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#TitleJournalYearCitations
1The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogrammingCell Research2012452
2The emergence of SARS-CoV-2 in Europe and North AmericaScience2020331
3Network Context and Selection in the Evolution to Enzyme SpecificityScience2012249
4Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cellsNature Genetics2019236
5The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemicScience2022192
6Ubiquitin-Mediated Response to Microsporidia and Virus Infection in C. elegansPLoS Pathogens2014184
7Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cellsProceedings of the National Academy of Sciences of the United States of America2012152
8Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial functionNature Communications2018129
9Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophaseNature Structural and Molecular Biology2019123
10The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2Science2022123
11Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coliScience2013111
12Timing the SARS-CoV-2 index case in Hubei provinceScience2021109
13Experimental selection of hypoxia-tolerant Drosophila melanogasterProceedings of the National Academy of Sciences of the United States of America2011105
14TreeCluster: Clustering biological sequences using phylogenetic treesPLoS ONE201999
15Systems biology analysis of longitudinal functional response of endothelial cells to shear stressProceedings of the National Academy of Sciences of the United States of America201795
16Ten simple rules for writing and sharing computational analyses in Jupyter NotebooksPLoS Computational Biology201986
17Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes riskNature Communications201982
18Technical Variations in Low-Input RNA-seq MethodologiesScientific Reports201475
19Properties of structural variants and short tandem repeats associated with gene expression and complex traitsNature Communications202067
20A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 ElementsPLoS Genetics201165
21Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New YorkNature Communications202165
22Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNANature202260
23AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplificationsNature Communications202049
24TET methylcytosine oxidases: new insights from a decade of researchJournal of Biosciences202049
25Subpixel colocalization reveals amyloid precursor protein-dependent kinesin-1 and dynein association with axonal vesiclesProceedings of the National Academy of Sciences of the United States of America201248
26FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequencesBioinformatics201945
27Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation TrajectoriesStem Cell Reports201944
28Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditionsProceedings of the National Academy of Sciences of the United States of America202143
29Quantitative Transcriptomics using Designed Primer-based AmplificationScientific Reports201338
30Immune DNA signature of T-cell infiltration in breast tumor exomesScientific Reports201630
31De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short ReadsPLoS ONE201029
32High-Resolution Mutational Profiling Suggests the Genetic Validity of Glioblastoma Patient-Derived Pre-Clinical ModelsPLoS ONE201325
33Fast and accurate distance‐based phylogenetic placement using divide and conquerMolecular Ecology Resources202225
34Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeatsNature Communications202022
35Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York CityNature Communications202222
36Identification of therapeutic targets for glioblastoma by network analysisOncogene201618
37Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brainCell Research202216
38Rapid Analysis of Saccharomyces cerevisiae Genome Rearrangements by Multiplex Ligation–Dependent Probe AmplificationPLoS Genetics201215
39The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situNpj Breast Cancer202213
40DEPP: Deep Learning Enables Extending Species Trees using Single GenesSystematic Biology202311
41A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISHNature Biotechnology20239
42Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seqNucleic Acids Research20218
43Wnt Pathway Activation Increases Hypoxia Tolerance during DevelopmentPLoS ONE20148
44Human Genetics to Identify Therapeutic Targets for NAFLD: Challenges and OpportunitiesFrontiers in Endocrinology20218
45A Two-State Model of Tree Evolution and Its Applications to Alu RetrotranspositionSystematic Biology20185
46Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021Journal of Infectious Diseases20225
47Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictionsNature Communications20225
48Tests of Selection in Pooled Case-Control Data: An Empirical StudyFrontiers in Genetics20113
49Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsamplingCell Systems20223
50Whole-genome CRISPR screening identifies PI3K/AKT as a downstream component of the oncogenic GNAQ–focal adhesion kinase signaling circuitryJournal of Biological Chemistry20233