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NEMO: cancer subtyping by integration of partial multi-omic data

Bioinformatics, 2019-09, Vol.35 (18), p.3348-3356

2019

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PlasClass improves plasmid sequence classification

PLoS computational biology, 2020-04, Vol.16 (4), p.e1007781-e1007781

2020

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DOMINO: a network‐based active module identification algorithm with reduced rate of false calls

Molecular systems biology, 2021-01, Vol.17 (1), p.e9593-n/a

2021

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Dissection of regulatory networks that are altered in disease via differential co-expression

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002955-e1002955

2013

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FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map

Genome Biology, 2018-05, Vol.19 (1), p.56-56, Article 56

2018

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Inaccuracy of the log‐rank approximation in cancer data analysis

Molecular systems biology, 2019-08, Vol.15 (8), p.e8754-n/a

2019

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PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets

BMC bioinformatics, 2019-12, Vol.20 (1), p.732-732, Article 732

2019

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Identification of functional modules using network topology and high-throughput data

BMC systems biology, 2007-01, Vol.1 (1), p.8-8, Article 8

2007

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Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Bioinformatics (Oxford, England), 2017-02, Vol.33 (4), p.475-482

2017

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Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases

Nature communications, 2024-04, Vol.15 (1), p.3147-3147

2024

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Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

Molecular systems biology, 2017-02, Vol.13 (2), p.910-n/a

2017

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Reconstructing cancer karyotypes from short read data: the half empty and half full glass

BMC bioinformatics, 2017-11, Vol.18 (1), p.488-488, Article 488

2017

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Quantification of protein half-lives in the budding yeast proteome

Proceedings of the National Academy of Sciences - PNAS, 2006-08, Vol.103 (35), p.13004-13009

2006

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Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets

Genome Research, 2008-07, Vol.18 (7), p.1180-1189

2008

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Parameterized syncmer schemes improve long-read mapping

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010638-e1010638

2022

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Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005777-e1005777

2017

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Discovering statistically significant biclusters in gene expression data

Bioinformatics, 2002-07, Vol.18 (suppl-1), p.S136-S144

2002

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MONET: Multi-omic module discovery by omic selection

PLoS computational biology, 2020-09, Vol.16 (9), p.e1008182-e1008182

2020

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Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate

PLoS computational biology, 2017-08, Vol.13 (8), p.e1005700-e1005700

2017

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Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

Genome research, 2016-05, Vol.26 (5), p.601

2016

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EXPANDER--an integrative program suite for microarray data analysis

BMC bioinformatics, 2005-09, Vol.6 (1), p.232-232, Article 232

2005

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Reduced changes in protein compared to mRNA levels across non-proliferating tissues

BMC genomics, 2017-04, Vol.18 (1), p.305-305, Article 305

2017

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Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD

PloS one, 2019-08, Vol.14 (8), p.e0219728-e0219728

2019

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Analysis of blood-based gene expression in idiopathic Parkinson disease

Neurology, 2017-10, Vol.89 (16), p.1676

2017

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NEMO: cancer subtyping by integration of partial multi-omic data

PlasClass improves plasmid sequence classification

DOMINO: a network‐based active module identification algorithm with reduced rate of false calls

Dissection of regulatory networks that are altered in disease via differential co-expression

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map

Inaccuracy of the log‐rank approximation in cancer data analysis

PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets

Identification of functional modules using network topology and high-throughput data

Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases

Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

Reconstructing cancer karyotypes from short read data: the half empty and half full glass

Quantification of protein half-lives in the budding yeast proteome

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets

Parameterized syncmer schemes improve long-read mapping

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

Discovering statistically significant biclusters in gene expression data

MONET: Multi-omic module discovery by omic selection

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture

EXPANDER--an integrative program suite for microarray data analysis

Reduced changes in protein compared to mRNA levels across non-proliferating tissues

Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD

Analysis of blood-based gene expression in idiopathic Parkinson disease

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