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Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

Scientific reports, 2016-11, Vol.6 (1), p.36812-36812, Article 36812

2016

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Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways

Nucleic acids research, 2018-10, Vol.46 (18), p.9496-9509

2018

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Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation

PloS one, 2017-09, Vol.12 (9), p.e0184850

2017

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Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose

Yeast (Chichester, England), 2015-01, Vol.32 (1), p.29-45

2015

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Identifying Personalized Metabolic Signatures in Breast Cancer

Metabolites, 2020-12, Vol.11 (1), p.20

2020

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Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

Proceedings of the National Academy of Sciences - PNAS, 2013-02, Vol.110 (9), p.3645-3650

2013

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CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data

PloS one, 2015-12, Vol.10 (12), p.e0144820-e0144820

2015

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Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data

BMC genomics, 2009-01, Vol.10 (1), p.53-53

2009

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Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes

Microbiology (Society for General Microbiology), 2007-11, Vol.153 (Pt 11), p.3864-3878

2007

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A regression model approach to enable cell morphology correction in high‐throughput flow cytometry

Molecular systems biology, 2011-09, Vol.7 (1), p.531-n/a

2011

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Exploiting combinatorial cultivation conditions to infer transcriptional regulation

BMC genomics, 2007-01, Vol.8 (1), p.25-25, Article 25

2007

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Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures

Applied and Environmental Microbiology, 2007-12, Vol.73 (23), p.7680-7692

2007

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Genome-wide analysis of effectors of peroxisome biogenesis

PloS one, 2010-08, Vol.5 (8), p.e11953

2010

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Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

Scientific reports, 2017-08, Vol.7 (1), p.8815-15, Article 8815

2017

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Abstract 2976: Comprehensive Pan-Genomic characterization of adrenocortical carcinoma

Cancer research (Chicago, Ill.), 2015-08, Vol.75 (15_Supplement), p.2976-2976

2015

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Fastbreak: a tool for analysis and visualization of structural variations in genomic data

EURASIP journal on bioinformatics & systems biology, 2012-10, Vol.2012 (1), p.15-8, Article 15

2012

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Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation

Genomics, proteomics & bioinformatics, 2007, Vol.5 (2), p.86-101

2007

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Author Correction: Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

Scientific reports, 2018-12, Vol.8 (1), p.17903-4, Article 17903

2018

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Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Cancer cell, 2016-08, Vol.30 (2), p.363-363

2016

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Abstract A44: A landscape of pharmacogenomic interactions in cancer

Clinical cancer research, 2017-01, Vol.23 (1_Supplement), p.A44-A44

2017

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Phylostratigraphic analysis of tumor and developmental transcriptomes reveals relationship between oncogenesis, phylogenesis and ontogenesis

Convergent science physical oncology, 2018-03, Vol.4 (2), p.25002

2018

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The Biomedical Data Translator Program: Conception, Culture, and Community

Clinical and translational science, 2019-03, Vol.12 (2), p.91-94

2019

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Abstract LB-240: SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer

Cancer research (Chicago, Ill.), 2015-08, Vol.75 (15_Supplement), p.LB-240-LB-240

2015

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Abstract 6548: Leveraging compact feature sets for TCGA-based molecular subtype classification on new samples

Cancer research (Chicago, Ill.), 2024-03, Vol.84 (6_Supplement), p.6548-6548

2024

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Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways

Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation

Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose

Identifying Personalized Metabolic Signatures in Breast Cancer

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes

A regression model approach to enable cell morphology correction in high‐throughput flow cytometry

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures

Genome-wide analysis of effectors of peroxisome biogenesis

Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

Abstract 2976: Comprehensive Pan-Genomic characterization of adrenocortical carcinoma

Fastbreak: a tool for analysis and visualization of structural variations in genomic data

Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation

Author Correction: Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Abstract A44: A landscape of pharmacogenomic interactions in cancer

Phylostratigraphic analysis of tumor and developmental transcriptomes reveals relationship between oncogenesis, phylogenesis and ontogenesis

The Biomedical Data Translator Program: Conception, Culture, and Community

Abstract LB-240: SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer

Abstract 6548: Leveraging compact feature sets for TCGA-based molecular subtype classification on new samples

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