Raquel (Kely) Norel  Raquel (Kely) Norel photo       

contact information

Research Staff Member @ Computational Biology Center
Thomas J. Watson Research Center, Yorktown Heights, NY USA
  +1dash914dash945dash1482

links



2017

Predicting human olfactory perception from chemical features of odor molecules
Keller, Andreas and Gerkin, Richard C and Guan, Yuanfang and Dhurandhar, Amit and Turu, Gabor and Szalai, Bence and Mainland, Joel D and Ihara, Yusuke and Yu, Chung Wen and Wolfinger, Russ and others
Science, eaal2014, American Association for the Advancement of Science, 2017
Abstract


2016

Reverse-engineering human olfactory perception from chemical features of odor molecules
Keller, Andreas and Gerkin, Richard C and Guan, Yuanfang and Dhurandhar, Amit and Turu, Gabor and Szalai, Bence and Mainland, Joel D and Ihara, Yusuke and Yu, Chung Wen and Wolfinger, Russ and others
bioRxiv, 082495, Cold Spring Harbor Labs Journals, 2016
Abstract

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins
Waks, Zeev and Weissbrod, Omer and Carmeli, Boaz and Norel, Raquel and Utro, Filippo and Goldschmidt, Yaara
Scientific Reports6, Nature Publishing Group, 2016
Abstract

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
D. P. Noren, B. L. Long, R. Norel, K. Rrhissorrakrai, K. Hess, C. W. Hu, A. J. Bisberg, A. Schultz, E. Engquist, L. Liu, X. Lin, G. M. Chen, H. Xie, G. A. Hunter, P. C. Boutros, O. Stepanov, T. Norman, S. H. Friend, G. Stolovitzky, S. Kornblau, A. A. Qutu
PLoS Comput. Biol. 12(6), e1004890, 2016

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin
R. Patro, R. Norel, R. J. Prill, J. Saez-Rodriguez, P. Lorenz, F. Steinbeck, B. Ziems, M. Lu?trek, N. Barbarini, A. Tiengo, R. Bellazzi, H. J. Thiesen, G. Stolovitzky, C. Kingsford
BMC Bioinformatics17, 155, 2016


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

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

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression
R. Kuffner, N. Zach, R. Norel, J. Hawe, D. Schoenfeld, L. Wang, G. Li, L. Fang, L. Mackey, O. Hardiman, M. Cudkowicz, A. Sherman, G. Ertaylan, M. Grosse-Wentrup, T. Hothorn, J. van Ligtenberg, J. H. Macke, T. Meyer, B. Scholkopf, L. Tran, R. Vaughan, G. S
Nat. Biotechnol. 33(1), 51--57, 2015

Inter-species pathway perturbation prediction via data-driven detection of functional homology
C. Hafemeister, R. Romero, E. Bilal, P. Meyer, R. Norel, K. Rhrissorrakrai, R. Bonneau, A. L. Tarca
Bioinformatics 31(4), 501--508, 2015

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge
A. Dayarian, R. Romero, Z. Wang, M. Biehl, E. Bilal, S. Hormoz, P. Meyer, R. Norel, K. Rhrissorrakrai, G. Bhanot, F. Luo, A. L. Tarca
Bioinformatics 31(4), 462--470, 2015

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge
M. Biehl, P. Sadowski, G. Bhanot, E. Bilal, A. Dayarian, P. Meyer, R. Norel, K. Rhrissorrakrai, M. D. Zeller, S. Hormoz
Bioinformatics 31(4), 453--461, 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

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


2014

Inter-species Inference of Gene Set Enrichment in Lung Epithelial Cells from Proteomic and Large Transcriptomic Data Sets
Sahand Hormoz, Gyan Bhanot, Michael Biehl, Erhan Bilal, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Adel Dayarian
Bioinformatics, btu569, Oxford Univ Press, 2014

The species translation challenge—a systems biology perspective on human and rat bronchial epithelial cells
Carine Poussin, Carole Mathis, Leonidas G Alexopoulos, Dimitris E Messinis, R\'emi HJ Dulize, Vincenzo Belcastro, Ioannis N Melas, Theodore Sakellaropoulos, Kahn Rhrissorrakrai, Erhan Bilal, others
Scientific Data1, Nature Publishing Group, 2014


