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119 peer-reviewed articles • 33,357 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
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1Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction
Briefings in Bioinformatics, 2024, 25,
6.666Citations (PDF)
2Prioritizing genomic variants pathogenicity via DNA, RNA, and protein-level features based on extreme gradient boosting
Human Genetics, 2024, 144, 253-263
2.92Citations (PDF)
3Deciphering cell types by integrating scATAC-seq data with genome sequences
Nature Computational Science, 2024, 4, 285-298
11.628Citations (PDF)
4VCAT: an integrated variant function annotation tools
Human Genetics, 2024, 143, 1311-1322
2.90Citations (PDF)
5Enhanced soluble expression and characterization of human N-acetylglucosaminyltransferase IVa in Escherichia coli
Enzyme and Microbial Technology, 2024, 181, 110524
3.61Citations (PDF)
6Fast and accurate protein intrinsic disorder prediction by using a pretrained language model
Briefings in Bioinformatics, 2023, 24,
6.620Citations (PDF)
7Capturing large genomic contexts for accurately predicting enhancer-promoter interactions
Briefings in Bioinformatics, 2022, 23,
6.632Citations (PDF)
8Cardiac ISL1-Interacting Protein, a Cardioprotective Factor, Inhibits the Transition From Cardiac Hypertrophy to Heart Failure
Frontiers in Cardiovascular Medicine, 2022, 9,
2.44Citations (PDF)
9Molecular Correlates of Venous Thromboembolism (VTE) in Ovarian Cancer
Cancers, 2022, 14, 1496
3.823Citations (PDF)
10Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections
Human Genetics, 2022, 142, 245-274
2.91Citations (PDF)
11Ab initio spillover compensation in mass cytometry data
Cytometry Part A: the Journal of the International Society for Analytical Cytology, 2021, 99, 899-909
2.519Citations (PDF)
12Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells
Blood, 2021, 137, 624-636
5.0276Citations (PDF)
13Sparse Subspace Clustering for Stream Data
IEEE Access, 2021, 9, 57271-57279
3.04Citations (PDF)
14GMP-Compliant Universal Antigen Presenting Cells (uAPC) Promote the Metabolic Fitness and Antitumor Activity of Armored Cord Blood CAR-NK Cells
Frontiers in Immunology, 2021, 12,
4.950Citations (PDF)
15MEDALT: single-cell copy number lineage tracing enabling gene discovery
Genome Biology, 2021, 22,
8.139Citations (PDF)
16Single-cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia
IScience, 2021, 24, 102186
3.558Citations (PDF)
17Spatially interacting phosphorylation sites and mutations in cancer
Nature Communications, 2021, 12,
13.720Citations (PDF)
18Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes
Frontiers in Immunology, 2021, 12,
4.917Citations (PDF)
19Extended live-cell barcoding approach for multiplexed mass cytometry
Scientific Reports, 2021, 11,
3.421Citations (PDF)
20Identification of Novel Single-Nucleotide Variants With Potential of Mediating Malfunction of MicroRNA in Congenital Heart Disease
Frontiers in Cardiovascular Medicine, 2021, 8,
2.45Citations (PDF)
21Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes
Nature Biotechnology, 2021, 39, 599-608
29.8822Citations (PDF)
22Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma
Nature Medicine, 2021, 27, 141-151
33.0246Citations (PDF)
23Dynamic Spatio-Temporal Graph-Based CNNs for Traffic Flow Prediction
IEEE Access, 2020, 8, 185136-185145
3.076Citations (PDF)
24Sex differences in oncogenic mutational processes
Nature Communications, 2020, 11,
13.794Citations (PDF)
25A robust benchmark for detection of germline large deletions and insertions
Nature Biotechnology, 2020, 38, 1347-1355
29.8404Citations (PDF)
26Latent periodic process inference from single-cell RNA-seq data
Nature Communications, 2020, 11,
13.755Citations (PDF)
27Systematic analysis to identify transcriptome-wide dysregulation of Alzheimer’s disease in genes and isoforms
Human Genetics, 2020, 140, 609-623
2.920Citations (PDF)
28Hybrid oncocytic/chromophobe renal tumors are molecularly distinct from oncocytoma and chromophobe renal cell carcinoma
