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Author Details

Jadwiga Bienkowska
Pfizer Global Research and Development La Jolla
1987
41
18
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37475004Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer.Genome Med2023
37169829Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation.Sci Rep2023
34520734Expanding control of the tumor cell cycle with a CDK2/4/6 inhibitor.Cancer Cell2021
32866155GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data.PLoS One2020
31898484Comparison of the molecular and cellular phenotypes of common mouse syngeneic models with human tumors.BMC Genomics2020
33268821Chemotherapy induces dynamic immune responses in breast cancers that impact treatment outcome.Nat Commun2020
32821942PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues.Nucleic Acids Res2020
30870493Model to improve specificity for identification of clinically-relevant expanded T cells in peripheral blood.PLoS One2019
30342468TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.BMC Bioinformatics2018
26113988BAFF (B cell activating factor) transcript level in peripheral blood of patients with SLE is associated with same-day disease activity as well as global activity over the next year.Lupus Sci Med2015
26098139Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.J Comput Biol2015
24336808ProbeSelect: selecting differentially expressed probes in transcriptional profile data.Bioinformatics2014
25405351Lymphotoxin-LIGHT pathway regulates the interferon signature in rheumatoid arthritis.PLoS One2014
23289891Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects.BMC Res Notes2013
22937800A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.Genome Biol2012
21130772iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions.J Mol Biol2011
22044682Lymphotoxin-beta receptor blockade reduces CXCL13 in lacrimal glands and improves corneal integrity in the NOD model of Sjögren's syndrome.Arthritis Res Ther2011
21423713Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis.PLoS Comput Biol2011
19541457Serious diabetes-specific emotional problems in patients with type 2 diabetes who have different levels of comorbid depression: a Polish study from the European Depression in Diabetes (EDID) Research Consortium.Eur Psychiatry2009
19699293Convergent Random Forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response.Genomics2009
18096641LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading.Protein Sci2008
18672051Experimental comparison and cross-validation of Affymetrix HT plate and cartridge array gene expression platforms.Genomics2008
18710876Optimal contact map alignment of protein-protein interfaces.Bioinformatics2008
18424034Comparative expression analysis of four breast cancer subtypes versus matched normal tissue from the same patients.J Steroid Biochem Mol Biol2008
17374850Estrogen receptors alpha and beta mediate distinct pathways of vascular gene expression, including genes involved in mitochondrial electron transport and generation of reactive oxygen species.Mol Endocrinol2007
17992745LTHREADER: prediction of ligand-receptor interactions using localized threading.Pac Symp Biocomput2007
15759620Gotrees: predicting go associations from protein domain composition using decision trees.Pac Symp Biocomput2005
15966858Computational characterization of proteins.Expert Rev Proteomics2005
14983069A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells?Protein Eng2003
12002223Using fold recognition to search for useful proteins: Bayesian approach to fold recognition.Brief Bioinform2002
11700563Crystal structure of the anthrax lethal factor.Nature2001
10902161Eliminating superfluous neighbor pairs while threading fold models.Pac Symp Biocomput2000
10861936Protein fold recognition by total alignment probability.Proteins2000
10582568Performance of threading scoring functions designed using new optimization method.J Comput Biol1999
10591096Filtered neighbors threading.Proteins1999
8985242Biology's new Rosetta stone.Nature1997
9278056Current limitations to protein threading approaches.J Comput Biol1997
9312128The von willebrand factor A3 domain does not contain a metal ion-dependent adhesion site motif.J Biol Chem1997
7603574Crystal structure of the zeta isoform of the 14-3-3 protein.Nature1995
10015453Light-cone quantization of the Liouville model.Phys Rev D Part Fields1993
10035828E2/M1 ratio of gamma N--> Delta (1232) transitions in a relativistic three-quark model.Phys Rev Lett1987
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Collaborators

Temple F Smith
Co-authored papers 7
Bonnie Berger
Massachusetts Institute of Technology
Co-authored papers 6
Wenyan Zhong
Oncology R&D
Co-authored papers 3
Jian Peng
University of Illinois
Co-authored papers 2
Jinbo Xu
Toyota Technological Institute at Chicago
Co-authored papers 2
Kai Wang
Pfizer Inc.
Co-authored papers 2
Ronenn Roubenoff
Co-authored papers 2
Todd VanArsdale
Oncology Research Unit, Inc.
Co-authored papers 2
Michelle Petri
Co-authored papers 2
Woong-Yang Park
Samsung Genome Institute, Samsung Medical Center
Co-authored papers 2
Michael E Mendelsohn
Co-authored papers 1
Dario Meluzzi
University of California San Diego
Co-authored papers 1
David DeCaprio
Broad Institute of Harvard and MIT
Co-authored papers 1
Thomas Paul
Co-authored papers 1
Richard H Karas
Co-authored papers 1
Vinayagam Arunachalam
Co-authored papers 1
Prashant Mali (CM4AI)
University of California San Diego
Co-authored papers 1
Jason F Kreisberg
University of California San Diego
Co-authored papers 1
Norbert Perrimon
Co-authored papers 1
Kyle Ford
University of California San Diego
Co-authored papers 1
Jarek Kostrowicki
Co-authored papers 1
Franak Batliwalla
Co-authored papers 1
Keith A Ching
Co-authored papers 1
Robert K Campbell
Serono Research Institute
Co-authored papers 1
Zhou Zhu
Co-authored papers 1
Michael A White
University of Georgia
Co-authored papers 1
Deanne Taylor
Co-authored papers 1
Brenton Munson
University of California San Diego
Co-authored papers 1
Rebecca Panwala
University of California San Diego
Co-authored papers 1
Kun Zhang
China Pharmaceutical University
Co-authored papers 1
Release 1.2