2013

On crowd-verification of biological networks
Sam Ansari, Jean Binder, Stephanie Boue, Anselmo Di Fabio, William Hayes, Julia Hoeng, Anita Iskandar, Robin Kleiman, Raquel Norel, Manuel C Peitsch, others
Bioinformatics and biology insights7, Libertas Academica Ltd, 2013

sbv IMPROVER diagnostic signature challenge: design and results
Rhrissorrakrai, Kahn and Rice, J Jeremy and Boue, Stephanie and Talikka, Marja and Bilal, Erhan and Martin, Florian and Meyer, Pablo and Norel, Raquel and Xiang, Yang and Stolovitzky, Gustavo and others
Systems Biomedicine 1(4), 196--207, Taylor & Francis, 2013

sbv IMPROVER Diagnostic Signature Challenge: Scoring strategies
Norel, Raquel and Bilal, Erhan and Conrad-Chemineau, Nathalie and Bonneau, Richard and de la Fuente, Alberto and Jurisica, Igor and Marbach, Daniel and Meyer, Pablo and Rice, J Jeremy and Tuller, Tamir and others
Systems Biomedicine 1(4), 208--216, Taylor & Francis, 2013

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
P. Meyer, G. Siwo, D. Zeevi, E. Sharon, R. Norel, E. Segal, G. Stolovitzky, G. Siwo, A. K. Rider, A. Tan, R. S. Pinapati, S. Emrich, N. Chawla, M. T. Ferdig, Y. A. Tung, Y. S. Chen, M. J. Chen, C. Y. Chen, J. M. Knight, S. M. Sahraeian, M. S. Esfahani, R.
Genome Res. 23(11), 1928--1937, 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

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

Critical assessment of automated flow cytometry data analysis techniques
Nima Aghaeepour, Greg Finak, Holger Hoos, Tim R Mosmann, Ryan Brinkman, Raphael Gottardo, Richard H Scheuermann, others
Nature methods 10(3), 228--238, Nature Publishing Group, 2013

Evaluation of methods for modeling transcription factor sequence specificity
M.T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T.R. Riley, J. Saez-Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, others
Nature biotechnology, Nature Publishing Group, 2013


2012

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification
P. Meyer, J. Hoeng, J. J. Rice, R. Norel, J. Sprengel, K. Stolle, T. Bonk, S. Corthesy, A. Royyuru, M. C. Peitsch, G. Stolovitzky
Bioinformatics 28(9), 1193--1201, 2012


2011

The self-assessment trap: can we all be better than average?
Norel, Raquel and Rice, John Jeremy and Stolovitzky, Gustavo
Molecular systems biology 7(1), 537, EMBO Press, 2011

The self-assessment trap: can we all be better than average?
R. Norel, J.J. Rice, G. Stolovitzky
Molecular Systems Biology 7(1), Nature Publishing Group, 2011

Verification of systems biology research in the age of collaborative competition
P. Meyer, L. G. Alexopoulos, T. Bonk, A. Califano, C. R. Cho, A. de la Fuente, D. de Graaf, A. J. Hartemink, J. Hoeng, N. V. Ivanov, H. Koeppl, R. Linding, D. Marbach, R. Norel, M. C. Peitsch, J. J. Rice, A. Royyuru, F. Schacherer, J. Sprengel, K. Stolle,
Nat. Biotechnol. 29(9), 811--815, 2011


2010

PUDGE: a flexible, interactive server for protein structure prediction
R Norel, D Petrey, B Honig
Nucleic acids research 38(suppl 2), W550--W554, Oxford Univ Press, 2010

Protein interface conservation across structure space
Q C Zhang, D Petrey, R Norel, B H Honig
Proceedings of the National Academy of Sciences 107(24), 10896, National Acad Sciences, 2010


2009

MicroRNA-23b cluster microRNAs regulate transforming growth factor-beta/bone morphogenetic protein signaling and liver stem cell differentiation by targeting Smads
C E Rogler, L LeVoci, T Ader, A Massimi, T Tchaikovskaya, R Norel, L E Rogler
Hepatology 50(2), 575--584, Wiley Online Library, 2009


2006



2005

cDNA microarray analysis of HBV transgenic mouse liver identifies genes in lipid biosynthetic and growth control pathways affected by HBV
M Hajjou, R Norel, R Carver, P Marion, J Cullen, L E Rogler, C E Rogler
Journal of medical virology 77(1), 57--65, Wiley Online Library, 2005


2004

RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples
C E Rogler, T Tchaikovskaya, R Norel, A Massimi, C Plescia, E Rubashevsky, P Siebert, L E Rogler
Nucleic acids research 32(15), e120--e120, Oxford Univ Press, 2004