Modern Pathology, 2019, 32, 1698-1707
4.850Citations (PDF)
29SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
Genome Research, 2019, 29, 1847-1859
4.6121Citations (PDF)
30Elevated Endogenous SDHA Drives Pathological Metabolism in Highly Metastatic Uveal Melanoma
2019, 60, 4187
51Citations (PDF)
31SCMarker: Ab initio marker selection for single cell transcriptome profiling
PLoS Computational Biology, 2019, 15, e1007445
3.139Citations (PDF)
32Dynamic clonal remodelling in breast cancer metastases is associated with subtype conversion
European Journal of Cancer, 2019, 120, 54-64
4.920Citations (PDF)
33Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy
Cancer Cell, 2019, 35, 851-867.e7
33.0212Citations (PDF)
34Multi-platform discovery of haplotype-resolved structural variation in human genomes
Nature Communications, 2019, 10,
13.7841Citations (PDF)
35Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes
BMC Medical Genomics, 2019, 12,
1.712Citations (PDF)
36Integrated transcriptomic–genomic tool Texomer profiles cancer tissues
Nature Methods, 2019, 16, 401-404
24.612Citations (PDF)
37Prospective Clinical Sequencing of Adult Glioma
Molecular Cancer Therapeutics, 2019, 18, 991-1000
1.918Citations (PDF)
38Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2
Cell, 2019, 176, 1310-1324.e10
33.691Citations (PDF)
39A novel immature natural killer cell subpopulation predicts relapse after cord blood transplantation
Blood Advances, 2019, 3, 4117-4130
5.034Citations (PDF)
40Identifying Common Genes, Cell Types and Brain Regions Between Diseases of the Nervous System
Frontiers in Genetics, 2019, 10,
2.36Citations (PDF)
41Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling
Nature Communications, 2019, 10,
13.7128Citations (PDF)
42Distinct Biological Types of Ocular Adnexal Sebaceous Carcinoma: HPV-Driven and Virus-Negative Tumors Arise through Nonoverlapping Molecular-Genetic Alterations
Clinical Cancer Research, 2019, 25, 1280-1290
6.855Citations (PDF)
43Comprehensive Characterization of Cancer Driver Genes and Mutations
Cell, 2018, 173, 371-385.e18
33.62,151Citations (PDF)
44Pathogenic Germline Variants in 10,389 Adult Cancers
Cell, 2018, 173, 355-370.e14
33.6829Citations (PDF)
45Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Cell Reports, 2018, 23, 227-238.e3
6.3588Citations (PDF)
46The Immune Landscape of Cancer
Immunity, 2018, 48, 812-830.e14
22.65,185Citations (PDF)
47Systematic Analysis of Splice-Site-Creating Mutations in Cancer
Cell Reports, 2018, 23, 270-281.e3
6.3234Citations (PDF)
48Untying the gordion knot of targeting MET in cancer
Cancer Treatment Reviews, 2018, 66, 95-103
9.522Citations (PDF)
49Systematic Functional Annotation of Somatic Mutations in Cancer
Cancer Cell, 2018, 33, 450-462.e10
33.0316Citations (PDF)
50Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell‐free DNA by next‐generation sequencing
Cancer, 2018, 124, 1061-1069
4.013Citations (PDF)
51Computational approaches for inferring tumor evolution from single-cell genomic data
Current Opinion in Systems Biology, 2018, 7, 16-25
1.442Citations (PDF)
52Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Genome Biology, 2018, 19,
8.150Citations (PDF)
53Hypervirulent group A Streptococcus emergence in an acaspular background is associated with marked remodeling of the bacterial cell surface
PLoS ONE, 2018, 13, e0207897
2.313Citations (PDF)
54Genetic biomarkers of sensitivity and resistance to venetoclax monotherapy in patients with relapsed acute myeloid leukemia
American Journal of Hematology, 2018, 93,
6.5138Citations (PDF)
55In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer
Nature Communications, 2018, 9,
13.745Citations (PDF)
56Metachronous Medulloblastoma in a Child With Successfully Treated Neuroblastoma: Case Report and Novel Findings of DNA Sequencing
Journal of the National Comprehensive Cancer Network: JNCCN, 2018, 16, 683-691
12.63Citations (PDF)
57Cancer driver mutation prediction through Bayesian integration of multi-omic data
PLoS ONE, 2018, 13, e0196939
2.326Citations (PDF)
58HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
Genome Research, 2017, 27, 793-800
4.633Citations (PDF)
59An Organismal CNV Mutator Phenotype Restricted to Early Human Development
Cell, 2017, 168, 830-842.e7
33.6112Citations (PDF)
60GenomeVIP: a cloud platform for genomic variant discovery and interpretation
Genome Research, 2017, 27, 1450-1459
4.618Citations (PDF)
61Ph-like acute lymphoblastic leukemia: a high-risk subtype in adults
Blood, 2017, 129, 572-581
5.0363Citations (PDF)
62A Population of Heterogeneous Breast Cancer Patient-Derived Xenografts Demonstrate Broad Activity of PARP Inhibitor in BRCA1/2 Wild-Type Tumors
Clinical Cancer Research, 2017, 23, 6468-6477
6.866Citations (PDF)
63Sarcomatoid Renal Cell Carcinoma Has a Distinct Molecular Pathogenesis, Driver Mutation Profile, and Transcriptional Landscape
Clinical Cancer Research, 2017, 23, 6686-6696
6.889Citations (PDF)
64Comprehensive Genomic Profiling of Metastatic Squamous Cell Carcinoma of the Anal Canal
Molecular Cancer Research, 2017, 15, 1542-1550
3.173Citations (PDF)
65Active Disclosure of Secondary Germline Findings to Deceased Research Participants’ Personal Representatives: Process and Outcomes
JCO Precision Oncology, 2017, , 1-5
1.94Citations (PDF)
66SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models
Genome Biology, 2017, 18,
8.1184Citations (PDF)
67BreakPoint Surveyor: a pipeline for structural variant visualization
Bioinformatics, 2017, 33, 3121-3122
4.75Citations (PDF)
68Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types
BMC Genomics, 2016, 17,
3.233Citations (PDF)
69Divergent viral presentation among human tumors and adjacent normal tissues
Scientific Reports, 2016, 6,
3.467Citations (PDF)
70Monovar: single-nucleotide variant detection in single cells
Nature Methods, 2016, 13, 505-507
24.6177Citations (PDF)
71Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set
BMC Medicine, 2016, 14,
7.1111Citations (PDF)
72Functional annotation of rare gene aberration drivers of pancreatic cancer
Nature Communications, 2016, 7,
13.784Citations (PDF)
73novoBreak: local assembly for breakpoint detection in cancer genomes
Nature Methods, 2016, 14, 65-67
24.6107Citations (PDF)
74ClinSeK: a targeted variant characterization framework for clinical sequencing
Genome Medicine, 2015, 7,
9.613Citations (PDF)
75Genome Modeling System: A Knowledge Management Platform for Genomics
PLoS Computational Biology, 2015, 11, e1004274
3.187Citations (PDF)
76Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms
Nature Communications, 2015, 6,
13.794Citations (PDF)
77Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations
Cancer Research, 2015, 75, 5341-5354
3.8160Citations (PDF)
78Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer
Cancer Letters, 2015, 357, 179-185
8.689Citations (PDF)
79RET Fusion as a Novel Driver of Medullary Thyroid Carcinoma
Journal of Clinical Endocrinology and Metabolism, 2015, 100, 788-793
4.078Citations (PDF)
80Clinical Actionability Enhanced through Deep Targeted Sequencing of Solid Tumors
Clinical Chemistry, 2015, 61, 544-553
1.191Citations (PDF)
81Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations
Genome Medicine, 2015, 7,
9.66Citations (PDF)
82A Decision Support Framework for Genomically Informed Investigational Cancer Therapy
Journal of the National Cancer Institute, 2015, 107,
4.6189Citations (PDF)
83An integrated map of structural variation in 2,504 human genomes
Nature, 2015, 526, 75-81
37.92,437Citations (PDF)
84TransVar: a multilevel variant annotator for precision genomics
Nature Methods, 2015, 12, 1002-1003
24.698Citations (PDF)
85Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours
Nature Communications, 2015, 6,
13.7178Citations (PDF)
86Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes
PLoS ONE, 2015, 10, e0136851
2.366Citations (PDF)
87Towards accurate characterization of clonal heterogeneity based on structural variation
BMC Bioinformatics, 2014, 15,
3.010Citations (PDF)
88TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
Genome Research, 2014, 24, 310-317
