Erhan Bilal  Erhan  Bilal photo       

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Thomas J. Watson Research Center, Yorktown Heights, NY USA

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2015

Implementation of Watson Genomic Analytics processing to improve the efficiency of interpreting whole genome sequencing data on patients with advanced cancers.
Koyama, Takahiko and Jones, Steven and Utro, Filippo and Ma, Yussanne and Rhrissorrakrai, Kahn and Shen, Yaoqing and Carmeli, Boaz and Jones, Martin and Waks, Zeev and Pleasance, Erin and others
ASCO Annual Meeting Proceedings, pp. e12549, 2015

DREAMTools: a Python package for scoring collaborative challenges [version 1; referees: awaiting peer review]
Cokelaer, Thomas and Bansal, Mukesh and Bare, Christopher and Bilal, Erhan and Bot, Brian M and Neto, Elias Chaibub and Eduati, Federica and G{"o}nen, Mehmet and Hill, Steven M and Hoff, Bruce and others
2015 - karrlab.org

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge
K. Rhrissorrakrai, V. Belcastro, E. Bilal, R. Norel, C. Poussin, C. Mathis, R. H. Dulize, N. V. Ivanov, L. Alexopoulos, J. J. Rice, M. C. Peitsch, G. Stolovitzky, P. Meyer, J. Hoeng
Bioinformatics 31(4), 471--483, 2015

A crowd-sourcing approach for the construction of species-specific cell signaling networks
E. Bilal, T. Sakellaropoulos, I. N. Melas, D. E. Messinis, V. Belcastro, K. Rhrissorrakrai, P. Meyer, R. Norel, A. Iskandar, E. Blaese, J. J. Rice, M. C. Peitsch, J. Hoeng, G. Stolovitzky, L. G. Alexopoulos, C. Poussin
Bioinformatics 31(4), 484--491, 2015


2014

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia
Thomas Trimarchi, Erhan Bilal, Panagiotis Ntziachristos, Giulia Fabbri, Riccardo Dalla-Favera, Aristotelis Tsirigos, Iannis Aifantis
Cell 158(3), 593--606, Elsevier, 2014


2013

sbv IMPROVER Diagnostic Signature Challenge: Scoring strategies
Raquel Norel, Erhan Bilal, Nathalie Conrad-Chemineau, Richard Bonneau, Alberto de la Fuente, Igor Jurisica, Daniel Marbach, Pablo Meyer, J Jeremy Rice, Tamir Tuller, others
Systems Biomedicine 1(4), 15--23, Landes Bioscience, 2013

sbv IMPROVER Diagnostics Signature Challenge: Design and results
Kahn Rhrissorrakrai, J Jeremy Rice, Stephanie Boue, Marja Talikka, Erhan Bilal, Florian Martin, Pablo Meyer, Raquel Norel, Yang Xiang, Gustavo Stolovitzky, others
Systems Biomedicine 1(4), 0--11, Landes Bioscience, 2013

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge
A. L. Tarca, M. Lauria, M. Unger, E. Bilal, S. Boue, K. Kumar Dey, J. Hoeng, H. Koeppl, F. Martin, P. Meyer, P. Nandy, R. Norel, M. Peitsch, J. J. Rice, R. Romero, G. Stolovitzky, M. Talikka, Y. Xiang, C. Zechner, A. Veliz-Cuba, J. Song, H. Nguyen, M. Zel
Bioinformatics 29(22), 2892--2899, 2013

Metabotropic Glutamate Receptor 1 Expression and Its Polymorphic Variants Associate with Breast Cancer Phenotypes
Madhura S Mehta, Sonia C Dolfi, Roman Bronfenbrener, Erhan Bilal, Chunxia Chen, Dirk Moore, Yong Lin, Hussein Rahim, Seena Aisner, Romona D Kersellius, others
PloS one 8(7), e69851, Public Library of Science, 2013

Translational systems biology understanding the limits of animal models as predictors of human biology
Carine Poussin, Leonidas Alexopoulos, Vincenzo Belcastro, Erhan Bilal, Carole Mathis, Pablo Meyer, Raquel Norel, Jeremy J Rice, Gustavo Stolovitzky, Julia Hoeng, others
EMBnet. journal 19(A), p--30, 2013

