other Phd Postdoc Other PMC6756480 2019 Nat_Genet 28 A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition Research article no yes yes yes GSE yes yes yes Package GitHub no yes 64 Male Associate Professor CS Postdoc Phd Other PMC6755913 2019 Nat_Genet 28 The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting Research article no yes yes yes GSE yes yes yes Package GitHub no yes 39 Female Associate Professor Other Phd Postdoc "Other, Genetics" PMC7451045 2019 Nat_Genet 28 Neuronal impact of patient-specific aberrant NRXN1α splicing Research article no yes yes yes "SRA,GEO" yes yes yes Package GitHub no yes 83 Female Professor Other Phd Phd Other PMC6949130 2019 Nat_Methods 31 DIA-NN: Neural networks and interference correction enable deep proteome coverage in high throughput Research article no yes yes yes other PRIDE yes yes yes Software GitHub no yes 32 Male Professor "Other, Genetics" Phd PMC7004891 2019 Nat_Methods 31 An adaptive excitation source for high speed multiphoton microscopy Research article no yes Available upon request upon request yes yes yes Matlab GitHub no no 21 Male Professor Other Phd Postdoc CS PMC6675608 2019 Nat_Methods 31 Gene expression atlas of a developing tissue by single cell expression correlation analysis Research article no yes yes yes GSE yes yes yes software GitHub yes Rmd single yes 32 Male Professor Other Postdoc Phd Other PMC7038986 2019 Nucleic_Acids_Res 11.5 Disentangling sRNA-Seq data to study RNA communication between species Research article no yes yes yes GEO no yes yes pipeline GitHub yes Rmd single no 66 Male Assistant Professor Other Phd Phd Other PMC7718714 2020 BMC_Bioinformatics 3.5 Regional registration of whole slide image stacks containing major histological artifacts Research article no yes no no yes yes yes Pipeline GitHub no partial 28 Male Head of Division Other Phd Phd CS PMC6979394 2020 Genome_Biol 11.7 CUBIC: an atlas of genetic architecture promises directed maize improvement Research article no yes yes yes SRA no yes yes Package GitHub no no 82 Male Professor "Other, Genetics" Phd Phd Other PMC7523332 2020 Genome_Med 11.1 Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions Research article no yes yes yes GEO yes yes yes Package GitHub no no 44 Male Assistant Professor Other Phd Phd Other PMC7036260 2020 Genome_Med 11.1 Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer Research article no yes yes yes GEO yes yes yes Analytical GitHub no yes 78 Male Professor "CS,Genetics" "MD,Postdoc" PMC7708171 2020 Genome_Med 11.1 Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study Research article no yes Available upon request upon request no yes yes Package GitHub yes Rmd multiple no 63 Male Head of Research Computational Biology Phd Phd Other PMC7416462 2020 Nat_Biotechnol 55 Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing Research article no yes yes yes GEO yes yes yes Analytical 10xGenomics yes notebook multiple yes 64 Female Assistant Professor "Other, Genetics" Phd Phd "Other, Genetics" PMC7541396 2020 Nat_Biotechnol 55 Analyzing the M. tuberculosis immune response by T cell receptor clustering with GLIPH2 and genome-wide antigen screening Research article no yes no no yes yes yes software downloadable file uncertain uncertain uncertain no 65 Male Professor Other Phd Phd "Other, Biotechnology" PMC7855056 2020 Nat_Biotechnol 55 A long-term study of AAV gene therapy in hemophilia A dogs identifies clonal expansions of transduced liver cells Research article no yes yes yes "SRA,other" Zenodo yes yes yes uncertain Zenodo no yes 42 Female Assistant Professor "Other, Genetics" Phd B.S Other PMC7610456 2020 Nat_Genet 38.3 The mutational signature profile of known and suspected human carcinogens in mice Research article no yes yes yes other ENA yes yes yes Analytical GitHub no yes 23 Male Senior Group Leader Other Phd Phd Other PMC7808397 2020 Nat_Genet 38.3 Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses Research article no yes Available upon request upon request yes yes yes Package GitHub no yes 66 Female Principal Investigator Other "MD, Phd" Postdoc "Other, Biostatistics" PMC7343625 2020 Nat_Genet 38.3 Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases Research article no yes yes yes other European Genotype Phenotype Archive yes yes yes Analytical GitHub no yes 70 Female Associate Professor Bioinformatics Phd PMC7796998 2020 Nat_Genet 38.3 Genetic screening for single-cell variability modulators driving therapy resistance Research article no yes yes yes GEO yes yes yes Package GitHub no yes 16 Male Professor Other Phd "MD, Phd" Other PMC7138649 2020 Nat_Genet 38.3 Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia Research article no yes yes yes GEO yes yes yes pipeline GitHub no yes 39 Male Professor "CS, Bioinformatics" Postdoc Phd "CS,Bioinformatics" PMC7192636 2020 Nat_Methods 28.6 Rapid mesoscale volumetric imaging of neural activity with synaptic resolution Research article no yes Available upon request upon request yes yes yes Matlab scripts Supplementary no yes 47 Female Associate Professor Other Postdoc Phd Other PMC7541687 2020 Nat_Methods 28.6 Detecting chromatin interactions between and along sister chromatids with SisterC Research article no yes yes yes GEO yes yes yes pipeline GitHub no no 6 Male Professor Other Phd Phd Other PMC7357298 2020 Nat_Methods 28.6 Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors Research article no yes yes yes GEO yes yes yes Analytical GitHub yes notebook multiple no 19 Male Professor Computational Neuroscience "Phd,MBA" Phd Other PMC7544197 2020 Nucleic_Acids_Res 17 Unbiased investigation of specificities of prime editing systems in human cells Research article no yes yes yes SRA yes yes yes Package GitHub no yes 47 Male Head Other Phd Phd Other PMC7945310 2021 Genome_Biol 15.1 Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction Research article no yes yes yes SRA yes yes yes Package Zenodo no yes 4 Male Professor "Other, Genetics" Postdoc Phd Other PMC8273981 2021 Genome_Biol 15.1 Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair Research article no yes yes yes SRA yes yes yes Shell Script GitHub no yes 3 Male Postdoc Reseacher "Other, Genetics" Phd Phd Other PMC7798263 2021 Genome_Biol 15.1 Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences Research article no yes yes yes Other PRIDE yes yes yes Package GitHub no yes 3 Male Associate Professor CS Postdoc Postdoc Bioinformatics PMC8375061 2021 Genome_Med 12 Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus Research article no yes yes yes other ENA yes yes yes Analytical Zenodo no yes 1 Male Associate Professor Phd Bioinformatics PMC8438989 2021 Genome_Med 12 Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study Research article no yes yes yes Other Genebank yes yes yes Package GitHub no yes 0 Male Head of Divison Other Postdoc Phd Other PMC8011839 2021 Nat_Genet 41.3 Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens. Research article no yes yes yes GEO yes yes yes Package GitHub no no 18 Male Professor Other Postdoc Phd Other PMC8038968 2021 Nat_Genet 41.3 Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution Research article no yes yes yes GEO yes yes yes Package GitHub no yes 6 Male Assistant Professor Other Phd Postdoc Other PMC7610396 2021 Nat_Genet 41.3 A Unique Bipartite Polycomb Signature Regulates Stimulus-Response Transcription during Development Research article no yes yes yes other ArrayExpress yes yes yes Package GitHub no yes 3 Male Professor Other Postdoc PMC7946813 2021 Nat_Genet 41.3 Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics Research article no yes yes yes GEO yes yes yes Package GitHub no yes 15 Male Professor Other Phd Phd "Other, Biomedical Science" PMC8148035 2021 Nat_Genet 41.3 Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction Research article no yes yes yes other dbgap yes yes yes Analytical GitHub no yes 44 Male Co-Leader Other ScD Phd "Other,Genetics" PMC7944648 2021 Nat_Genet 41.3 Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics Research article no yes yes yes SRA "dbgap,ENA" yes yes yes Analytical GitHub no yes 11 Male Head