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Publications

22 peer-reviewed articles • 43,767 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
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1A genome scale transcriptional regulatory model of the human placenta
Science Advances, 2024, 10, eadf3411
8.315Citations (PDF)
2Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types
Cell Reports, 2020, 32, 108029
4.629Citations (PDF)
3Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis
Molecular Cell, 2020, 78, 960-974.e11
9.097Citations (PDF)
4Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate
Cell Stem Cell, 2019, 24, 812-820.e5
12.4128Citations (PDF)
5Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders
Cell Systems, 2019, 8, 122-135.e7
3.944Citations (PDF)
6Reproducible big data science: A case study in continuous FAIRness
PLoS ONE, 2019, 14, e0213013
1.632Citations (PDF)
7Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus
Neuron, 2018, 99, 64-82.e7
8.9586Citations (PDF)
8Orchestrating high-throughput genomic analysis with Bioconductor
Nature Methods, 2015, 12, 115-121
14.82,823Citations (PDF)
9CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
F1000Research, 2015, 4, 478
0.470Citations (PDF)
10VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.
Bioinformatics, 2014, 30, 2076-8
3.3282Citations (PDF)
11Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways
PLoS ONE, 2013, 8, e52884
1.616Citations (PDF)
12Differential Plasma Glycoproteome of p19ARF Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform
Clinical Proteomics, 2008, 4, 105-116
2.510Citations (PDF)
13General transcription factor specified global gene regulation in archaea
Proceedings of the National Academy of Sciences of the United States of America, 2007, 104, 4630-4635
5.4100Citations (PDF)
14A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
Cell, 2007, 131, 1354-1365
24.4269Citations (PDF)
15The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
Genome Biology, 2006, 7, 1-16
5.1434Citations (PDF)
16Derivation of genetic interaction networks from quantitative phenotype data
Genome Biology, 2005, 6, 1-10
5.1108Citations (PDF)
17Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
Genome Research, 2004, 14, 2221-2234
3.5281Citations (PDF)
18Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
Genome Biology, 2004, 5, 1-15
5.139Citations (PDF)
19System-based proteomic analysis of the interferon response in human liver cells
Genome Biology, 2004, 5, 1-15
5.166Citations (PDF)
20Proteomic analysis of human prostasomes
Prostate, 2003, 56, 150-161
1.7224Citations (PDF)
21Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Genome Research, 2003, 13, 2498-2504
3.541,162Citations (PDF)
22Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach
Proceedings of the National Academy of Sciences of the United States of America, 2002, 99, 14913-14918
5.4114Citations (PDF)