Improving breast cancer survival analysis through competition-based multidimensional modeling
Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A Logsdon, Gaurav Pandey, Benjamin A Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H Mecham, others
2013

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer
Adam A Margolin, Erhan Bilal, Erich Huang, Thea C Norman, Lars Ottestad, Brigham H Mecham, Ben Sauerwine, Michael R Kellen, Lara M Mangravite, Matthew D Furia, others
Science translational medicine 5(181), 181re1--181re1, American Association for the Advancement of, 2013


2012

GenomicTools: a computational platform for developing high-throughput analytics in genomics
A. Tsirigos, N. Haiminen, E. Bilal, F. Utro
Bioinformatics 28(2), 282--283, Oxford University Press, 2012
Abstract

ErbB2, EphrinB1, Src kinase and PTPN13 signaling complex regulates MAP kinase signaling in human cancers
Paola D Vermeer, Megan Bell, Kimberly Lee, Daniel W Vermeer, Byrant G Wieking, Erhan Bilal, Gyan Bhanot, Ronny I Drapkin, Shridar Ganesan, Aloysius J Klingelhutz, others
PloS one 7(1), e30447, Public Library of Science, 2012

Amplified loci on chromosomes 8 and 17 predict early relapse in ER-positive breast cancers
Erhan Bilal, Kristen Vassallo, Deborah Toppmeyer, Nicola Barnard, Inga H Rye, Vanessa Almendro, Hege Russnes, Anne-Lise B\orresen-Dale, Arnold J Levine, Gyan Bhanot, others
PloS one 7(6), e38575, Public Library of Science, 2012


2011

Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers.
Agnieszka K Witkiewicz, Jessica Kline, Maria Queenan, Jonathan R Brody, Aristotelis Tsirigos, S Pavlides, F Sotgia, MP Lisanti
Cell cycle (Georgetown, Tex.) 10(11), 2011


2010

Identification of the YES1 Kinase as a Therapeutic Target in Basal-Like Breast Cancers
Erhan Bilal, Gabriela Alexe, Ming Yao, Lei Cong, Atul Kulkarni, Vasudeva Ginjala, Deborah Toppmeyer, Shridar Ganesan, Gyan Bhanot
Genes \& cancer 1(10), 1063, SAGE Publications, 2010

From data to bench to bedside: therapeutic targets in breast cancer
Erhan Bilal
Ph.D. Thesis, 2010


2009

Abnormalities of 53BP1 in Basal-Like Breast Cancer.
A Aly, Q Yang, E Bilal, M Yao, G Bhanot, D Toppmeyer, B Haffty, S Ganesan
CANCER RESEARCH, pp. 578S--578S, 2009

NF-kappa B Activation in Breast Cancer Occurs Via Different Mechanisms in Triple Negative and HER2+ Tumors with Lymphocytic Infiltrate
VR Tadigotla, G Alexe, N Sethi, E Bilal, CL Huang, S Monti, P Tamayo, C DeLisi, G Bhanot, S Ganesan
CANCER RESEARCH, pp. 590S--590S, 2009

BA1 Subclass of Basal-Like Breast Cancer Is Characterized by Upregulation of Interferon-Related Genes and Is Enriched for BRCA1-Associated Cancers.
S Ganesan, G Alexe, E Bilal, H Liu, G Bhanot
CANCER RESEARCH, pp. 863S--863S, 2009


2008

Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan
Erhan Bilal, Raul Rabadan, Gabriela Alexe, Noriyuki Fuku, Hitomi Ueno, Yutaka Nishigaki, Yasunori Fujita, Masafumi Ito, Yasumichi Arai, Nobuyoshi Hirose, others
PLoS One 3(6), e2421, Public Library of Science, 2008


2007

Enrichment of longevity phenotype in mtDNA haplogroups D4b2b, D4a, and D5 in the Japanese population
Gabriela Alexe, Noriyuki Fuku, Erhan Bilal, Hitomi Ueno, Yutaka Nishigaki, Yasunori Fujita, Masafumi Ito, Yasumichi Arai, Nobuyoshi Hirose, Gyan Bhanot, others
Human genetics 121(3), 347--356, Springer, 2007