Other Postdoc Postdoc Bioinformatics PMC7611018 2021 Nat_Methods 48 Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells Research article no yes yes yes other EMDB yes yes yes Software GitHub no yes 39 Female Group Leader Other Postdoc Postdoc CS PMC8107123 2021 Nat_Methods 48 Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning Research article no yes yes yes other zenodo yes yes yes Pipeline GitHub yes notebook multiple no 16 Male Professor Other Postdoc Phd Other PMC7954905 2021 Nat_Methods 48 Joint profiling of histone modifications and transcriptome in single cells from mouse brain Research article no yes yes yes GEO yes yes yes Pipeline GitHub no yes 20 Male Professor Other Phd Phd Other PMC7954949 2021 Nat_Methods 48 Joint probabilistic modeling of single-cell multi-omic data with totalVI Research article no yes yes yes GEO yes yes yes Analytical GitHub yes notebook multiple yes 31 Male Associate Professor Other Phd Phd CS PMC8272231 2021 Nat_Methods 48 Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia Research article no yes yes yes GSE PRIDE yes yes yes Package GitHub yes Rmd multiple yes 2 Male Professor "Other, Genetics" "MD, Phd" Postdoc Other PMC5059998 2016 Genome_Biol 11.2 Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements Research article no yes yes yes GEO yes yes yes Protocol GitHub no 61 Male Associate Professor Other Phd Phd Other PMC5032245 2016 Genome_Biol 11.2 Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms Research article no yes yes yes other EGA no yes yes Package GitHub yes Rmd multiple 92 Male Professor Other PostDoc Phd Other PMC5143225 2016 Nat_Biotechnol 42 Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation Research article no no no no no yes yes Pipeline GitHub yes Rmd Single 127 Male Professor Other Phd Phd Computational Biology PMC5125825 2016 Nat_Biotechnol 42 Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions Research article no no yes yes other GSE no yes yes Pipeline GitHub no 118 Male Professor CS Phd Phd CS PMC5101133 2016 Nat_Biotechnol 42 Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling Research article no no yes yes other Excel Sheets no yes yes Analytical GitHub no 100 Male Professor Other PostDoc MD Other PMC5423094 2016 Nat_Methods 25 RESA identifies mRNA regulatory sequences with high resolution Research article no yes yes yes other SRP no yes yes Pipeline GitHub no 37 Male Professor Other PostDoc Phd Other Genetics PMC5330809 2016 Nat_Methods 25 Massively multiplex single-cell Hi-C Research article no yes yes yes GEO no yes yes Analytical GitHub no 421 Male Professor Other-Genetics MD-Phd Phd Other PMC4772672 2016 Nat_Methods 25 Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis Research article no yes yes yes GEO no yes yes Package GitHub yes Rmd Multiple 323 Male Associate Professor Other Computational Biology and Genomics PostDoc PostDoc Bioinformatics PMC5745977 2017 BMC_Bioinformatics 2.6 "A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy" Research article no yes yes yes other GB-eaSy pipeline yes yes yes Pipeline GitHub no 51 Male Professor Other Phd Phd Bioinformatics PMC5366155 2017 Genome_Biol 11.6 MeDeCom: discovery and quantification of latent components of heterogeneous methylomes Research article no yes yes yes GEO yes yes yes Package GitHub yes Rmd Single 72 Male Professor Postdoc PMC5709945 2017 Genome_Biol 11.6 OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps Research article no yes yes yes other Zenodo yes yes yes Pipeline GitHub no 28 Male Professor CS Postdoc PMC5473967 2017 Genome_Biol 11.6 Translational contributions to tissue specificity in rhythmic and constitutive gene expression Research article no yes yes yes GEO yes yes yes Analytical GitHub no 43 Male Associate Professor Other Postdoc Phd Other PMC5260019 2017 Genome_Med 9 "Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal" Research article no yes yes yes other CBI Sequence Read Archive repository yes yes yes Pipeline GitHub no 36 Female Professor Other Phd Phd Other PMC5800952 2017 Nat_Biotechnol 36 Orthologous CRISPR-Cas9 enzymes for Combinatorial Genetic Screens Research article no yes yes yes other zip file yes yes yes Pipeline GitHub no 201 Male Director of Research Other Phd Phd Other PMC5334791 2017 Nat_Methods 27 Pooled CRISPR screening with single-cell transcriptome read-out Research article no yes yes yes other gb file yes yes yes Analytical "GitHub, Supplementary" no 557 Male Professor Bioinformatics Postdoc Phd Other PMC5766199 2017 Nucleic_Acids_Res 11.6 CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome Research article no no no no no yes yes Pipeline GitHub no 37 Male Professor Bioinformatics Postdoc Phd Bioinformatics PMC5984373 2018 Genome_Biol 12 UMI-count modeling and differential expression analysis for single-cell RNA sequencing Research article no yes yes yes GEO yes yes yes Pipeline Other (Bitbucket) yes Rmd Single 63 Male Assistant Member Other Computational Biology Postdoc Postdoc CS PMC5872584 2018 Genome_Med 11 Elevated polygenic burden for autism is associated with differential DNA methylation at birth Research article no yes no (Available upon request) upon request yes yes yes Analytical GitHub no 77 Male Professor "Other, Genetics" Postdoc Phd "Other, Genetics" PMC6488461 2018 Nat_Biotechnol 32 Identification of spatially associated subpopulations by combining scRNA-seq and sequential fluorescence in situ hybridization data Research article no no yes yes GEO no yes yes Tool Bitbucket no 141 Male Professor Other Postdoc Phd Other PMC6380887 2018 Nat_Methods 28.5 Inferring single-trial neural population dynamics using sequential auto-encoders Research article no yes no (Available upon request) upon request yes yes yes Pipeline GitHub no 353 Male Adjunt Professor "Other, Computational Neuroscience" Postdoc Postdoc Other PMC5990454 2018 Nat_Methods 28.5 Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads Research article no yes yes yes SRA yes yes yes Pipeline GitHub no 66 Female Professor Other Postdoc Postdoc "Other, Genetics" PMC6152898 2018 Nat_Methods 28.5 Improved Ribo-seq enables identification of cryptic translation events Research article no yes yes yes other PXD yes yes yes Pipeline GitHub 100 Male PMC5254078 2016 Bioinformatics 7.3 FoldAtlas: a repository for genome-wide RNA structure probing data Research article no yes yes yes SRA yes yes yes Pipeline/Software code/Tool no GitHub no 13 Female Group Leader Other PostDoc PMC6661746 2019 Genome_Med 11 Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data Research article no yes yes yes Geo yes yes yes Pipeline Other (Website) no no 66 Male Professor "Other,Biomedical Engineering" Phd Postdoc Bioinformatics PMC6612848 2019 Bioinformatics 5.6 Large-scale mammalian genome rearrangements coincide with chromatin interactions Research article yes no yes no (No access on BitBucket) no pipeline BitBucket no no 56 Male Professor CS Postdoc Postdoc CS PMC6937815 2019 BMC_Bioinformatics 3.8 Benchmarking the PEPOP methods for mimicking discontinuous epitopes Research article yes yes no no no no no no no 62 Female Deputy Director Other Phd PMC6886252 2019 BMC_Bioinformatics 3.8 Liver tumor segmentation in CT volumes using an adversarial densely connected network Research article yes yes no no no no no no no 33 Male Professor CS Phd Phd CS PMC6821021 2019 BMC_Bioinformatics 3.8 Predicting protein inter-residue contacts using composite likelihood maximization and deep learning Research article yes yes yes no (link does Not work) no no no no no 59 Male Associate Professor CS Phd Postdoc CS PMC6929343 2019 BMC_Bioinformatics 3.8 An automated 3D modeling pipeline for constructing 3D models of MONOGENEAN HARDPART using machine learning techniques Research article yes yes no no no no no no no 36 Female Associate Professor "CS, Bioinformatics" Phd Phd Bioinformatics PMC6557762 2019 BMC_Bioinformatics 3.8 A new fruit fly optimization algorithm enhanced support vector machine for diagnosis of breast cancer based on high-level features Research article yes yes no no no no no no no 49 Male Associate Chief Physician Other MD PMC6528302 2019 BMC_Bioinformatics 