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Enhanced regulatory sequence prediction using gapped k-mer features

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003711-e1003711

2014

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Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma

Cancer cell, 2017-07, Vol.32 (1), p.101-114.e8

2017

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Inferring clonal evolution of tumors from single nucleotide somatic mutations

BMC bioinformatics, 2014-02, Vol.15 (1), p.35-35, Article 35

2014

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QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

Genome Biology, 2018-03, Vol.19 (1), p.45-45, Article 45

2018

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BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

PLoS computational biology, 2015-06, Vol.11 (6), p.e1004333-e1004333

2015

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High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

Molecular cell, 2018-02, Vol.69 (3), p.517-532.e11

2018

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A practical guide to cancer subclonal reconstruction from DNA sequencing

Nature methods, 2021-02, Vol.18 (2), p.144-155

2021

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Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy

Cell, 2021-01, Vol.184 (1), p.226-242.e21

2021

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Evaluation of methods for modeling transcription factor sequence specificity

Nature biotechnology, 2013-02, Vol.31 (2), p.126-134

2013

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PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

Genome Biology, 2015-02, Vol.16 (1), p.35-35, Article 35

2015

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Cytoscape Web: an interactive web-based network browser

Bioinformatics, 2010-09, Vol.26 (18), p.2347-2348

2010

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GeneMANIA: Fast gene network construction and function prediction for Cytoscape [version 1; peer review: 2 approved]

F1000 research, 2014, Vol.3, p.153-153

2014

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Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity

Nature communications, 2021-01, Vol.12 (1), p.335-335, Article 335

2021

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The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

Nucleic acids research, 2010-07, Vol.38 (Web Server issue), p.W214-W220

2010

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Deep Learning-driven research for drug discovery: Tackling Malaria

PLoS computational biology, 2020-02, Vol.16 (2), p.e1007025-e1007025

2020

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Machine learning and computer vision approaches for phenotypic profiling

The Journal of cell biology, 2017-01, Vol.216 (1), p.65-71

2017

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Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood

Nature communications, 2021-08, Vol.12 (1), p.4921-4921, Article 4921

2021

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Similarity regression predicts evolution of transcription factor sequence specificity

Nature genetics, 2019-06, Vol.51 (6), p.981-989

2019

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Regional mutational signature activities in cancer genomes

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010733-e1010733

2022

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Using expression profiling data to identify human microRNA targets

Nature methods, 2007-12, Vol.4 (12), p.1045-1049

2007

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RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

Methods (San Diego, Calif.), 2017-04, Vol.118-119, p.3-15

2017

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Dynamic modularity in protein interaction networks predicts breast cancer outcome

Nature biotechnology, 2009-02, Vol.27 (2), p.199-204

2009

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Clusternomics: Integrative context-dependent clustering for heterogeneous datasets

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005781-e1005781

2017

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Enhanced regulatory sequence prediction using gapped k-mer features

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma

Inferring clonal evolution of tumors from single nucleotide somatic mutations

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

A practical guide to cancer subclonal reconstruction from DNA sequencing

Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy

Evaluation of methods for modeling transcription factor sequence specificity

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

Cytoscape Web: an interactive web-based network browser

GeneMANIA: Fast gene network construction and function prediction for Cytoscape [version 1; peer review: 2 approved]

Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

Deep Learning-driven research for drug discovery: Tackling Malaria

Machine learning and computer vision approaches for phenotypic profiling

Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood

A compendium of RNA-binding motifs for decoding gene regulation

Similarity regression predicts evolution of transcription factor sequence specificity

Regional mutational signature activities in cancer genomes

Using expression profiling data to identify human microRNA targets

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

Dynamic modularity in protein interaction networks predicts breast cancer outcome

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets

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