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A Whole-Cell Computational Model Predicts Phenotype from Genotype

Cell, 2012-07, Vol.150 (2), p.389-401

2012

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“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation

Molecular cell, 2022-11, Vol.82 (21), p.3970-3984

2022

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Reproductive Proteomics Comes of Age

Molecular & cellular proteomics, 2019-03, Vol.18 (Suppl 1), p.S1-S5

Karr, Timothy L.

2019

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Functional Diversity and Evolution of the Drosophila Sperm Proteome

Molecular & cellular proteomics, 2022-10, Vol.21 (10), p.100281-100281, Article 100281

2022

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SBML Level 3: an extensible format for the exchange and reuse of biological models

Molecular systems biology, 2020-08, Vol.16 (8), p.e9110-n/a

2020

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Building Structural Models of a Whole Mycoplasma Cell

Journal of molecular biology, 2022-01, Vol.434 (2), p.167351-167351, Article 167351

2022

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Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

Nucleic acids research, 2021-01, Vol.49 (D1), p.D516-D522

2021

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SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Bioinformatics (Oxford, England), 2021-11, Vol.37 (21), p.3702-3706

2021

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Prolonged and tunable residence time using reversible covalent kinase inhibitors

Nature chemical biology, 2015-07, Vol.11 (7), p.525-531

2015

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RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Nucleic acids research, 2021-07, Vol.49 (W1), p.W597-W602

2021

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Emerging whole-cell modeling principles and methods

Current opinion in biotechnology, 2018-06, Vol.51, p.97-102

2018

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The Drosophila Neprilysin 4 gene is essential for sperm function following sperm transfer to females

Genes & Genetic Systems, 2021/08/01, Vol.96(4), pp.177-186

2021

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p300 is an obligate integrator of combinatorial transcription factor inputs

Molecular cell, 2024-01, Vol.84 (2), p.234-243.e4

2024

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Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

Bioinformatics, 2008-09, Vol.24 (18), p.2044-2050

2008

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Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation

Molecular ecology, 2020-11, Vol.29 (22), p.4428-4441

2020

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Sperm proteomics reveals intensified selection on mouse sperm membrane and acrosome genes

Molecular biology and evolution, 2010-06, Vol.27 (6), p.1235-1246

2010

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Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

Briefings in bioinformatics, 2021-09, Vol.22 (5)

2021

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Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

PLoS computational biology, 2015-05, Vol.11 (5), p.e1004096-e1004096

2015

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The Rhesus Macaque (Macaca mulatta) Sperm Proteome

Molecular & cellular proteomics, 2013-11, Vol.12 (11), p.3052-3067

2013

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Identification and characterization of the zebra finch (Taeniopygia guttata) sperm proteome

Journal of proteomics, 2019-02, Vol.193, p.192-204

2019

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The Old and the New: Discovery Proteomics Identifies Putative Novel Seminal Fluid Proteins in Drosophila

Molecular & cellular proteomics, 2019-03, Vol.18 (Suppl 1), p.S23-S33

2019

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Comparative Sperm Proteomics in Mouse Species with Divergent Mating Systems

Molecular biology and evolution, 2017-06, Vol.34 (6), p.1403-1416

2017

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Cu(II) Binding to Monomeric, Oligomeric, and Fibrillar Forms of the Alzheimer’s Disease Amyloid-β Peptide

Biochemistry (Easton), 2008-04, Vol.47 (17), p.5006-5016

2008

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Placental transcriptomic signatures of prenatal and preconceptional maternal stress

Molecular psychiatry, 2024-04, Vol.29 (4), p.1179-1191

2024

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A Whole-Cell Computational Model Predicts Phenotype from Genotype

“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation

Reproductive Proteomics Comes of Age

Functional Diversity and Evolution of the Drosophila Sperm Proteome

SBML Level 3: an extensible format for the exchange and reuse of biological models

H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers

Building Structural Models of a Whole Mycoplasma Cell

Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Prolonged and tunable residence time using reversible covalent kinase inhibitors

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Emerging whole-cell modeling principles and methods

The Drosophila Neprilysin 4 gene is essential for sperm function following sperm transfer to females

p300 is an obligate integrator of combinatorial transcription factor inputs

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation

Sperm proteomics reveals intensified selection on mouse sperm membrane and acrosome genes

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

The Rhesus Macaque (Macaca mulatta) Sperm Proteome

Identification and characterization of the zebra finch (Taeniopygia guttata) sperm proteome

The Old and the New: Discovery Proteomics Identifies Putative Novel Seminal Fluid Proteins in Drosophila

Comparative Sperm Proteomics in Mouse Species with Divergent Mating Systems

Cu(II) Binding to Monomeric, Oligomeric, and Fibrillar Forms of the Alzheimer’s Disease Amyloid-β Peptide

Placental transcriptomic signatures of prenatal and preconceptional maternal stress

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