3.8 Weekly ILI patient ratio change prediction using news articles with support vector machine Research article yes yes no no no no no no no 19 Female Team Leader "Other, Biotechnology" Phd PMC6827178 2019 BMC_Bioinformatics 3.8 Predictive modelling using pathway scores: robustness and significance of pathway collections Research article yes yes no no no no no no no 25 Male Professor Other Postdoc PMC6463664 2019 Genome_Biol 9.5 Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency Research article yes yes no no no no no no no 54 Male Professor Other Phd Phd Bioinformatics PMC6631995 2019 Genome_Biol 9.5 "Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation" Research article yes yes no no no no no no no 54 Male Senior Investigator Computational Biology Phd Phd "Other,Information Technology" PMC6698742 2019 Nucleic_Acids_Res 11.5 Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise Research article yes no no no no no no no no 80 Male Assistant Professor Other MS MS Bioinformatics PMC7145579 2019 Nucleic_Acids_Res 11.5 TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites Research article yes no no no no no no no no 37 Male Professor Other Phd Phd Bioinformatics PMC7646399 2020 BMC_Bioinformatics 3.5 "Developing the novel bioinformatics algorithms to systematically investigate the connections among survival time, key genes and proteins for Glioblastoma multiforme" Research article yes yes no no no no 53 Male Professor CS Postdoc PMC7367324 2020 BMC_Bioinformatics 3.5 Deep user identification model with multiple biometric data Research article yes yes no no no no 14 Male Associate Professor "Other, Information Technology" Phd Phd Other PMC7671827 2020 BMC_Bioinformatics 3.5 Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks Research article yes yes no no no no 21 Male Professor Bioinformatics Phd Phd CS PMC7778890 2020 Nucleic_Acids_Res 17 "RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions" Research article yes yes no no no no 53 Male Professor Other Postdoc PMC7779005 2020 Nucleic_Acids_Res 17 DualSeqDB: the host–pathogen dual RNA sequencing database for infection processes Research article yes yes no no no no 26 Male Associate Professor Other Postdoc Phd Bioinformatics PMC7989618 2021 Bioinformatics 6.6 COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases Research article yes no no no no no 13 Male Professor Other "MD, Phd" Phd CS PMC8052714 2021 BMC_Bioinformatics 3.4 Cancer immune control dynamics: a clinical data driven model of systemic immunity in patients with metastatic melanoma Research article yes yes no no no no 0 Male Faculty Other "MD,Phd" MD Other PMC8011138 2021 BMC_Bioinformatics 3.4 Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression Research article yes yes no no no no 2 Male Professor Postdoc Other PMC7852121 2021 BMC_Bioinformatics 3.4 Search for SINE repeats in the rice genome using correlation-based position weight matrices Research article yes yes no no no 0 Male Professor Other Phd Phd Bioinformatics PMC8340473 2021 Genome_Biol 15.1 Community-wide hackathons to identify central themes in single-cell multi-omics Research article yes no no no no no 1 Female Director of Division "Other, Computational Biology" Phd Phd Other PMC7845089 2021 Genome_Med 12 Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later Research article yes yes no no no no 7 Male Professor Other Phd Phd Bioinformatics PMC7611259 2021 Nat_Genet 41.3 Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect Research article yes yes no no no no 29 PMC7897485 2021 Nucleic_Acids_Res 19.3 A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis’ Research article yes no no no no no 7 Female Associate Professor Other Postdoc PMC5139036 2016 BMC_Bioinformatics 2.5 Integrating mean and variance heterogeneities to identify differentially expressed genes Research article yes yes no no no 4 Male Assistant Professor Other PostDoc Phd Biostatistics PMC4826549 2016 BMC_Bioinformatics 2.5 Structured feature selection using coordinate descent optimization Research article yes no no no no 28 Male Professor Phd CS PMC5259871 2016 BMC_Bioinformatics 2.5 Dynamic epigenetic mode analysis using spatial temporal clustering Research article yes yes no no no 3 PMC5075203 2016 BMC_Bioinformatics 2.5 Subcellular protein expression models for microsatellite instability in colorectal adenocarcinoma tissue images Research article yes yes yes no (Available upon request) no 1 Male Professor CS Phd Phd PMC5259813 2016 BMC_Bioinformatics 2.5 "Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features" Research article yes yes supplementary file no no (Available upon request) no 26 Female Associate Professor CS and Bioinformatics Phd Phd Biomedical Informatics PMC4934005 2016 Genome_Biol 11.2 Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome Research article yes no Babraham website no no no 105 Male Professor Other Phd PMC5006368 2016 Genome_Biol 11.2 Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders Research article yes yes other website no no no 193 PMC4734871 2016 Genome_Biol 11.2 External signals shape the epigenome Research article yes no no no no 1 PMC4823857 2016 Genome_Biol 11.2 Design and computational analysis of single-cell RNA-sequencing experiments Research article yes no no no no 443 Female Professor Other Mathematics Phd Phd Other Statistics PMC4964047 2016 Genome_Biol 11.2 Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans Research article yes yes no no no 7 Male Assistant Professor "Other , Biological Sciences" Phd Phd Bioinformatics PMC4797182 2016 Genome_Med 7.1 Exploring the implications of distinct mutational signatures and mutation rates in aging and cancer Research article yes no no no no 16 Male Professor Other Phd PMC4835935 2016 Genome_Med 7.1 Microbiome mediation of infections in the cancer setting Research article yes no no no no 72 Male Professor Other MD MD Other PMC4992240 2016 Genome_Med 7.1 Migraine genetics: from genome-wide association studies to translational insights Research article yes no no no no 25 Male Associate Member Other MD and Phd Phd Computational Biology PMC5041586 2016 Genome_Med 7.1 qKAT: a high-throughput qPCR method for KIR gene copy number and haplotype determination Research article yes yes no no (Available upon request) no 17 PMC5513182 2016 Nat_Biotechnol 42 Blood pressure regulation by CD4+ lymphocytes expressing choline acetyltransferase Research article yes no no no (Available upon request) no 56 Male Professor Other MD MD and Phd Other PMC4811732 2016 Nat_Genet 28 "Mutations in nuclear pore genes NUP93, NUP205, and XPO5 cause steroid resistant nephrotic syndrome" Research article yes no no no no 142 Male Professor Other MD PMC5238942 2016 Nat_Genet 28 Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages Research article yes yes no no no 286 Male Associate Professor Other PostDoc Phd CS PMC5042855 2016 Nat_Genet 28 Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast Research article yes no no no no 66 Male Professor Other Phd Phd Other PMC5042863 2016 Nat_Genet 28 "The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals" Research article yes no supplementary file no no no 353 Female Professor Other PostDoc PMC5131845 2016 Nat_Genet 28 Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer Research article yes no no no no 127 Male Other Other Phd Phd Other PMC5045719 2016 Nat_Methods 25 DSBCapture: in situ capture and direct sequencing of dsDNA breaks Research article yes no no no (Available upon request) no Pipeline Others(Supplementary) no 108 Male Professor Other Phd PMC5001604 2016 Nucleic_Acids_Res 10.2 Splice-switching antisense oligonucleotides as therapeutic drugs Research article yes no no no no 317 Female Professor Other PostDoc Phd Other PMC4838366 2016 Nucleic_Acids_Res 10.2 "Defective histone supply causes condensin-dependent chromatin alterations, SAC activation and chromosome decatenation impairment " Research article yes no no no no 15 Male Phd Phd Other Molecular Biology and Genetics PMC4987919 2016 Nucleic_Acids_Res 10.2 BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization Research article yes no no no no 24 