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Author Details

Theo A Knijnenburg
Allen Institute for Cell Science
2006
44
23
PMIDPaper TitleJournal TitlePublished Year
36599983Integrated intracellular organization and its variations in human iPS cells.Nature2023
36599983Integrated intracellular organization and its variations in human iPS cells.Nature2023
35041651A deep generative model of 3D single-cell organization.PLoS Comput Biol2022
35045296A functional module states framework reveals transcriptional states for drug and target prediction.Cell Rep2022
35041651A deep generative model of 3D single-cell organization.PLoS Comput Biol2022
35045296A functional module states framework reveals transcriptional states for drug and target prediction.Cell Rep2022
33982016Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer.STAR Protoc2021
33982016Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer.STAR Protoc2021
33396819Identifying Personalized Metabolic Signatures in Breast Cancer.Metabolites2020
33396819Identifying Personalized Metabolic Signatures in Breast Cancer.Metabolites2020
30833390Genomic and molecular characterization of preterm birth.Proc Natl Acad Sci U S A2019
30833390Genomic and molecular characterization of preterm birth.Proc Natl Acad Sci U S A2019
29617664Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.Cell Rep2018
30401823Epigenetic profiling for the molecular classification of metastatic brain tumors.Nat Commun2018
30107528Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways.Nucleic Acids Res2018
30538266Author Correction: Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes.Sci Rep2018
29617664Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.Cell Rep2018
30107528Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways.Nucleic Acids Res2018
30401823Epigenetic profiling for the molecular classification of metastatic brain tumors.Nat Commun2018
30538266Author Correction: Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes.Sci Rep2018
28821810Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes.Sci Rep2017
28821810Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes.Sci Rep2017
28922390Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.PLoS One2017
28170390Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.PLoS Comput Biol2017
28170390Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.PLoS Comput Biol2017
28922390Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.PLoS One2017
27047537Using Incomplete Trios to Boost Confidence in Family Based Association Studies.Front Genet2016
27047537Using Incomplete Trios to Boost Confidence in Family Based Association Studies.Front Genet2016
27172896Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance.Clin Cancer Res2016
27165744Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.Cancer Cell2016
27397505A Landscape of Pharmacogenomic Interactions in Cancer.Cell2016
27505681Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.Cancer Cell2016
27876821Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.Sci Rep2016
27587659Combining dependent P-values with an empirical adaptation of Brown's method.Bioinformatics2016
27876821Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.Sci Rep2016
27587659Combining dependent P-values with an empirical adaptation of Brown's method.Bioinformatics2016
27397505A Landscape of Pharmacogenomic Interactions in Cancer.Cell2016
27505681Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.Cancer Cell2016
27172896Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance.Clin Cancer Res2016
27165744Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.Cancer Cell2016
24733517Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.Yeast2015
25656847SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.Cell Res2015
26369414A multilevel pan-cancer map links gene mutations to cancer hallmarks.Chin J Cancer2015
26679347CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.PLoS One2015
26061751Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.N Engl J Med2015
24733517Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.Yeast2015
26369414A multilevel pan-cancer map links gene mutations to cancer hallmarks.Chin J Cancer2015
26679347CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.PLoS One2015
26061751Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.N Engl J Med2015
25656847SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.Cell Res2015
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Collaborators

Ilya Shmulevich
Institute for Systems Biology
Co-authored papers 19
Lodewyk F A Wessels
University Medical Centre Mannheim, University of Heidelberg
Co-authored papers 13
Brady Bernard
Co-authored papers 6
Andrew D Cherniack
Dana-Farber Cancer Institute
Co-authored papers 5
Amy G Robertson
Present address: Dxige Research Inc.
Co-authored papers 4
Rehan Akbani
The University of Texas MD Anderson Cancer Center
Co-authored papers 4
Katherine A Hoadley
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
Co-authored papers 4
David L Gibbs
Institute for Systems Biology
Co-authored papers 4
Matthew Meyerson
Broad Institute
Co-authored papers 3
David A Wheeler
Baylor College of Medicine
Co-authored papers 3
Nyasha Chambwe
Institute of Molecular Medicine, Feinstein Institutes for Medical Research
Co-authored papers 3
Stephen A Ramsey
Oregon State University
Co-authored papers 3
John D Aitchison
Center for Global Infectious Disease Research, Seattle Children's Research Institute
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Kalle Leinonen
Co-authored papers 3
Peter W Laird
Van Andel Institute
Co-authored papers 3
Bradley A Murray
Co-authored papers 3
Olena Morozova
University of California Santa Cruz Genomics Institute
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Siyuan Zheng
Greehey Children's Cancer Research Institute
Co-authored papers 3
Roel G W Verhaak
Yale School of Medicine
Co-authored papers 3
Richard Kreisberg
Co-authored papers 3
Ultan McDermott
Wellcome Sanger Institute
Co-authored papers 3
Gordon B Mills
Knight Cancer Institute, Oregon Health and Sciences University
Co-authored papers 3
Giovanni Ciriello
University of Lausanne (UNIL)
Co-authored papers 3
Mathew J Garnett
Wellcome Sanger Institute
Co-authored papers 3
Alan Aderem
Seattle Children's Research Institute
Co-authored papers 3
Richard A Moffitt
Stony Brook University, and Stony Brook Cancer Center
Co-authored papers 2
Tobias Else
Harvard Medical School
Co-authored papers 2
Greg Eley
Co-authored papers 2
David J Dilworth
Institute for Systems Biology
Co-authored papers 2
Christina Yau
University of California San Francisco
Co-authored papers 2
Release 1.2