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Items: 42

1.

SPEECH MARKERS FOR CLINICAL ASSESSMENT OF COCAINE USERS.

Agurto C, Norel R, Pietrowicz M, Parvaz M, Kinreich S, Bachi K, Cecchi G, Goldstein RZ.

Proc IEEE Int Conf Acoust Speech Signal Process. 2019 May;2019:6391-6394. doi: 10.1109/icassp.2019.8682691. Epub 2019 Apr 17.

2.

Detection of acute 3,4-methylenedioxymethamphetamine (MDMA) effects across protocols using automated natural language processing.

Agurto C, Cecchi GA, Norel R, Ostrand R, Kirkpatrick M, Baggott MJ, Wardle MC, Wit H, Bedi G.

Neuropsychopharmacology. 2020 Apr;45(5):823-832. doi: 10.1038/s41386-020-0620-4. Epub 2020 Jan 24.

3.

Analyzing progression of motor and speech impairment in ALS.

Agurto C, Ahmad O, Cecchi GA, Norel R, Pietrowicz M, Eyigoz EK, Mosmiller E, Baxi E, Rothstein JD, Roy P, Berry J, Maragakis NJ.

Conf Proc IEEE Eng Med Biol Soc. 2019 Jul;2019:6097-6102. doi: 10.1109/EMBC.2019.8857300.

PMID:
31947236
4.

Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.

Kueffner R, Zach N, Bronfeld M, Norel R, Atassi N, Balagurusamy V, Di Camillo B, Chio A, Cudkowicz M, Dillenberger D, Garcia-Garcia J, Hardiman O, Hoff B, Knight J, Leitner ML, Li G, Mangravite L, Norman T, Wang L; ALS Stratification Consortium, Xiao J, Fang WC, Peng J, Yang C, Chang HJ, Stolovitzky G.

Sci Rep. 2019 Jan 24;9(1):690. doi: 10.1038/s41598-018-36873-4.

5.

Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing.

Patel NM, Michelini VV, Snell JM, Balu S, Hoyle AP, Parker JS, Hayward MC, Eberhard DA, Salazar AH, McNeillie P, Xu J, Huettner CS, Koyama T, Utro F, Rhrissorrakrai K, Norel R, Bilal E, Royyuru A, Parida L, Earp HS, Grilley-Olson JE, Hayes DN, Harvey SJ, Sharpless NE, Kim WY.

Oncologist. 2018 Feb;23(2):179-185. doi: 10.1634/theoncologist.2017-0170. Epub 2017 Nov 20.

6.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

Neurol Genet. 2017 Jul 11;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug.

7.

Predicting human olfactory perception from chemical features of odor molecules.

Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R, Vens C, Schietgat L, De Grave K, Norel R; DREAM Olfaction Prediction Consortium, Stolovitzky G, Cecchi GA, Vosshall LB, Meyer P.

Science. 2017 Feb 24;355(6327):820-826. doi: 10.1126/science.aal2014. Epub 2017 Feb 20.

8.

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins.

Waks Z, Weissbrod O, Carmeli B, Norel R, Utro F, Goldschmidt Y.

Sci Rep. 2016 Dec 23;6:38988. doi: 10.1038/srep38988.

9.

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.

Noren DP, Long BL, Norel R, Rrhissorrakrai K, Hess K, Hu CW, Bisberg AJ, Schultz A, Engquist E, Liu L, Lin X, Chen GM, Xie H, Hunter GA, Boutros PC, Stepanov O; DREAM 9 AML-OPC Consortium, Norman T, Friend SH, Stolovitzky G, Kornblau S, Qutub AA.

PLoS Comput Biol. 2016 Jun 28;12(6):e1004890. doi: 10.1371/journal.pcbi.1004890. eCollection 2016 Jun.

10.

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.

BMC Bioinformatics. 2016 Apr 8;17:155. doi: 10.1186/s12859-016-1008-7.

11.

DREAMTools: a Python package for scoring collaborative challenges.

Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.

Version 2. F1000Res. 2015 Oct 9 [revised 2016 Jan 1];4:1030. doi: 10.12688/f1000research.7118.2. eCollection 2015.