Male Professor Other Phd Phd Other PMC5379749 2017 BMC_Bioinformatics 2.6 Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments Research article yes yes yes no (Link Expired) no 31 Male VP Other Masters Phd Other PMC5773911 2017 BMC_Bioinformatics 2.6 Predicting enhancers with deep convolutional neural networks Research article yes yes no no (Available upon request) no 73 PMC5568075 2017 BMC_Bioinformatics 2.6 A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification Research article yes yes yes no (Link Expired) no 0 PMC5260008 2017 BMC_Bioinformatics 2.6 FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples Research article yes yes no no (Link Expired) no 7 Female Assistant Professor Bioinformatics Phd Phd CS PMC5663038 2017 Genome_Biol 11.6 Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. Research article yes yes no no no 10 Male Professor Phd Computational Biology PMC5412043 2017 Genome_Biol 11.6 Unraveling the clonal hierarchy of somatic genomic aberrations Research article yes yes dbGaP no no no 98 Female Professor Other Phd Phd Other PMC5320668 2017 Genome_Biol 11.6 epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data Research article yes yes yes no (Link Expired) no 9 Male Professor Other Postdoc Postdoc Other PMC5561556 2017 Genome_Med 9 A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications Research article yes no no no no 504 Male Researcher Other Phd Phd Other PMC5729609 2017 Genome_Med 9 Mapping a shared genetic basis for neurodevelopmental disorders Research article yes no no no no 24 Male Associate Professor Other Postdoc Bioinformatics PMC5477758 2017 Genome_Med 9 Computing patient data in the cloud: practical and legal considerations for genetics and genomics research in Europe and internationally Research article yes no no no no 32 Male Head of Department Other Postdoc Phd Other PMC5704398 2017 Genome_Med 9 Recurrent de novo mutations in neurodevelopmental disorders: properties and clinical implications Research article yes yes no no no 99 Male Professor "Other, Molecular Genetics" Phd Phd Other Statistical Genetics PMC5462879 2017 Nat_Biotechnol 36 In vivo genome editing and organoid transplantation models of colorectal cancer Research article yes no no no no 227 Male Associate Professor Other "MD, Postdoc" Postdoc Other PMC5388574 2017 Nat_Biotechnol 36 Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions Research article yes no no no no 596 Male Professor Other Phd Phd Other PMC5621629 2017 Nat_Genet 27.2 Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis Research article yes yes UK Biobank no no no 311 Male Professor Other Statistical Genetics Phd Phd Genetics PMC5737898 2017 Nucleic_Acids_Res 11.6 LDB1-mediated enhancer looping can be established independent of mediator and cohesin Research article yes no no no no 42 Female Senior Investigator Phd Phd Other Molecular Genetics PMC5389708 2017 Nucleic_Acids_Res 11.6 Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization Research article yes no no no no 41 Female Professor Other Postdoc Postdoc Other PMC5753376 2017 Nucleic_Acids_Res 11.6 The SysteMHC Atlas project Research article yes no no no no 104 Male Assistant Professor Bioinformatics Postdoc Postdoc Other PMC6038323 2018 BMC_Bioinformatics 3 A deep learning approach to bilingual lexicon induction in the biomedical domain Research article yes no yes no (Available upon request) no 11 Female Professor CS Phd Phd CS PMC6245584 2018 BMC_Bioinformatics 3 Computational discovery of direct associations between GO terms and protein domains Research article yes yes GODomainMiner no no no 4 Female Research Officer CS Phd Phd CS PMC6020218 2018 BMC_Bioinformatics 3 ToTem: a tool for variant calling pipeline optimization Research article yes no yes no (Link expired) no 1 Female Professor Phd Other Genetics PMC5796405 2018 BMC_Bioinformatics 3 Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures Research article yes no yes no (Link expired) no 13 Male Professor Other Postdoc Phd Other PMC6203279 2018 Genome_Biol 12 Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors Research article yes yes no no no 26 Male Senior Investigator Other Phd PMC5759268 2018 Genome_Biol 12 Epigenetic supersimilarity of monozygotic twin pairs Research article yes yes no no no 69 Male Professor Other Genetics Postdoc Phd CS PMC5815211 2018 Genome_Biol 12 Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species Research article yes yes no no no 45 Male Professor Other Epigenetics Postdoc Phd Other PMC6097284 2018 Genome_Biol 12 Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data Research article yes yes URGI no no no 167 Male Leader Bioinformatics Postdoc PMC5870483 2018 Genome_Biol 12 Pulling the genome in opposite directions to dissect gene networks Research article yes no no no no 1 Male Professor Other Genetics Phd Phd Other PMC6036703 2018 Genome_Biol 12 Splicing heterogeneity: separating signal from noise Research article yes no no no no 43 Male Senior Investigator Other Postdoc Phd PMC6162943 2018 Genome_Med 11 Advanced model systems and tools for basic and translational human immunology Research article yes no no no no 66 Male Professor Other Phd Phd Other PMC5902843 2018 Genome_Med 11 Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing Research article yes yes no no no 26 Male Professor Other Phd MS Other PMC6309089 2018 Genome_Med 11 Polygenic risk scores: a biased prediction? Research article yes no no no no 82 Male Professor Other Postdoc Phd "Other, Genetics" PMC5968547 2018 Genome_Med 11 Antifungal immune responses: emerging host–pathogen interactions and translational implications Research article yes no no no no 9 Male Professor Other Postdoc Phd "Other, Genetics" PMC6208080 2018 Genome_Med 11 "Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers " Research article yes yes no no no 83 Male Assistant Professor Other Phd Phd Other PMC6526074 2018 Nat_Biotechnol 32 RNAi Modulation of Placental sFLT1 for the Treatment of Preeclampsia. Research article yes no no no no 104 Female Professor Other Postdoc Postdoc Other PMC5898373 2018 Nat_Genet 25.5 Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes Research article yes yes DIAGRAM consortium no no no 291 Male Executive Director Other MD Phd Other PMC5896734 2018 Nat_Genet 25.5 Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis Research article yes no UK Biobank no no no 182 Female Group Leader "Other, Genetics" Postdoc PMC5934350 2018 Nat_Genet 25.5 Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits Research article yes no UK Biobank no no no 202 Male Professor Other Phd Phd "Other, Genetics" PMC5935235 2018 Nat_Genet 25.5 Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition Research article yes yes no no no 113 Male Executive Director Other MD Phd "Other, Genetics" PMC5942247 2018 Nat_Genet 25.5 A large electronic health record-based genome-wide study of serum lipids Research article yes yes UK Biobank no no no 197 Male Professor "Other, Biomaths" Phd Phd CS PMC6345375 2018 Nat_Methods 28.5 Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging Research article yes yes no no no 123 Male Professor Other Postdoc Postdoc Other PMC6204345 2018 Nat_Methods 28.5 All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition Research article yes no yes no (Available upon request) no Analytical 24 Male Professor Other Phd Phd Other PMC6212719 2018 Nucleic_Acids_Res 11.2 RbpA relaxes promoter selectivity of M. tuberculosis RNA polymerase Research article yes no no no no 14 Postdoc Other PMC6009581 2018 Nucleic_Acids_Res 11.2 "Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species" Research article yes yes no no no 8 Phd Bioinformatics PMC4908329 2016 Bioinformatics 7.3 A convex optimization approach for identification of human tissue-specific interactomes Research article yes yes no (Link Expired) no no 12 Male Professor CS Phd Phd CS PMC4908319 2016 Bioinformatics 7.3 Privacy-preserving microbiome analysis using secure computation Research article yes yes no (Link Expired) no no 22 Male Professor Cs Phd PMC4920110 2016 Bioinformatics 7.3 Phasing for medical sequencing using rare variants