Publications

Publications

2016 Publications

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood disease.  Rong ChenLisong ShiJörg HakenbergBrian NaughtonPamela SklarJianguo ZhangHanlin ZhouLifeng TianOm PrakashMathieu LemirePatrick SleimanWei-yi ChengWanting ChenHardik ShahYulan ShenMenachem FromerLarsson OmbergMatthew A DeardorffElaine ZackaiJason R BobeElissa LevinThomas J HudsonLeif GroopJun WangHakon HakonarsonAnne WojcickiGeorge A DiazLisa EdelmannEric E Schad Stephen H Friend. Nature Biotechnology, April 11, 2016. doi:10.1038/nbt.3514

First, design for data sharing. John Wilbanks & Stephen Friend. Nature Biotechnology. March 3, 2016. doi:10.1038/nbt.3516

The mPower study, Parkinson disease mobile data collected using ResearchKit. Brian M. Bot, Christine Suver, Elias Chaibub Neto, Michael Kellen, Arno Klein, Christopher Bare, Megan Doerr, Abhishek Pratap, John Wilbanks, E. Ray Dorsey, Stephen H. Friend & Andrew D. Trister. Scientific Data, Mar 3, 2016. doi:10.1038/sdata.2016.11

Smartphones as new tools in the management and understanding of Parkinson’s disease. Andrew D Trister, E Ray Dorsey & Stephen H Friend. NPJ Parkinson’s Disease. March 3, 2016

Empirical assessment of causal network inference 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 W, Taylor D, Hu CW, Long BL, Noren DP, Bisberg A, 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. Nature Methods, Feb 22, 2016. doi:10.1038/nmeth.3773

The PsychENCODE project. Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters M, White KP, Gerstein MB, Amiri A, Armoskus C, et al.Nature Neuroscience. November 25, 2015. doi:10.1038/nn.4156

The consensus molecular subtypes of colorectal cancer. Guinney, J., Dienstmann, R., Wang X., de Reyniès, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., Bot, B.M., Morris, J.S., Simon, I.M., Gerster, S., Fessler, E., De Sousa, F., Melo, E., et al. Nature Medicine. 12 October 2015. Doi: 10.1038/nm.3967

rCGH : a comprehensive array-based genomic profile platform for precision medicine. Commo F, Guinney J, Ferte C; Bot B, Lefebvre C, Soria JC, Andre F. Bioinformatics. 2015; doi: 10.1093/bioinformatics/btv718.

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability. Bahnassawy L, Perumal TM, Gonzalez-Cano L, Hillje AL, Taher L, Makalowski W, Suzuki Y, Fuellen G, del Sol A, Schwamborn JC. Scientific Reports. November 25, 2015. doi: 10.1038/srep13456

The NIH BD2K center for big data in translational genomics. Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van’t Veer L, Wold B, & Haussler D. JAMIA, 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047

App-enabled trial participation: Tectonic shift or tepid rumble? Friend, S. Science Translational Medicine. 22 July 2015. doi:10.1126/scitranslmed.aab1206

Safety and Activity of the First-in-Class Sym004 Anti-EGFR Antibody Mixture in Patients with Refractory Colorectal Cancer. Dienstmann R, Patnaik A, Garcia-Carbonero R, Cervantes A, Benavent M, Roselló S, Tops BB, van der Post RS, Argilés G, Skartved NJ, Hansen UH, Hald R, Pedersen MW, Kragh M, Horak ID, Braun S, Van Cutsem E, Tolcher AW, Tabernero J. Cancer Discov. 2015 Jun;5(6):598-609. doi: 10.1158/2159-8290.CD-14-1432. PMID: 25962717

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Adam D Ewing, Kathleen E Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, Takafumi N Yamaguchi, J Christopher Bare, Christine P’ng, Daryl Waggott, Veronica Y Sabelnykova, ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Michael R Kellen, Thea C Norman, David Haussler, Stephen H Friend, Gustavo Stolovitzky, Adam A Margolin, Joshua M Stuart & Paul C Boutros. Nature Methods, May 18, 2015. doi:10.1038/nmeth.3407

Heterogeneity of driver genes and therapeutic implications in colorectal cancer. Dienstmann R. & Cervantest, A. Annals of Ocology. May 12, 2015. doi: 10.1093/annonc/mdv229. PMID: 25969371

Personalizing Colon Cancer Adjuvant Therapy: Selecting Optimal Treatments for Individual Patients. Dienstmann R, Salazar R & Tabernero J. J Clin Oncol. 2015 Jun 1;33(16):1787-1796. doi: 10.1200/JCO.2014.60.0213. PMID: 25918287

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. Kald Abdallah, Charles Hugh-Jones, Thea Norman, Stepen Friend, Gustavo Stolovitzsky. The Oncologist. March 16, 2015, doi:10.1634/theoncologist.2015-0054

