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Lag penalized weighted correlation for time series clustering

BMC bioinformatics, 2020-01, Vol.21 (1), p.21-21, Article 21

2020

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Network inference with Granger causality ensembles on single-cell transcriptomics

Cell reports (Cambridge), 2022-02, Vol.38 (6), p.110333-110333, Article 110333

2022

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Opportunities and obstacles for deep learning in biology and medicine

Journal of the Royal Society interface, 2018-04, Vol.15 (141), p.20170387

2018

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Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004879-e1004879

2016

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Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus

PLoS biology, 2022-12, Vol.20 (12), p.e3001934

2022

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Linking the signaling cascades and dynamic regulatory networks controlling stress responses

Genome research, 2013-02, Vol.23 (2), p.365-376

2013

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Open collaborative writing with Manubot

PLoS computational biology, 2019-06, Vol.15 (6), p.e1007128

2019

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Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism

PLoS pathogens, 2017-03, Vol.13 (3), p.e1006256-e1006256

2017

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HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B

PLoS pathogens, 2023-07, Vol.19 (7), p.e1011492-e1011492

2023

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Automating parameter selection to avoid implausible biological pathway models

NPJ systems biology and applications, 2021-02, Vol.7 (1), p.12-12, Article 12

2021

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DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

BMC systems biology, 2012-08, Vol.6 (1), p.104-104

2012

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Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference

Cell systems, 2024-08, Vol.15 (8), p.673-675

Gitter, Anthony

2024

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A network-based approach for predicting missing pathway interactions

PLoS computational biology, 2012-08, Vol.8 (8), p.e1002640-e1002640

2012

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Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Cell reports (Cambridge), 2018-09, Vol.24 (13), p.3607-3618

2018

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Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

PLoS computational biology, 2018-05, Vol.13 (5), p.e1006088-e1006088

2018

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Multitask learning of signaling and regulatory networks with application to studying human response to flu

PLoS computational biology, 2014-12, Vol.10 (12), p.e1003943-e1003943

2014

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Studying and modelling dynamic biological processes using time-series gene expression data

Nature reviews. Genetics, 2012-08, Vol.13 (8), p.552-564

2012

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The Coming of Age of Nucleic Acid Vaccines during COVID-19

mSystems, 2023-04, Vol.8 (2), p.e0092822-e0092822

2023

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Predicting kinase inhibitors using bioactivity matrix derived informer sets

PLoS computational biology, 2019-08, Vol.15 (8), p.e1006813-e1006813

2019

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Inferring signaling pathways with probabilistic programming

Bioinformatics, 2020-12, Vol.36 (Supplement_2), p.i822-i830

2020

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Backup in gene regulatory networks explains differences between binding and knockout results

Molecular systems biology, 2009-06, Vol.5 (1), p.276-n/a

2009

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Identification and Development of Therapeutics for COVID-19

mSystems, 2021-12, Vol.6 (6), p.e0023321-e0023321

2021

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Application of Traditional Vaccine Development Strategies to SARS-CoV-2

mSystems, 2023-04, Vol.8 (2), p.e0092722

2023

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Neural networks to learn protein sequence–function relationships from deep mutational scanning data

Proceedings of the National Academy of Sciences - PNAS, 2021-11, Vol.118 (48), p.1-12

2021

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Lag penalized weighted correlation for time series clustering

Network inference with Granger causality ensembles on single-cell transcriptomics

Opportunities and obstacles for deep learning in biology and medicine

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

Open collaborative writing with Manubot

Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism

HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B

Automating parameter selection to avoid implausible biological pathway models

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference

A network-based approach for predicting missing pathway interactions

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

Multitask learning of signaling and regulatory networks with application to studying human response to flu

Studying and modelling dynamic biological processes using time-series gene expression data

The Coming of Age of Nucleic Acid Vaccines during COVID-19

Predicting kinase inhibitors using bioactivity matrix derived informer sets

Inferring signaling pathways with probabilistic programming

Backup in gene regulatory networks explains differences between binding and knockout results

Identification and Development of Therapeutics for COVID-19

Application of Traditional Vaccine Development Strategies to SARS-CoV-2

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

Neural networks to learn protein sequence–function relationships from deep mutational scanning data

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