and large haplotype reference panels Research article yes yes no (Link Expired) no no 21 Male Director Other Phd Phd Other Machine Learning PMC5351549 2016 Bioinformatics 7.3 Training alignment parameters for arbitrary sequencers with LAST-TRAIN Research article yes yes no (Link not accessible) no Tool no 54 Male Professor Bioinformatics PostDoc Phd Bioinformatics PMC6540526 2019 Genome_Med 11 Prognostic value of B cells in cutaneous melanoma Research article yes yes no no no no 50 Male Assistant Professor Other MD Phd Bioinformatics PMC4889955 2016 Nucleic_Acids_Res 10.2 The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes Research article yes no no no no 67 Male Professor Other PostDoc Phd Other PMC6030935 2018 Nucleic_Acids_Res 11.2 IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding Research article yes no no yes yes Pipeline Other (Website) no no 575 Female Professor Other Postdoc Postdoc Other PMC6612824 2019 Bioinformatics 5.6 Prediction of mRNA subcellular localization using deep recurrent neural networks Research article yes no yes yes yes Package GitHub no no 46 Male Professor CS Postdoc Phd CS PMC6792070 2019 Bioinformatics 5.6 The TMCrys server for supporting crystallization of transmembrane proteins Research article yes no yes yes yes Package GitHub no no 13 Male Member Other Phd Phd Molecular Genetics PMC6612899 2019 Bioinformatics 5.6 PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors Research article yes no yes yes yes Package GitHub no yes 29 Male Director of Reseach CS Phd Phd Other PMC6612898 2019 Bioinformatics 5.6 MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks Research article yes no yes yes yes tool GitHub no no 42 Male Lecturer CS Phd MS CS PMC6954654 2019 Bioinformatics 5.6 scRNABatchQC: multi-samples quality control for single cell RNA-seq data Research article yes no yes yes yes Package GitHub no yes 9 Male Chair Biostatistics Phd Phd Bioinformatics PMC6761931 2019 Bioinformatics 5.6 GREP: genome for REPositioning drugs Research article yes no yes yes yes Package GitHub no yes 12 Male Professor Statistical genetics "MD,Phd" Phd Genetics PMC6612875 2019 Bioinformatics 5.6 Representation transfer for differentially private drug sensitivity prediction Research article yes no yes yes yes Package GitHub no yes 32 Male Professor CS Phd PMC6612853 2019 Bioinformatics 5.6 Drug repositioning based on bounded nuclear norm regularization Research article yes no yes yes yes Tool GitHub no yes 29 Male Professor CS Phd Phd CS PMC6761967 2019 Bioinformatics 5.6 Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction Research article yes no no yes yes Tool GitHub no no 43 Male Professor CS Postdoc Phd CS PMC6734328 2019 BMC_Bioinformatics 3.8 BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus Research article yes yes yes yes yes Package GitHub no yes 72 Female Professor Other Postdoc Md Other PMC6941187 2019 BMC_Bioinformatics 3.8 Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments Research article yes no yes yes yes tool GitHub no yes 37 Male Professor CS Phd Phd Bioinformatics PMC6421703 2019 BMC_Bioinformatics 3.8 MGSEA – a multivariate Gene set enrichment analysis Research article yes yes yes yes yes tool downloadable file no no 30 Male Associate Researcher CS Phd Postdoc Bioinformatics PMC6423771 2019 Genome_Biol 9.5 Measuring the reproducibility and quality of Hi-C data Research article yes yes yes yes yes Package GitHub + Zenodo no yes 48 Male Professor CS Phd Postdoc Computional Biology PMC6472072 2019 Genome_Biol 9.5 Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data Research article yes yes yes yes yes tool Zenodo no yes 10 Female Head Other Phd Phd Bioinformatics PMC6927181 2019 Genome_Biol 9.5 normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression Research article yes yes yes yes yes Package GitHub no yes 39 Male Associate Professor "Other, Statistics" Phd Postdoc Computional Biology PMC6883653 2019 Genome_Biol 9.5 ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning Research article yes yes yes yes yes Package GitHub + Zenodo no yes 23 Male Professor Other Phd PMC6927166 2019 Genome_Biol 9.5 tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies Research article yes yes yes yes yes Package GitHub + Zenodo no yes 62 PMC6917484 2019 Nat_Genet 28 The impact of short tandem repeat variation on gene expression Research article yes yes yes yes yes Package GitHub yes notebook multiple yes 68 Female Assistant Professor "CS, Bioinformatics" Phd Phd Bioinformatics PMC6726478 2019 Nat_Genet 28 Inferring whole-genome histories in large population datasets Research article yes yes yes yes yes Package GitHub yes notebook single yes 60 Male Professor Other BA Postdoc CS PMC7610650 2019 Nat_Genet 28 Determining protein structures using deep mutagenesis Research article yes yes yes yes yes Package GitHub no yes 73 Male Professor Other Postdoc Phd Other PMC7098173 2019 Nat_Methods 31 Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data Research article yes yes yes yes yes Package GitHub no yes 54 Male Professor CS Phd Phd CS PMC7145620 2019 Nucleic_Acids_Res 11.5 CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies Research article yes no no yes yes pipeline GitHub no yes 57 Male Professor Bioinformatics Postdoc Phd Other PMC7355292 2020 Bioinformatics 6.9 MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model Research article yes no yes yes yes Package github no no 48 Male Professor CS Phd MS CS PMC7355262 2020 Bioinformatics 6.9 Unsupervised topological alignment for single-cell multi-omics integration Research article yes no yes yes yes Package GitHub no no 27 Male Professor Other Phd Phd Bioinformatics PMC7355291 2020 Bioinformatics 6.9 Copy number evolution with weighted aberrations in cancer Research article yes no yes yes yes Package GitHub no no 60 Male Professor Other Phd Phd CS PMC7750928 2020 Bioinformatics 6.9 LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation Research article yes no yes yes yes Package GitHub no yes 23 Male Associate Professor Phd CS PMC8336998 2020 Bioinformatics 6.9 quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories Research article yes no yes yes yes Package GitHub no yes 8 Male Phd Bioinformatics PMC8352503 2020 Bioinformatics 6.9 MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection Research article yes no yes yes yes Package GitHub no no 17 Female Professor Other Postdoc Phd Bioinformatics PMC7355251 2020 Bioinformatics 6.9 TopicNet: a framework for measuring transcriptional regulatory network change Research article yes no yes yes yes Package GitHub no yes 47 Male Professor Bioinformatics Postdoc Postdoc Bioinformatics PMC7320608 2020 Bioinformatics 6.9 gplas: a comprehensive tool for plasmid analysis using short-read graphs Research article yes no yes yes yes Package gitlab no no 15 Female Head of Group Bioinformatics Postdoc Phd Bioinformatics PMC7355259 2020 Bioinformatics 6.9 The locality dilemma of Sankoff-like RNA alignments Research article yes no yes yes yes Package GitHub yes notebook multiple yes 29 Male Professor CS Phd MS Bioinformatics PMC8097688 2020 Bioinformatics 6.9 selectBoost: a general algorithm to enhance the performance of variable selection methods Research article yes no yes yes yes Pipeline CRAN no no 52 Female Lecturer Other Phd Phd Other PMC7288679 2020 BMC_Bioinformatics 3.5 PhyteByte: identification of foods containing compounds with specific pharmacological properties Research article yes yes no yes yes Tool GitHub yes notebook multiple yes 25 Male Assistant Professor Other Phd Postdoc Other PMC7372900 2020 BMC_Bioinformatics 3.5 LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks Research article yes yes no yes yes Package GitHub no yes 43 Male Associate Professor Phd Other PMC7191778 2020 BMC_Bioinformatics 3.5 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome Research article yes yes no yes yes Matlab GitHub no no 46 Male Assistant Professor Other Phd Phd Other PMC7014945 2020 BMC_Bioinformatics 3.5 GARS: Genetic Algorithm for the identification of a Robust Subset of features in high-dimensional datasets Research article yes yes yes yes yes