selected publications
- CNCDatabase: a database of non-coding cancer drivers. Nucleic acids research. 2020 Academic Article GET IT
- Lineage Reversion Drives WNT Independence in Intestinal Cancer. Cancer discovery. 2020 Academic Article GET IT
- Loss-of-function tolerance of enhancers in the human genome. PLoS genetics. 2020 Academic Article GET IT
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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: 1 -
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: 5 -
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Nature.
2020
Academic Article
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Times cited: 56 -
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.
Communications biology.
2020
Academic Article
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Times cited: 15 - Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature communications. 2020 Academic Article GET IT
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Genomic basis for RNA alterations in cancer.
Nature.
2020
Academic Article
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Times cited: 40 -
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Nature communications.
2020
Academic Article
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Times cited: 6 -
Integrative pathway enrichment analysis of multivariate omics data.
Nature communications.
2020
Academic Article
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Times cited: 5 -
Pan-cancer analysis of whole genomes.
Nature.
2020
Academic Article
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Times cited: 186 -
Pathway and network analysis of more than 2500 whole cancer genomes.
Nature communications.
2020
Academic Article
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Times cited: 9 -
Patterns of somatic structural variation in human cancer genomes.
Nature.
2020
Academic Article
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Times cited: 39 -
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.
Cell systems.
2019
Academic Article
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Times cited: 9 -
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Cell.
2018
Academic Article
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Times cited: 82 -
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: 29 -
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Cell.
2018
Academic Article
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Times cited: 425 -
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: 26 -
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: 15 -
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: 5 -
Inherited determinants of early recurrent somatic mutations in prostate cancer.
Nature communications.
2017
Academic Article
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Times cited: 13 -
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.
Nature genetics.
2017
Academic Article
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Times cited: 28 -
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 -
Non-coding genetic variation in cancer.
Current opinion in systems biology.
2017
Review
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Times cited: 16 -
Cancer genomics: Hard-to-reach repairs.
Nature.
2016
Article
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Times cited: 3 -
Role of non-coding sequence variants in cancer.
Nature reviews. Genetics.
2016
Review
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Times cited: 220 -
The Molecular Taxonomy of Primary Prostate Cancer.
Cell.
2015
Academic Article
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Times cited: 1169 -
A global reference for human genetic variation.
Nature.
2015
Review
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Times cited: 5034 -
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: 34 -
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Nature communications.
2014
Academic Article
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Times cited: 169 -
Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.
PLoS pathogens.
2014
Academic Article
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Times cited: 11 -
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Genome biology.
2014
Academic Article
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Times cited: 148 - Learning to swim in a sea of genomic data. Genome biology. 2013 Academic Article GET IT
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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: 239 -
Interpretation of genomic variants using a unified biological network approach.
PLoS computational biology.
2013
Academic Article
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Times cited: 103 -
An integrated map of genetic variation from 1,092 human genomes.
Nature.
2012
Academic Article
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Times cited: 4919 -
An integrated encyclopedia of DNA elements in the human genome.
Nature.
2012
Academic Article
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Times cited: 8660 -
Architecture of the human regulatory network derived from ENCODE data.
Nature.
2012
Academic Article
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Times cited: 939 -
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: 44 -
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: 744 -
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: 734 -
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: 655 -
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: 52 - A map of human genome variation from population-scale sequencing. Nature. 2010 Academic Article GET IT
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Segmental duplications in the human genome reveal details of pseudogene formation.
Nucleic acids research.
2010
Academic Article
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Times cited: 19 -
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: 30 -
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: 35 -
Computational analysis of membrane proteins: the largest class of drug targets.
Drug discovery today.
2009
Review
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Times cited: 156 -
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: 18 -
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: 97 -
Pseudofam: the pseudogene families database.
Nucleic acids research.
2008
Academic Article
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Times cited: 26 -
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: 31 - 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
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A physicochemical model for analyzing DNA sequences.
Journal of chemical information and modeling.
2006
Conference Paper
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Times cited: 16