12.

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression.

Küffner R, Zach N, Norel R, Hawe J, Schoenfeld D, Wang L, Li G, Fang L, Mackey L, Hardiman O, Cudkowicz M, Sherman A, Ertaylan G, Grosse-Wentrup M, Hothorn T, van Ligtenberg J, Macke JH, Meyer T, Schölkopf B, Tran L, Vaughan R, Stolovitzky G, Leitner ML.

Nat Biotechnol. 2015 Jan;33(1):51-7. doi: 10.1038/nbt.3051. Epub 2014 Nov 2.

PMID:
25362243
13.

A crowd-sourcing approach for the construction of species-specific cell signaling networks.

Bilal E, Sakellaropoulos T, Melas IN, Messinis DE, Belcastro V, Rhrissorrakrai K, Meyer P, Norel R, Iskandar A, Blaese E, Rice JJ, Peitsch MC, Hoeng J, Stolovitzky G, Alexopoulos LG, Poussin C; Challenge Participants.

Bioinformatics. 2015 Feb 15;31(4):484-91. doi: 10.1093/bioinformatics/btu659. Epub 2014 Oct 7.

14.

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge.

Rhrissorrakrai K, Belcastro V, Bilal E, Norel R, Poussin C, Mathis C, Dulize RH, Ivanov NV, Alexopoulos L, Rice JJ, Peitsch MC, Stolovitzky G, Meyer P, Hoeng J.

Bioinformatics. 2015 Feb 15;31(4):471-83. doi: 10.1093/bioinformatics/btu611. Epub 2014 Sep 17.

15.

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets.

Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A.

Bioinformatics. 2015 Feb 15;31(4):492-500. doi: 10.1093/bioinformatics/btu569. Epub 2014 Aug 24.

16.

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Hafemeister C, Romero R, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Bonneau R, Tarca AL.

Bioinformatics. 2015 Feb 15;31(4):501-8. doi: 10.1093/bioinformatics/btu570. Epub 2014 Aug 22.

17.

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge.

Dayarian A, Romero R, Wang Z, Biehl M, Bilal E, Hormoz S, Meyer P, Norel R, Rhrissorrakrai K, Bhanot G, Luo F, Tarca AL.

Bioinformatics. 2015 Feb 15;31(4):462-70. doi: 10.1093/bioinformatics/btu490. Epub 2014 Jul 23.

18.

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.

Biehl M, Sadowski P, Bhanot G, Bilal E, Dayarian A, Meyer P, Norel R, Rhrissorrakrai K, Zeller MD, Hormoz S.

Bioinformatics. 2015 Feb 15;31(4):453-61. doi: 10.1093/bioinformatics/btu407. Epub 2014 Jul 3.

19.

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

Poussin C, Mathis C, Alexopoulos LG, Messinis DE, Dulize RH, Belcastro V, Melas IN, Sakellaropoulos T, Rhrissorrakrai K, Bilal E, Meyer P, Talikka M, Boué S, Norel R, Rice JJ, Stolovitzky G, Ivanov NV, Peitsch MC, Hoeng J.

Sci Data. 2014 Jun 10;1:140009. doi: 10.1038/sdata.2014.9. eCollection 2014.

20.

On Crowd-verification of Biological Networks.

sbv IMPROVER project team (in alphabetical order), Ansari S, Binder J, Boue S, Di Fabio A, Hayes W, Hoeng J, Iskandar A, Kleiman R, Norel R, O'Neel B, Peitsch MC, Poussin C, Pratt D, Rhrissorrakrai K, Schlage WK, Stolovitzky G, Talikka M.

Bioinform Biol Insights. 2013 Oct 10;7:307-25. doi: 10.4137/BBI.S12932. eCollection 2013.

21.

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.

Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C; IMPROVER DSC Collaborators.

Bioinformatics. 2013 Nov 15;29(22):2892-9. doi: 10.1093/bioinformatics/btt492. Epub 2013 Aug 20.

22.

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.

Meyer P, Siwo G, Zeevi D, Sharon E, Norel R; DREAM6 Promoter Prediction Consortium, Segal E, Stolovitzky G.