Package GitHub no yes 35 PMC7068914 2020 BMC_Bioinformatics 3.5 Dynamic incorporation of prior knowledge from multiple domains in biomarker discovery Research article yes yes yes yes yes Package GitHub no yes 27 Female Assistant Professor Other MD Phd Other PMC7444084 2020 Genome_Biol 11.7 GBAT: a gene-based association test for robust detection of trans-gene regulation Research article yes yes yes yes yes Package GitHub no yes 42 Male Associate Professor Bioinformatics Phd Postdoc "Other, Genetics" PMC7384222 2020 Genome_Biol 11.7 Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics Research article yes no no yes yes Package GitHub no no 33 Male Professor "Other, Biostatistics" Phd Postdoc CS PMC7477834 2020 Genome_Biol 11.7 Long-read-based human genomic structural variation detection with cuteSV Research article yes yes yes yes yes Package Zenodo no yes 53 Male Professor CS MS BS Bioinformatics PMC7104480 2020 Genome_Biol 11.7 Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome Research article yes yes ENCODE yes yes yes Package Zenodo/GitHub no yes 54 Male Professor CS Phd Postdoc CS PMC7291511 2020 Genome_Biol 11.7 SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins Research article yes no no yes yes Package GitHub yes (partial) Rmd single no 81 Female Professor Other Phd Phd Other PMC7236505 2020 Genome_Biol 11.7 tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing Research article yes yes yes yes yes Software GitHub no yes 138 Female Professor Other Phd Phd Bioinformatics PMC7017486 2020 Genome_Biol 11.7 Genotyping structural variants in pangenome graphs using the vg toolkit Research article yes yes yes yes yes Package Zenodo/GitHub no yes 61 Male Associate Professor CS Postdoc Phd Other PMC7081711 2020 Genome_Med 11.1 Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL Research article yes yes yes yes yes Package GitHub no no 94 Male Professor Phd Phd Bioinformatics PMC7768597 2020 Genome_Med 11.1 Statistical power in COVID-19 case-control host genomic study design Research article yes yes yes yes yes Package GitHub no yes 29 Female Associate Professor "Other, Biostatistics" Postdoc Phd Other Statistics PMC7687775 2020 Genome_Med 11.1 Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases Research article yes yes yes yes yes Package Zenodo/GitHub no yes 65 Male Director of Research "Other, Genetics" Phd Phd PMC7878194 2020 Nat_Biotechnol 55 Context-aware dimensionality reduction deconvolutes gut microbial community dynamics Research article yes yes yes yes yes Tool GitHub yes notebook multiple yes 18 Male Professor Other Phd Phd Bioinformatics PMC7343608 2020 Nat_Genet 38.3 Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics Research article yes yes yes yes yes Package GitHub no yes 67 Male Associate Professor CS Phd Phd "Other, Biostatistics" PMC7610467 2020 Nat_Genet 38.3 Evolutionary dynamics of neoantigens in growing tumors Research article yes yes yes yes yes Package Zenodo no yes 19 Male Professor Other Postdoc Postdoc "Other, Bioinformatics" PMC7610464 2020 Nat_Genet 38.3 Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases Research article yes yes yes yes yes Package GitHub no yes 59 Male Professor Other Postdoc Phd Other PMC8073243 2020 Nat_Methods 28.6 Supervised enhancer prediction with epigenetic pattern recognition and targeted validation Research article yes yes yes yes yes Package GitHub no yes 24 Male Professor Bioinformatics Postdoc Phd Other PMC7437817 2020 Nat_Methods 28.6 Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq Research article yes yes yes yes yes Package GitHub no yes 37 Female Professor Bioinformatics Phd Postdoc CS PMC7897472 2020 Nucleic_Acids_Res 17 Entropy subspace separation-based clustering for noise reduction (ENCORE) of scRNA-seq data Research article yes yes no yes yes software GitHub no no 38 Male Professor Other Phd Postdoc Other PMC8136008 2021 Bioinformatics 6.6 VisuaLife: library for interactive visualization in rich web applications Research article yes no yes yes yes Package BitBucket no no 1 Male Faculty Other Phd MS Other PMC8428582 2021 Bioinformatics 6.6 "Mercator: a pipeline for multi-method, unsupervised visualization and distance generation" Research article yes yes yes yes yes Pipeline CRAN yes Rmd multiple uncertain 2 Male Professor Other Postdoc Postdoc Bioinformatics PMC8406877 2021 Bioinformatics 6.6 Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction Research article yes no yes yes yes Package GitHub no yes 1 Male Professor Other MSc Phd Other PMC8135978 2021 Bioinformatics 6.6 Alignment free sequence comparison methods and reservoir host prediction Research article yes no yes yes yes Package GitHub no yes 0 Male Professor Other Phd MS CS PMC8034537 2021 Bioinformatics 6.6 EM-stellar: benchmarking deep learning for electron microscopy image segmentation Research article yes no yes yes yes Jupyter Notebook github yes notebook multiple yes 2 Male Senior Lecturer Other Phd Phd Other PMC8388021 2021 Bioinformatics 6.6 BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R Research article yes yes yes yes yes Package GitHub no no 3 Male Principle Scientist Other Postdoc Postdoc Other PMC8136078 2021 Bioinformatics 6.6 SeRenDIP-CE: sequence-based interface prediction for conformational epitopes Research article yes no yes no yes Pipeline Other (Website) no no 2 Male Assistant Professor Bioinformatics Postdoc Phd Bioinformatics PMC8034526 2021 Bioinformatics 6.6 The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators Research article yes no no yes yes Package gitlab no no 5 Male Group Leader Bioinformatics Phd MSc Bioinformatics PMC8388031 2021 Bioinformatics 6.6 CuBlock: a cross-platform normalization method for gene-expression microarrays Research article yes no yes yes yes Pipeline Other (Website) uncertain uncertain uncertain uncertain 1 Male Adjunct Professor Other Phd Phd Bioinformatics PMC8254361 2021 BMC_Bioinformatics 3.4 PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity Research article yes yes yes yes yes Package GitHub no yes 0 Male Research Assistant Other MSc MS CS PMC7936459 2021 BMC_Bioinformatics 3.4 SomatoSim: precision simulation of somatic single nucleotide variants Research article yes yes no yes yes Package GitHub no no 1 Male Director Other MD BS Other PMC8220828 2021 BMC_Bioinformatics 3.4 A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns Research article yes yes yes yes yes Package GitHub no no 0 Male Professor "Other, Genetics" "MD,Phd" Phd Other PMC7877041 2021 BMC_Bioinformatics 3.4 Ranking cancer drivers via betweenness-based outlier detection and random walks Research article yes yes no yes yes Pipeline GitHub no yes 0 Female Associate Professor CS Phd Phd Other PMC8340394 2021 BMC_Bioinformatics 3.4 Maximum parsimony reconciliation in the DTLOR model Research article yes yes yes yes yes Package GitHub no no 0 Male Professor CS Phd Phd Other PMC7869453 2021 BMC_Bioinformatics 3.4 NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences Research article yes yes no yes yes Tool GitHub no no 1 Male Emiretus Professor Other Phd Postdoc CS PMC8296540 2021 BMC_Bioinformatics 3.4 METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs Research article yes yes yes yes yes Pipeline GitHub no no 1 Male Assistant Professor CS Postdoc Postdoc "CS,Bioinformatics" PMC8004462 2021 Genome_Biol 15.1 Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders Research article yes yes yes yes yes Analytical GitHub no yes 4 Male Fellow "Other,Genetics" Phd Phd Other PMC8218388 2021 Genome_Biol 15.1 SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies Research article yes yes yes yes yes Pipeline GitHub no yes 1 Male Associate Professor Other Phd Phd Biostatistics PMC7988935 2021 Genome_Med 12 CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells Research article yes yes yes yes yes Package GitHub no yes 1 Female Assistant Professor "Other,Genetics" Postdoc Phd CS PMC8127495 2021 Genome_Med 12 An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility Research article yes yes no yes yes Package GitHub no no 8 Male Associate Professor Other "MD,Phd" Phd Other PMC8383430 2021 Genome_Med 