selected publications
- Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. Science (New York, N.Y.). 2024 Academic Article GET IT
- Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data. Cell systems. 2024 Academic Article GET IT
- TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. 2024 GET IT
- Recapitulation of patient-specific 3D chromatin conformation using machine learning. Cell reports methods. 2023 Academic Article GET IT
- Impulsivity and Risk-Taking Behavior in School-Going Adolescents. Cureus. 2023 Academic Article GET IT
- ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer. Science advances. 2023 Academic Article GET IT
- Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers. Nature communications. 2022 Academic Article GET IT
- Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic viruses. The Journal of clinical investigation. 2022 Academic Article GET IT
- Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets. Science (New York, N.Y.). 2022 Academic Article GET IT
- Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proceedings of the National Academy of Sciences of the United States of America. 2021 Academic Article GET IT
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Developmental chromatin programs determine oncogenic competence in melanoma.
Science (New York, N.Y.).
2021
Academic Article
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Times cited: 1 - Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell reports. 2021 Academic Article GET IT
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CNCDatabase: a database of non-coding cancer drivers.
Nucleic acids research.
2021
Academic Article
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Times cited: 9 -
Lineage Reversion Drives WNT Independence in Intestinal Cancer.
Cancer discovery.
2020
Academic Article
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Times cited: 47 -
Loss-of-function tolerance of enhancers in the human genome.
PLoS genetics.
2020
Academic Article
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Times cited: 7 -
DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.
Genome biology.
2020
Academic Article
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Times cited: 36 -
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.
Cell.
2020
Academic Article
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Times cited: 88 -
Analyses of non-coding somatic drivers in 2,658Â cancer whole genomes.
Nature.
2020
Academic Article
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Times cited: 368 -
Genomic basis for RNA alterations in cancer.
Nature.
2020
Academic Article
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Times cited: 272 -
Pan-cancer analysis of whole genomes.
Nature.
2020
Academic Article
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Times cited: 1741 -
Pathway and network analysis of more than 2500 whole cancer genomes.
Nature communications.
2020
Academic Article
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Times cited: 69 -
Patterns of somatic structural variation in human cancer genomes.
Nature.
2020
Academic Article
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Times cited: 457 -
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.
Cell systems.
2019
Academic Article
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Times cited: 50 -
FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications.
American journal of human genetics.
2018
Academic Article
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Times cited: 60 -
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Cell.
2018
Academic Article
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Times cited: 1309 -
MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene.
The Journal of pathology.
2017
Academic Article
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Times cited: 76 -
Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.
Genome biology.
2017
Academic Article
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Times cited: 25 -
Health beliefs regarding pediatric cerebral palsy among caregivers in Botswana: A qualitative study.
Child: care, health and development.
2017
Academic Article
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Times cited: 9 -
Inherited determinants of early recurrent somatic mutations in prostate cancer.
Nature communications.
2017
Academic Article
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Times cited: 27 -
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.
Nature genetics.
2017
Academic Article
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Times cited: 47 -
Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.
Current protocols in bioinformatics.
2017
Academic Article
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Times cited: 1 -
Role of non-coding sequence variants in cancer.
Nature reviews. Genetics.
2016
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Times cited: 250 -
The Molecular Taxonomy of Primary Prostate Cancer.
Cell.
2015
Academic Article
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Times cited: 2263 -
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
Nucleic acids research.
2015
Academic Article
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Times cited: 54 -
Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.
PLoS pathogens.
2014
Academic Article
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Times cited: 18 -
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Genome biology.
2014
Academic Article
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Times cited: 245 -
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Science (New York, N.Y.).
2013
Academic Article
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Times cited: 290 -
Interpretation of genomic variants using a unified biological network approach.
PLoS computational biology.
2013
Academic Article
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Times cited: 132 -
An integrated encyclopedia of DNA elements in the human genome.
Nature.
2012
Academic Article
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Times cited: 12676 -
Architecture of the human regulatory network derived from ENCODE data.
Nature.
2012
Academic Article
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Times cited: 1144 -
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
Bioinformatics (Oxford, England).
2012
Academic Article
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Times cited: 54 -
A systematic survey of loss-of-function variants in human protein-coding genes.
Science (New York, N.Y.).
2012
Academic Article
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Times cited: 940 -
A user's guide to the encyclopedia of DNA elements (ENCODE).
PLoS biology.
2011
Academic Article
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Times cited: 902 -
Mapping copy number variation by population-scale genome sequencing.
Nature.
2011
Academic Article
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Times cited: 875 -
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Science (New York, N.Y.).
2010
Academic Article
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Times cited: 765 -
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Genome research.
2010
Academic Article
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Times cited: 56 -
Segmental duplications in the human genome reveal details of pseudogene formation.
Nucleic acids research.
2010
Academic Article
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Times cited: 24 -
Using semantic web rules to reason on an ontology of pseudogenes.
Bioinformatics (Oxford, England).
2010
Academic Article
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Times cited: 19 -
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus.
Biochimica et biophysica acta.
2010
Academic Article
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Times cited: 37 -
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.
BMC genomics.
2009
Academic Article
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Times cited: 44 -
Computational analysis of membrane proteins: the largest class of drug targets.
Drug discovery today.
2009
Information Resource
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Times cited: 199 -
Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.
Journal of virology.
2009
Academic Article
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Times cited: 21 -
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus.
Proceedings of the National Academy of Sciences of the United States of America.
2009
Academic Article
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Times cited: 109 -
Pseudofam: the pseudogene families database.
Nucleic acids research.
2008
Academic Article
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Times cited: 35 -
Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics.
Nano letters.
2008
Academic Article
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Times cited: 35 - Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study. The journal of physical chemistry. B. 2006 Academic Article GET IT
- Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. The journal of physical chemistry. B. 2006 Academic Article GET IT