Genome Res. 2013 Nov;23(11):1928-37. doi: 10.1101/gr.157420.113. Epub 2013 Aug 15.

23.

Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.

24.

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification.

Meyer P, Hoeng J, Rice JJ, Norel R, Sprengel J, Stolle K, Bonk T, Corthesy S, Royyuru A, Peitsch MC, Stolovitzky G.

Bioinformatics. 2012 May 1;28(9):1193-201. doi: 10.1093/bioinformatics/bts116. Epub 2012 Mar 14. Review.

25.

The self-assessment trap: can we all be better than average?

Norel R, Rice JJ, Stolovitzky G.

Mol Syst Biol. 2011 Oct 11;7:537. doi: 10.1038/msb.2011.70. No abstract available.

26.

Verification of systems biology research in the age of collaborative competition.

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.

Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. No abstract available.

PMID:
21904331
27.

Protein interface conservation across structure space.

Zhang QC, Petrey D, Norel R, Honig BH.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10896-901. doi: 10.1073/pnas.1005894107. Epub 2010 Jun 1.

28.

PUDGE: a flexible, interactive server for protein structure prediction.

Norel R, Petrey D, Honig B.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W550-4. doi: 10.1093/nar/gkq475. Epub 2010 Jun 4.

29.

MicroRNA-23b cluster microRNAs regulate transforming growth factor-beta/bone morphogenetic protein signaling and liver stem cell differentiation by targeting Smads.

Rogler CE, Levoci L, Ader T, Massimi A, Tchaikovskaya T, Norel R, Rogler LE.

Hepatology. 2009 Aug;50(2):575-84. doi: 10.1002/hep.22982.

PMID:
19582816
30.
31.

cDNA microarray analysis of HBV transgenic mouse liver identifies genes in lipid biosynthetic and growth control pathways affected by HBV.

Hajjou M, Norel R, Carver R, Marion P, Cullen J, Rogler LE, Rogler CE.

J Med Virol. 2005 Sep;77(1):57-65.

PMID:
16032730
32.

RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples.

Rogler CE, Tchaikovskaya T, Norel R, Massimi A, Plescia C, Rubashevsky E, Siebert P, Rogler LE.

Nucleic Acids Res. 2004 Aug 25;32(15):e120.

33.
34.

Electrostatic aspects of protein-protein interactions.

Sheinerman FB, Norel R, Honig B.

Curr Opin Struct Biol. 2000 Apr;10(2):153-9. Review.

PMID:
10753808
35.

Small molecule recognition: solid angles surface representation and molecular shape complementarity.

Norel R, Wolfson HJ, Nussinov R.

Comb Chem High Throughput Screen. 1999 Aug;2(4):223-37.

PMID:
10469882
36.

Examination of shape complementarity in docking of unbound proteins.

Norel R, Petrey D, Wolfson HJ, Nussinov R.

Proteins. 1999 Aug 15;36(3):307-17.

PMID:
10409824
37.

Two distinct binding sites for globotriaosyl ceramide on verotoxins: identification by molecular modelling and confirmation using deoxy analogues and a new glycolipid receptor for all verotoxins.

Nyholm PG, Magnusson G, Zheng Z, Norel R, Binnington-Boyd B, Lingwood CA.

Chem Biol. 1996 Apr;3(4):263-75. Erratum in: Chem Biol 1996 Jan;3(1):503.

38.
39.

Shape complementarity at protein-protein interfaces.

Norel R, Lin SL, Wolfson HJ, Nussinov R.

Biopolymers. 1994 Jul;34(7):933-40.

PMID:
8054472
40.

Molecular surface recognition by a computer vision-based technique.

Norel R, Fischer D, Wolfson HJ, Nussinov R.

Protein Eng. 1994 Jan;7(1):39-46.

PMID:
8140093
41.

Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition.

Fischer D, Norel R, Wolfson H, Nussinov R.

Proteins. 1993 Jul;16(3):278-92.

PMID:
8394000
42.

A model for the adjustment of the mitotic clock by cyclin and MPF levels.

Norel R, Agur Z.

Science. 1991 Mar 1;251(4997):1076-8.

PMID:
1825521

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