12 Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain Research article yes yes no yes yes pipeline GitHub no yes 12 Male Associate Professor "Other,Genetics" Phd BSc Bioinformatics PMC7610386 2021 Nat_Genet 41.3 "Genome-wide meta-analysis, fine-mapping, and integrative prioritization implicate new Alzheimer’s disease risk genes" Research article yes yes yes yes yes Analytical GitHub no yes 42 Male Head of Research "Other, Genetics" Postdoc Postdoc "Other, Genetics" PMC8035334 2021 Nat_Methods 48 Deep Learning-Based Point-Scanning Super-Resolution Imaging Research article yes yes yes yes yes Pipeline GitHub yes notebook multiple no 36 Male Assistant Professor Other Postdoc MS Other PMC7611169 2021 Nat_Methods 48 Structured illumination microscopy with noise-controlled image reconstructions Research article yes yes yes yes yes Pipeline GitHub no no 3 Male Professor Other Phd Phd Other PMC8262695 2021 Nucleic_Acids_Res 19.3 GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA Research article yes yes no yes yes Package GitHub no yes 12 PMC8287924 2021 Nucleic_Acids_Res 19.3 Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii Research article yes yes no yes yes Analytical Supplementary no no 1 Male Professor Other Postdoc PMC5018371 2016 Bioinformatics 7.3 TarPmiR: a new approach for microRNA target site prediction Research article yes yes TarPmiR website yes yes yes Software Other(Website) no 124 PMC4908323 2016 Bioinformatics 7.3 Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap Research article yes yes Ribomap website yes yes yes Software "Other(Website), GitHub" no 34 Male Professor CS Phd CS PMC5043639 2016 BMC_Bioinformatics 2.5 Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs Research article yes yes yes yes yes Pipeline GitHub no 7 Male Professor CS Phd Post Doc Bioinformatics PMC5123383 2016 BMC_Bioinformatics 2.5 A fuzzy method for RNA-Seq differential expression analysis in presence of multireads Research article yes yes yes yes yes Pipeline Other(Website) no 16 Male Researcher Bioinformatics and Biological Science NM Phd CS PMC5020541 2016 BMC_Bioinformatics 2.5 CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data Research article yes no yes yes yes Package Others (Website) no 66 Male Professor Engineering Phd Phd Bioinformatics PMC5054559 2016 Genome_Biol 11.2 Prediction of gestational age based on genome-wide differentially methylated regions Research article yes yes NIPH website yes yes yes Package Zenodo yes Rmd single 101 Male Professor Other Epidemiology Phd Phd Bioinformatics PMC4872356 2016 Genome_Med 7.1 An adaptive association test for microbiome data Research article yes yes yes yes yes Package GitHub yes 69 Male Professor CS Phd Phd Biostatistics PMC4784276 2016 Genome_Med 7.1 CoINcIDE: A framework for discovery of patient subtypes across multiple datasets Research article yes yes supplementary file yes yes yes Package Bioconductor yes 31 Male Associate Professor Bioinformatics Phd Phd Biomedical Informatics PMC4900928 2016 Nat_Biotechnol 42 Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch Research article yes no GitHub no yes yes Analytical GitHub no 154 Male Associate Professor CS Phd Phd Other PMC4900911 2016 Nat_Biotechnol 42 Systematic comparison of CRISPR-Cas9 and RNAi screens for essential genes Research article yes no supplementary file no yes yes Pipeline Other (Bitbucket) no 330 Male Associate Professor Other PostDoc Phd Other PMC5207801 2016 Nat_Genet 28 Detection and interpretation of shared genetic influences on 42 human traits Research article yes no supplementary file no yes yes Tool GitHub no 922 Male Research Fellow Other Phd Phd Human Genetics PMC5042848 2016 Nat_Genet 28 noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer Research article yes no no yes yes Tool GitHub 79 Male Professor Other PostDoc Phd Other PMC5040167 2016 Nat_Genet 28 Network-based inference of protein activity helps functionalize the genetic landscape of cancer Research article yes no no yes yes Package Bioconductor yes Rmd Single 465 Male Chair Other Phd Phd Other PMC4817234 2016 Nat_Genet 28 A multiple phenotype imputation method for genetic studies Research article yes no no yes yes Pipeline Other(Website) no 82 Male Professor Other Statistics Phd Phd Other Statistics PMC4854847 2016 Nat_Methods 25 Inferring causal molecular networks: empirical assessment through a community-based effort Research article yes yes HPN-DREAM website no yes yes Web Tool Others(Supplementary) no 212 Male Head Other Machine Learning PostDoc Phd Statistics and Complexity Science PMC5199618 2016 Nat_Methods 25 TACO produces robust multi-sample transcriptome assemblies from RNA-seq Research article yes yes TACO website yes yes yes Tool GitHub no 107 Male MD-Phd MD-Phd Others PMC5008461 2016 Nat_Methods 25 TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics Research article yes yes Peptide Atlas no yes yes Software GitHub no 144 Male Professor Other Phd Phd Other Computational Biology PMC5199621 2016 Nat_Methods 25 novoBreak: local assembly for breakpoint detection in cancer genomes Research article yes no yes yes yes Pipeline Other(Sourceforge) no 99 Male Associate Professor Other Phd Phd CS and Bioinformatics PMC4930141 2016 Nat_Methods 25 Data-driven hypothesis weighting increases detection power in genome-scale multiple testing Research article yes no yes yes yes Pipeline Other(Website) yes Rmd Single 384 Male Other Cheminformatics PostDoc Phd Other Statistics PMC4987952 2016 Nucleic_Acids_Res 10.2 3D-GNOME: an integrated web service for structural modeling of the 3D genome Research article yes no no yes yes Web Tool 35 Male Professor Other PostDoc Phd PMC4937319 2016 Nucleic_Acids_Res 10.2 Redundans: an assembly pipeline for highly heterozygous genomes Research article yes no no yes yes Pipeline GitHub no 324 Male Professor Bioinformatics Phd Phd PMC4987948 2016 Nucleic_Acids_Res 10.2 Heatmapper: web-enabled heat mapping for all Research article yes no no yes yes Software GitHub no 1283 Male Professor Other Phd PMC5860066 2017 Bioinformatics 5.4 OMSim: a simulator for optical map data Research article yes yes yes yes yes Tool GitHub no 12 Male Associate Professor Bioinformatics PostDoc Masters Bioinformatics PMC5870698 2017 Bioinformatics 5.4 HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens Research article yes yes yes yes yes Analytical GitHub no 5 Male Head of Division Other PostDoc Masters Other PMC6031019 2017 Bioinformatics 5.4 GDSCTools for mining pharmacogenomic interactions in cancer Research article yes yes no yes yes Software GitHub yes notebook Multiple 34 Male Group Leader Other PostDoc Phd CS PMC5860120 2017 Bioinformatics 5.4 Kart: a divide-and-conquer algorithm for NGS read alignment Research article yes yes yes yes yes Pipeline GitHub no 39 Male Chair Professor CS Phd Postdoc CS and Bioinformatics PMC5870853 2017 Bioinformatics 5.4 "cyvcf2: fast, flexible variant analysis with Python" Research article yes yes yes yes yes Analytical GitHub no 41 Male Professor CS Phd PMC5860161 2017 Bioinformatics 5.4 FALCON: a toolbox for the fast contextualization of logical networks Research article yes yes yes yes yes Pipeline GitHub no 12 Male Professor Postdoc Bioinformatics PMC5905622 2017 Bioinformatics 5.4 SimulaTE: simulating complex landscapes of transposable elements of populations Research article yes yes yes yes yes Tool Other (Sourceforge) no 6 Male Professor Other Phd PMC5870603 2017 Bioinformatics 5.4 "Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data" Research article yes yes yes yes yes Pipeline Other (Website) no 11 Female Research Scientist Other Phd Postdoc PMC5870860 2017 Bioinformatics 5.4 Threshold-seq: a tool for determining the threshold in short RNA-seq datasets Research article yes yes yes yes yes Tool Other (Website) no 11 Male Professor CS Phd Phd Other PMC5860361 2017 Bioinformatics 5.4 graphkernels: R and Python packages for graph comparison Research article yes yes yes yes yes Package Others (Website) no 53 Male Professor CS Phd Postdoc Bioinformatics PMC5697234 2017 BMC_Bioinformatics 2.6 Synima: a Synteny imaging tool for annotated genome assemblies