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Items: 1 to 50 of 131

1.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.

Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2.

PMID:
31209238
2.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A.

Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018.

3.

Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement.

Wunsch BH, Kim SC, Gifford SM, Astier Y, Wang C, Bruce RL, Patel JV, Duch EA, Dawes S, Stolovitzky G, Smith JT.

Lab Chip. 2019 Apr 23;19(9):1567-1578. doi: 10.1039/c8lc01408f.

PMID:
30920559
4.

Mitochondrial origins of fractional control in regulated cell death.

Santos LC, Vogel R, Chipuk JE, Birtwistle MR, Stolovitzky G, Meyer P.

Nat Commun. 2019 Mar 21;10(1):1313. doi: 10.1038/s41467-019-09275-x.

5.

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.

6.

Integrated nanoscale deterministic lateral displacement arrays for separation of extracellular vesicles from clinically-relevant volumes of biological samples.

Smith JT, Wunsch BH, Dogra N, Ahsen ME, Lee K, Yadav KK, Weil R, Pereira MA, Patel JV, Duch EA, Papalia JM, Lofaro MF, Gupta M, Tewari AK, Cordon-Cardo C, Stolovitzky G, Gifford SM.

Lab Chip. 2018 Dec 4;18(24):3913-3925. doi: 10.1039/c8lc01017j.

PMID:
30468237
7.

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC.

Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

8.

A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.

Hansen J, Meretzky D, Woldesenbet S, Stolovitzky G, Iyengar R.

Sci Rep. 2017 Dec 18;7(1):17689. doi: 10.1038/s41598-017-16627-4.

9.

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology.

Chen X, Houten S, Allette K, Sebra RP, Stolovitzky G, Losic B.

Pac Symp Biocomput. 2018;23:8-19.

10.

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.

Seyednasrollah F, Koestler DC, Wang T, Piccolo SR, Vega R, Greiner R, Fuchs C, Gofer E, Kumar L, Wolfinger RD, Kanigel Winner K, Bare C, Neto EC, Yu T, Shen L, Abdallah K, Norman T, Stolovitzky G, Soule HR, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Elo LL, Zhou FL, Guinney J, Costello JC; Prostate Cancer DREAM Challenge Community.

JCO Clin Cancer Inform. 2017 Nov;1:1-15. doi: 10.1200/CCI.17.00018.

11.

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.

Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA.

Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4.

12.

The inconvenience of data of convenience: computational research beyond post-mortem analyses.

Azencott CA, Aittokallio T, Roy S; DREAM Idea Challenge Consortium, Norman T, Friend S, Stolovitzky G, Goldenberg A.

Nat Methods. 2017 Sep 29;14(10):937-938. doi: 10.1038/nmeth.4457. No abstract available.

PMID:
28960198
13.

Broken flow symmetry explains the dynamics of small particles in deterministic lateral displacement arrays.

Kim SC, Wunsch BH, Hu H, Smith JT, Austin RH, Stolovitzky G.

Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):E5034-E5041. doi: 10.1073/pnas.1706645114. Epub 2017 Jun 12.

14.

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.

15.

Wafer-scale integration of sacrificial nanofluidic chips for detecting and manipulating single DNA molecules.

Wang C, Nam SW, Cotte JM, Jahnes CV, Colgan EG, Bruce RL, Brink M, Lofaro MF, Patel JV, Gignac LM, Joseph EA, Rao SP, Stolovitzky G, Polonsky S, Lin Q.

Nat Commun. 2017 Jan 23;8:14243. doi: 10.1038/ncomms14243.

16.

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.

Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC; Prostate Cancer Challenge DREAM Community.

Lancet Oncol. 2017 Jan;18(1):132-142. doi: 10.1016/S1470-2045(16)30560-5. Epub 2016 Nov 16.

17.

Nanoscale lateral displacement arrays for the separation of exosomes and colloids down to 20 nm.

Wunsch BH, Smith JT, Gifford SM, Wang C, Brink M, Bruce RL, Austin RH, Stolovitzky G, Astier Y.

Nat Nanotechnol. 2016 Nov;11(11):936-940. doi: 10.1038/nnano.2016.134. Epub 2016 Aug 1.

PMID:
27479757
18.

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Oct 10;7:13205. doi: 10.1038/ncomms13205. No abstract available.

19.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Erratum in: Nat Commun. 2016 Oct 10;7:13205.

20.

Crowdsourcing biomedical research: leveraging communities as innovation engines.

Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G.

Nat Rev Genet. 2016 Jul 15;17(8):470-86. doi: 10.1038/nrg.2016.69. Review.

21.

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.

22.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S; Alzheimer's Disease Neuroimaging Initiative.

Alzheimers Dement. 2016 Jun;12(6):645-53. doi: 10.1016/j.jalz.2016.02.006. Epub 2016 Apr 11.

23.

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.

24.

Voices of biotech.

Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T.

Nat Biotechnol. 2016 Mar;34(3):270-5. doi: 10.1038/nbt.3502. No abstract available.