Sparse expression bases in cancer reveal tumor drivers. Logsdon BA, Gentles AJ, Miller CP, Blau CA, Becker PS, Lee SI. Nucleic Acids Res. 2015. Feb 15. doi: 10.1093/nar/gku1290. PMCID: PMC4330344

Assessing the scale of tumor heterogeneity by complete hierarchical segmentation of MRI. Gensheimer MF, Doulas HS, Ermoian RE, Trister, AD. Phys Med Biol. 2015 Feb 7. doi: 10.1088/0031-9155/60/3/977. PMID: 25575341

Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors. Dienstmann R, Jang IS, Bot B, Friend S & Guinney J. Cancer Discov 2015, 5(2): 118-123. doi: 10.1158/2159-8290.CD-14-1118. PMID: 25656898

Bayesian Network Reconstruction using Systems Genetics Data: Comparison of MCMC Methods. Shinya Tasaki, Ben Sauerwine, Bruce Hoff, Hiroyoshi Toyoshiba, Chris Gaiteri, and Elias Chaibub Neto. Genetics. January 28, 2015. doi: 10.1534/genetics.114.172619

Diversity matters: Historical lessons. Dhami G, Gao W, and Trister AD. J Am Coll Radiology. January 2015. DOI: http://dx.doi.org/10.1016/j.jacr.2014.09.023

Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology. Commo F, Ferte C, Soria JC, Friend SH, Andre F and Guinney J. Ann Oncol 2015, 26(3): 582-588. doi: 10.1093/annonc/mdu582. Epub 2014 Dec 23. PMID: 25538175

Response to “Tumor cells in search for glutamate: an alternative explanation for increased invasiveness of IDH1 mutant gliomas”. Trister A, Scott J, Rockne R, Yagle K, Johnston SK, Hawkins-Daarud A, Baldock A, Swanson KR. Neuro Oncol. 2014 Dec;16(12):1670-1/ doi: 10.1093/neuonc/nou290. PMID: 25398942

Social interactomes for enabling research communities. Guinney J, Dienstmann R, Ferté C, Friend S, McCormick F. Cancer Discov (November 2014);4(11):1265-8.

Patient-specific metrics of invasiveness reveal significant prognostic benefit of resection in a predictable subset of gliomas. Baldock AL, Ahn S, Rockne R, Johnston S, Neal M, Corwin D, Clark-Swanson K, Sterin G, Trister AD, Malone H, Ebiana V, Sonabend AM, Mrugala M, Rockhill JK, Silbergeld DL, Lai A, Cloughesy T, McKhann G 2nd, Bruce JN, Rostomily RC, Canoll P, Swanson KR. PLoS One. 2014; Oct 28; 9(10):e99057. doi: 10.1371/journal.pone.0099057. PMID: 25350742

Molecular Markers Identify Subtypes of Stage III Colon Cancer Associated with Patient Outcomes.  Sinocrope FA, Shi Q, Smyrk TC, Thibodeau SN, Dienstmann R, Guinney J, Bot BM, Tejbar S, Delorenzi M, Goldberg RM, Mahoney MR, Sargent DJ, Alberts SR. Gastroenterology. October 8, 2014. doi:10.1053/j.gastro.2014.09.041

Simulation studies as designed experiments: the comparison of penalizede regression models in the “large p, small n” setting. Chaibub Neto E, Bare JC, Margolin AA (October, 2014). PLoS ONE 9(10): e107957. doi:10.1371/journal.pone.0107957

Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements. Tustison, NJ, Cook, PA, Klein, A, Song, G, Das, SR, Duda, JT, Kandel, BM, van Strien, N, Stone, JR, Gee, JC, Avants, BB. NeuroImage. October 1, 2014. doi.org.10.1016/j.neuroimage.2014.05.044

Game design for bioinformatics and cyberinfrastructure learning: a parallel computing case study. Perry D, Robinson J, Cruz S, Cecilia Aragon C, Ting J, Chowning C & Peters M. Concurrency and Computation: Practice and Experience, 26(13). 10 September 2014. doi: 10.1002/cpe.3261

Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-Seq. Huang Y, Hu Y and Liu J. BMC Bioinformatics (September 2014), 15(Suppl 9):S3 doi:10.1186/1471-2105-15-S9-S3

Phase I/IIa study evaluating the safety, efficacy, pharmacokinetics, and pharmacodynamics of lucitanib in advanced solid tumors. Soria JC, DeBraud F, Bahleda R, Adamo B, Andre F, Dienstmann R, Delmonte A, Cereda R, Isaacson J, Litten J, Allen A, Dubois F, Saba C, Robert R, D’Incalci M, Zucchetti M, Camboni MG, Tabernero J. Ann Oncol (September 5, 2014);25(11):2244-51.