Research article yes yes yes yes yes Tool GitHub no 33 Male Lecturer Bioinformatics Phd PMC5721689 2017 BMC_Bioinformatics 2.6 Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach Research article yes yes yes yes yes Pipeline GitHub no 1 Male Professor Other Phd Phd Other PMC5490186 2017 BMC_Bioinformatics 2.6 ISVASE: identification of sequence variant associated with splicing event using RNA-seq data Research article yes yes ISVASE yes yes yes Tool Other(Sourceforge) no 0 Male Professor PMC5353803 2017 BMC_Bioinformatics 2.6 microclass: an R-package for 16S taxonomy classification Research article yes no no yes yes Package Other(Website) yes Rmd Single 18 Male Associate Professor Phd Informatics PMC5657048 2017 Genome_Biol 11.6 McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes Research article yes yes yes yes yes Pipeline GitHub no 23 Male Professor CS Postdoc Phd CS PMC5404673 2017 Genome_Med 9 PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories Research article yes yes Nectar Australian yes yes yes Pipeline GitHub no 35 Male Professor Other Phd Phd Other PMC5607865 2017 Nat_Biotechnol 36 GuideScan software for improved single and paired CRISPR guide RNA design Research article yes no no yes yes Software Other (BitBucket) no 164 Male Member Other "MD, Phd" "MD, Phd" Bioinformatics PMC5395419 2017 Nat_Genet 27.2 "Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data" Research article yes yes yes yes yes Pipeline GitHub no 274 Male Professor CS Phd Phd Other PMC6026581 2017 Nat_Methods 27 Interactome INSIDER: a structural interactome browser for genomic studies Research article yes yes yes yes Tool GitHub yes notebook single 114 Male Professor Bioinformatics Postdoc Phd Computational Biology PMC5564216 2017 Nat_Methods 27 CrY2H-seq: a massively-multiplexed assay for deep coverage interactome mapping Research article yes no yes yes yes Analytical Supplementary no 123 Male Professor Other Postdoc Phd Other PMC6662083 2018 Bioinformatics 4.5 CASMAP: detection of statistically significant combinations of SNPs in association mapping Research article yes no yes yes yes Package GitHub yes "Rmd, ipynb" Multiple 10 Male Professor CS Postdoc Phd Computational Biology PMC6581432 2018 Bioinformatics 4.5 MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs) Research article yes no yes yes yes Pipeline GitHub no 29 Male Professor Bioinformatics Phd Phd Bioinformatics PMC6022719 2018 Bioinformatics 4.5 Deconvolution and phylogeny inference of structural variations in tumor genomic samples Research article yes no yes yes yes Pipeline GitHub no 34 Male Professor CS Postdoc MS Computational Biology PMC6022601 2018 Bioinformatics 4.5 Association mapping in biomedical time series via statistically significant shapelet mining Research article yes no yes yes yes Pipeline GitHub no 24 Male Professor CS Postdoc Phd Bioinformatics PMC6041755 2018 Bioinformatics 4.5 Network-based integration of multi-omics data for prioritizing cancer genes Research article yes no yes yes yes Pipeline GitHub no 95 Male Professor CS Postdoc MS CS PMC6247942 2018 Bioinformatics 4.5 MolArt: a molecular structure annotation and visualization tool Research article yes no yes yes yes Pipeline GitHub no 17 Male Head and Professor Other Phd Postdoc CS PMC6129310 2018 Bioinformatics 4.5 CaSiAn: a Calcium Signaling Analyzer tool Research article yes no yes yes yes Tool GitHub no 11 Male Associate Professor Other Postdoc Phd CS PMC6022688 2018 Bioinformatics 4.5 Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies Research article yes no yes yes yes Pipeline GitHub no 9 Male Assistant Professor CS Phd Phd CS PMC6022691 2018 Bioinformatics 4.5 Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge Research article yes no yes yes yes Pipeline GitHub yes notebook Multiple 15 Male Assistant Professor Other Electrical and Computer Engineering Phd Phd Other Electrical and Computer Engineering PMC6084591 2018 Bioinformatics 4.5 ONETOOL for the analysis of family-based big data Research article yes no yes yes yes Pipeline Other (Website) no 21 Male Professor Other Postdoc Phd Other Biostatistics PMC6020255 2018 BMC_Bioinformatics 3 ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies Research article yes no yes yes yes Pipeline GitHub no 1 Male Professor CS Phd Phd CS PMC5998916 2018 BMC_Bioinformatics 3 Computing the family-free DCJ similarity Research article yes no yes yes yes Pipeline GitHub no 4 Male Professor Bioinformatics Postdoc Phd CS PMC6134797 2018 BMC_Bioinformatics 3 Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data Research article yes yes yes yes yes Pipeline GitHub no 32 Female Professor Other Phd MS Other PMC6247705 2018 BMC_Bioinformatics 3 ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events Research article yes yes Google Drive no yes yes Tool GitHub no 30 Female Professor CS and Bioinformatics Phd Phd CS PMC6003080 2018 BMC_Bioinformatics 3 Taxonomy-aware feature engineering for microbiome classification Research article yes no yes yes yes Pipeline GitHub no 52 Male Associate Professor CS Phd Phd CS and Bioinformatics PMC6286514 2018 BMC_Bioinformatics 3 GOnet: a tool for interactive Gene Ontology analysis Research article yes no yes yes yes Tool GitHub no 134 Male Professor Other Phd PMC6109350 2018 Genome_Med 11 Exploring the pre-immune landscape of antigen-specific T cells Research article yes yes immune access yes yes yes Analytical GitHub yes Rmd Multiple 27 Male Head Other Phd PMC5992758 2018 Genome_Med 11 A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing Research article yes yes cisCall yes yes yes Tool GitHub no 19 Male Professor Other "MD, Postdoc" Phd Other PMC6436528 2018 Nat_Biotechnol 32 Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Research article yes no supplementary no yes yes GitHub 895 Female Program Lead "Other, Genetics" Postdoc Postdoc Other PMC6590076 2018 Nat_Biotechnol 32 Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions Research article yes yes ProteomeXchange no yes yes Analytical GitHub no 23 Male Associate Professor Other Phd Phd Other PMC6330062 2018 Nat_Genet 25.5 High resolution genetic mapping of putative causal interactions between regions of open chromatin Research article yes no European Nucleotide Archive yes yes yes Pipeline GitHub no 63 Male Group Leader "Other, Genetics" Phd Postdoc "Other, Genetics" PMC6624853 2018 Nat_Methods 28.5 Analyzing complex single molecule emission patterns with deep learning Research article yes yes yes yes yes Software GitHub 55 Male Assistant Professor Other Phd Phd Other PMC6235447 2018 Nat_Methods 28.5 Species-level functional profiling of metagenomes and metatranscriptomes Research article yes yes Human Microbiome Project yes yes yes Pipeline GitHub no 874 Male Professor CS Phd Phd Bioinformatics PMC6076999 2018 Nat_Methods 28.5 Genome-wide SWAp-tag yeast libraries for proteome exploration Research article yes yes Loqate database yes yes yes Analytical yes GitHub no 103 Female Professor "Other, Genetics" Phd Postdoc Other PMC6289068 2018 Nat_Methods 28.5 Deep Generative Modeling for Single-cell Transcriptomics Research article yes yes GitHub yes yes yes Analytical GitHub yes notebook Multiple 693 Male Associate Professor Other Phd Phd CS PMC4908351 2016 Bioinformatics 7.3 Genome assembly from synthetic long read clouds Research article yes yes yes yes Pipeline/Software code/Tool no (Figures don't look like they were generated by code) GitHub no 35 Male Emeritus Professor CS Phd Post Doc CS PMC4908349 2016 Bioinformatics 7.3 RNAiFold2T: Constraint Programming design of thermo-IRES switches Research article yes yes yes yes Pipeline/Software code/Tool no GitHub no 12 Male Professor "Other, courtesy Professor of Computer Science" Phd Phd CS and Bioinformatics PMC6822339 2019 Genome_Med 11 pTuneos: prioritizing tumor neoantigens from next-generation sequencing data Research article yes yes yes yes yes Package GitHub no no 55 Female Associate Professor Bioinformatics Phd PMC6916105 2019 Genome_Med 11 FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures Research article yes yes yes yes yes Package GitHub no yes 68 Male Professor