4.690Citations (PDF)
89BreakDancer: Identification of Genomic Structural Variation from Paired‐End Read Mapping
Current Protocols in Bioinformatics, 2014, 45,
3.3156Citations (PDF)
90Bias from removing read duplication in ultra-deep sequencing experiments
Bioinformatics, 2014, 30, 1073-1080
4.746Citations (PDF)
91Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Nature, 2014, 512, 155-160
37.91,010Citations (PDF)
92Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
New England Journal of Medicine, 2013, 368, 2059-2074
34.54,867Citations (PDF)
93A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival
Genes and Development, 2013, 27, 1462-1472
4.683Citations (PDF)
94CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features
PLoS ONE, 2013, 8, e77945
2.3117Citations (PDF)
95SomaticSniper: identification of somatic point mutations in whole genome sequencing data
Bioinformatics, 2012, 28, 311-317
4.7656Citations (PDF)
96BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Bioinformatics, 2012, 28, 1923-1924
4.757Citations (PDF)
97Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells
Cell Stem Cell, 2012, 10, 570-582
16.4206Citations (PDF)
98Whole-genome analysis informs breast cancer response to aromatase inhibition
Nature, 2012, 486, 353-360
37.9993Citations (PDF)
99Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers
Cell, 2012, 150, 1121-1134
33.61,117Citations (PDF)
100Clonal Architecture of Secondary Acute Myeloid Leukemia
New England Journal of Medicine, 2012, 366, 1090-1098
34.5736Citations (PDF)
101Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Nature, 2012, 481, 506-510
37.91,931Citations (PDF)
102The Origin and Evolution of Mutations in Acute Myeloid Leukemia
Cell, 2012, 150, 264-278
33.61,506Citations (PDF)
103CREST maps somatic structural variation in cancer genomes with base-pair resolution
Nature Methods, 2011, 8, 652-654
24.6476Citations (PDF)
104Mapping copy number variation by population-scale genome sequencing
Nature, 2011, 470, 59-65
37.91,078Citations (PDF)
105Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene
JAMA - Journal of the American Medical Association, 2011, 305, 1577
16.5239Citations (PDF)
106Identification of a Novel <emph type="ital">TP53</emph> Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML
JAMA - Journal of the American Medical Association, 2011, 305, 1568
16.5150Citations (PDF)
107Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression
Journal of Clinical Investigation, 2011, 121, 1445-1455
10.691Citations (PDF)
108Genome remodelling in a basal-like breast cancer metastasis and xenograft
Nature, 2010, 464, 999-1005
37.91,114Citations (PDF)
109CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
Bioinformatics, 2010, 26, 464-469
4.760Citations (PDF)
110VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Bioinformatics, 2009, 25, 2283-2285
4.71,372Citations (PDF)
111BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Nature Methods, 2009, 6, 677-681
24.61,464Citations (PDF)
112Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome
New England Journal of Medicine, 2009, 361, 1058-1066
34.52,139Citations (PDF)
113Somatic mutations affect key pathways in lung adenocarcinoma
Nature, 2008, 455, 1069-1075
37.92,801Citations (PDF)
114DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
Nature, 2008, 456, 66-72
37.91,342Citations (PDF)
115PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
Genome Research, 2007, 17, 659-666
4.677Citations (PDF)
116On the detection of functionally coherent groups of protein domains with an extension to protein annotation
BMC Bioinformatics, 2007, 8,
3.06Citations (PDF)
117Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular Dynamics and Molecular Field Analysis
Journal of Proteome Research, 2006, 5, 32-43
3.473Citations (PDF)
118Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain
PLoS Computational Biology, 2006, 2, e1
3.1158Citations (PDF)
119Simultaneous recognition of words and prosody in the Boston University Radio Speech Corpus
Speech Communication, 2005, 46, 418-439
2.136Citations (PDF)