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Author: Mark Gerstein

Rankings

  • All-time downloads: 41,627 (rank: 965 out of 404,161)
  • Categories:
    • bioinformatics: 9,309 (rank: 646 out of 34,272)
    • cell biology: 696 (rank: 8,949 (tie) out of 30,511)
    • evolutionary biology: 297 (rank: 15,294 (tie) out of 20,691)
    • genomics: 31,325 (rank: 243 out of 42,763)

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Preprints

Multi-platform discovery of haplotype-resolved structural variation in human genomes

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Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

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Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

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Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

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Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

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Nearly all new protein-coding predictions in the CHESS database are not protein-coding

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Determining the impact of putative loss-of-function variants in protein-coding genes

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An integrative ENCODE resource for cancer genomics

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Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

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A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation

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Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

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Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols

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STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions

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MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

genomics more details view paper
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microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis

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SVFX: a machine-learning framework to quantify the pathogenicity of structural variants

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Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

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sigLASSO: optimizing cancer mutation signatures jointly with sampling likelihood

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HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps

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GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner

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Storing and analyzing a genome on a blockchain

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Genomic variants concurrently listed in a somatic and a germline mutation database have implications for disease-variant discovery and genomic privacy

genomics more details view paper
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Epigenome-based Splicing Prediction using a Recurrent Neural Network

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To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq

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TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements

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Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients

genomics more details view paper
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Cyclic and Multilevel Causation in Evolutionary Processes

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Leveraging protein dynamics to identify cancer mutational hotspots in 3D-structures

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Bayesian Structural Time Series for Biomedical Sensor Data: A Flexible Modeling Framework for Evaluating Interventions

bioinformatics more details view paper
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FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data

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DiNeR: a Differential Graphical Model for analysis of co-regulation Network Rewiring

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Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients

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NIMBus: a Negative Binomial Regression based Integrative Method for Mutation Burden Analysis

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Privacy-preserving genotype imputation with fully homomorphic encryption

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