PMID:
26963549
25.

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22.

26.

Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Oct;33(10):1109. doi: 10.1038/nbt1015-1109a. No abstract available.

PMID:
26448092
27.

Prediction of human population responses to toxic compounds by a collaborative competition.

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.

Nat Biotechnol. 2015 Sep;33(9):933-40. doi: 10.1038/nbt.3299. Epub 2015 Aug 10. Erratum in: Nat Biotechnol. 2015 Oct;33(10):1109. Friend, Stephen; Dearry, Allen; Simeonov, Anton; Tice, Raymond R; Rusyn, Ivan; Wright, Fred A; Stolovitzky, Gustavo; Xie, Yang; and Saez-Rodriguez, Julio [Added].

28.

Noise-driven causal inference in biomolecular networks.

Prill RJ, Vogel R, Cecchi GA, Altan-Bonnet G, Stolovitzky G.

PLoS One. 2015 Jun 1;10(6):e0125777. doi: 10.1371/journal.pone.0125777. eCollection 2015.

29.

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P.

PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May.

30.

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC.

Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18.

31.

Preface: RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2014 Special Issue.

Califano A, Kellis M, Stolovitzky G.

J Comput Biol. 2015 Apr;22(4):251-2. doi: 10.1089/cmb.2015.020P. No abstract available.

PMID:
25844665
32.

The Prostate Cancer DREAM Challenge: A Community-Wide Effort to Use Open Clinical Trial Data for the Quantitative Prediction of Outcomes in Metastatic Prostate Cancer.

Abdallah K, Hugh-Jones C, Norman T, Friend S, Stolovitzky G.

Oncologist. 2015 May;20(5):459-60. doi: 10.1634/theoncologist.2015-0054. Epub 2015 Mar 16. No abstract available.

33.

Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels.

Wang C, Bruce RL, Duch EA, Patel JV, Smith JT, Astier Y, Wunsch BH, Meshram S, Galan A, Scerbo C, Pereira MA, Wang D, Colgan EG, Lin Q, Stolovitzky G.

ACS Nano. 2015 Feb 24;9(2):1206-18. doi: 10.1021/nn507350e. Epub 2015 Jan 29.

PMID:
25626162
34.

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.

35.

Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria.

Meyer P, Cecchi G, Stolovitzky G.

BMC Syst Biol. 2014 Dec 14;8:131. doi: 10.1186/s12918-014-0131-1.

36.

A community computational challenge to predict the activity of pairs of compounds.

Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community.

Nat Biotechnol. 2014 Dec;32(12):1213-22. doi: 10.1038/nbt.3052. Epub 2014 Nov 17.

37.

Fixed-gap tunnel junction for reading DNA nucleotides.

Pang P, Ashcroft BA, Song W, Zhang P, Biswas S, Qing Q, Yang J, Nemanich RJ, Bai J, Smith JT, Reuter K, Balagurusamy VS, Astier Y, Stolovitzky G, Lindsay S.

ACS Nano. 2014 Dec 23;8(12):11994-2003. doi: 10.1021/nn505356g. Epub 2014 Nov 12.

38.

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
39.

Toward better benchmarking: challenge-based methods assessment in cancer genomics.

Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G.

Genome Biol. 2014 Sep 17;15(9):462. doi: 10.1186/s13059-014-0462-7.

40.

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.

41.

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.

42.

Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales.

Bai J, Wang D, Nam SW, Peng H, Bruce R, Gignac L, Brink M, Kratschmer E, Rossnagel S, Waggoner P, Reuter K, Wang C, Astier Y, Balagurusamy V, Luan B, Kwark Y, Joseph E, Guillorn M, Polonsky S, Royyuru A, Papa Rao S, Stolovitzky G.

Nanoscale. 2014 Aug 7;6(15):8900-6. doi: 10.1039/c3nr06723h.

PMID:
24964839
43.

Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages.

Luan B, Wang C, Royyuru A, Stolovitzky G.

Nanotechnology. 2014 Jul 4;25(26):265101. doi: 10.1088/0957-4484/25/26/265101. Epub 2014 Jun 12.

PMID:
24920303
44.

A community effort to assess and improve drug sensitivity prediction algorithms.

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.

Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

45.

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue.

Califano A, Kellis M, Stolovitzky G.

J Comput Biol. 2014 May;21(5):371-2. doi: 10.1089/cmb.2014.009p. No abstract available.

PMID:
24784777
46.

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.

Nat Genet. 2014 Apr;46(4):318-319. doi: 10.1038/ng.2932. No abstract available.

47.

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.

Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J.

BMC Syst Biol. 2014 Feb 7;8:13. doi: 10.1186/1752-0509-8-13.

48.

Regulating the transport of DNA through biofriendly nanochannels in a thin solid membrane.

Wang D, Harrer S, Luan B, Stolovitzky G, Peng H, Afzali-Ardakani A.

Sci Rep. 2014 Feb 5;4:3985. doi: 10.1038/srep03985.

49.

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.

50.

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.

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