2003

940 HBV replication increases steady state MRNA level of selected lipid biosynthesis genes in HBV transgenic mouse liver
M Hajjou, R Norel, R Carver, P Marion, J Cullen, L E Rogler, C E Rogler
Hepatology38, 610, Elsevier, 2003

271 Embryonic hepatoblasts share patterns of gene expression with other stem cell populations
T Ader, R Norel, C E Rogler, L E Rogler
Hepatology38, 286--287, Elsevier, 2003


2001

Protein-Ligand Interactions: Energetic Contributions and Shape Complementarity
Chung-Jung Tsai, Raquel Norel, Haim J Wolfson, Jacob V Maizel, Ruth Nussinov
Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, 2001

Electrostatic contributions to protein--protein interactions: fast energetic filters for docking and their physical basis
R Norel, F Sheinerman, D Petrey, B Honig
Protein Science 10(11), 2147--2161, Wiley Online Library, 2001


2000

Electrostatic aspects of protein--protein interaction
FB Scheinerman, R Norel, B Honig
Curr Opin Struct Biol10, 153--159, 2000

Electrostatic aspects of protein--protein interactions
F B Sheinerman, R Norel, B Honig
Current Opinion in Structural Biology 10(2), 153--159, Elsevier, 2000


1999

Small Molecule Recognition: Solid Angles Surface Representation and Molecular Shape Complementarity
Norel, R. Wolfson, H. J. Nussinov, R.
COMBINATORIAL CHEMISTRY AND HIGH THROUGHPUT SCREENING 2(4), 223-236, BENTHAM SCIENCE PUBLICSHERS, 1999

Examination of shape complementarity in docking of unbound proteins
R Norel, D Petrey, H J Wolfson, R Nussinov
Proteins: Structure, Function, and Bioinformatics 36(3), 307--317, Wiley Online Library, 1999


1998

[Invited Lecture] Structural motifs in the interior and on the surfaces of protein monomers and at protein-protein interfaces
R Nussinov, R Norel, B Sandak, G Verbitsky, H J Wolfson
German Conference on Bioinformatics, 1998

Algorithms for Protein Docking
R Norel
Ph.D. Thesis, 1998

Molecular surface variability and induced conformational changes upon protein-protein association
R Norel, S L Lin, D Xu, H J Wolfson, R Nussinov
Journal of Biomolecular Structure and Dynamics 16(1), 33--35, Guilderland, NY: Adenine Press,[c1983-, 1998


1996



1995

Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking
R Norel, S L Lin, H J Wolfson, R Nussinov, others
Journal of molecular biology 252(2), 263--274, London, New York, Academic Press., 1995


1994

Molecular surface recognition by a computer vision-based technique
R Norel, D Fischer, H J Wolfson, R Nussinov
Protein engineering 7(1), 39--46, Oxford Univ Press, 1994

Shape complementarity at protein--protein interfaces
R Norel, S L Lin, H J Wolfson, R Nussinov
Biopolymers 34(7), 933--940, Wiley Online Library, 1994


1993

3-d docking of protein molecules
D Fischer, R Norel, R Nussinov, H Wolfson
Combinatorial Pattern Matching, pp. 20--34, 1993

Surface motifs by a computer vision technique: searches, detection, and implications for protein--ligand recognition
D Fischer, R Norel, H Wolfson, R Nussinov
Proteins: Structure, Function, and Bioinformatics 16(3), 278--292, Wiley Online Library, 1993


1991

A model for the adjustment of the mitotic clock by cyclin and MPF levels
R Norel, Z Agur
Science 251(4997), 1076--1078, American Association for the Advancement of Science, 1991


Year Unknown

Nucleic acids research Volume: 32 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2004
C E Rogler, T Tchaikovskaya, R Norel, A Massimi, C Plescia, E Rubashevsky, P Siebert, L E Rogler
Detail:, 0

Protein--Ligand Interactions: Energetic Contributions and Shape Complementarity
C J Tsai, R Norel, H J Wolfson, J V Maizel, R Nussinov
eLS, Wiley Online Library, 0

Wolfson, and Nussinov, R.,(1994). Surface motifs by a Computer Vision Technique: Searches, Detection and Implications for Protein Ligand Recognition
DR Fisher, RH Norel
Protein: Structure, Function and Genetics16, 278--292, 0