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. Gönen M and Margolin A A. Bioinformatics (September 1, 2014) 30 (17): i556-i563. doi: 10.1093/bioinformatics/btu464

Periostin is a novel therapeutic target that predicts and regulates glioma malignancy. Mikheev AM, Mikheeva SA, Trister AD, Tokita MJ, Emerson SN, Parada CA, Born DE, Carnemolla B, Frankel S, Kim DH, Oxford RG, Kosai Y, Tozer-Fink KR, Manning TC, Silber JR, Rostomily RC. Neuro Oncol. 2014; 2014 Aug 19. pii: nou16. doi: 10.1093/neuonc/nou161. PMID: 25140038

Functional kinomics identifies candidate therapeutic targets in head and neck cancer. Moser R, Xu C, Kao M, Annis J, Lerma LA, Schaupp CM, Gurley KE, Jang IS, Biktasova A, Yarbrough WG, Margolin AA, Grandori C, Kemp CJ, Méndez E. Clin Cancer Res. 2014 Aug 15;20(16):4274-88. doi: 10.1158/1078-0432.CCR-13-2858

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin. Hoadley KA, Yau C, , DM Cherniack AD. D, S., Leiserson MDM, Beifang Niu, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, LJ, N, Laird PW, BJ, Ding L, A. Robertson G, Byers LA, Mills GB, Weinstein JN, C, Chen Z, EA, The Cancer Genome Atlas Research Network, Benz CC, Charles M. Perou CM, Stuart J (August 14, 2014). Cell, 1–16. doi:10.1016/j.cell.2014.06.049

Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, Zhang B, Zhang C, Lamb JR, Xie T, Suver C, Molony C, Melquist S, Johnson AD, Fan G, Stone DJ, Schadt EE, Casaccia P, Emilsson V, Zhu J. Mol Syst Biol. 2014 Jul 30;10(7):743. doi: 10.15252/msb.2014530

Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep. Klein, BA, Stiegler, M, Klein, A, Tautz, J. PlosOne (July 16,2014). doi:10.1371/journal.pone.0102316

Optimal design of trials to demonstrate the utility of genomically-guided therapy: putting Precision Cancer Medicine to the test. Dienstmann R, Rodon J, Tabernero J. Mol Oncol. 2014 Jul 15. pii: S1574-7891(14)00150-1. doi: 10.1016/j.molonc.2014.06.014

Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H. Nat Biotechnol. 2014 Jul;32(7):644-52. doi: 10.1038/nbt.2940. Epub 2014 Jun 22. PMID: 2495290.

Invasion and proliferation kinetics in enhancing gliomas predict IDH1 mutation status. Baldock AL, Yagle K, Born DE, Ahn S, Trister AD, Neal M, Johnston SK, Bridge CA, Basanta D, Scott J, Malone H, Sonabend AM, Canoll P, Mrugala MM, Rockhill JK, Rockne RC, Swanson KR. Neuro Oncol. (June 16, 2014); 16(6):779-86. doii: 10.1093/neuonc/nou027. PMID: 24832620

Clues from the resilient. Stephen H. Friend and Eric E. Schadt. Science. May 30, 2014, Vol. 344 no. 6187, doi: 10.1126/science.1255648

Describing high-order statistical dependence using “Concurrence Topology,” with application to functional MRI brain data. Ellis, SP, Klein, A. Homology, Homotopy and Applications v(16) pp. 245-264 (May 27, 2014). doi.org/10.4310/HHA.2014.v16.n1.a14

Citizens as partners in the use of clinical data. Wilbanks J, Kellen M and Suver C. O’Reilly Radar May 6, 2014

TGR analysis in phase I clinical trials–letter. Dienstmann R, Tabernero J. Clin Cancer Res. 2014 May 1;20(9):2495-6. doi: 10.1158/1078-0432. CCR-13-3455. PMID: 24789035

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer. Kemp CJ, Moore JM, Moser R, Bernard B, Teater M, Smith LE, Rabaia NA, Gurley KE, Guinney J, Busch SE, Shaknovich R, Lobanenkov VV, Liggitt D, Shmulevich I, Melnick A, Filippova GN. Cell Rep. 2014 May 22;7(4):1020-9. doi: 10.1016/j.celrep.2014.04.004. Epub 2014 May 1. PMID: 24794443

Standardized decision support in next generation sequencing reports of somatic cancer variants. Dienstmann R, Dong F, Borger D, Dias-Santagata D, Ellisen LW, Le LP, Iafrate AJ. Mol Oncol. 2014 Apr 4. pii: S1574-7891(14)00069-6. doi: 10.1016/j.molonc.2014.03.021.

Synapse elimination and learning rules co-regulated by MHC class I H2-Db. Lee H, Brott BK, Kirkby LA, Adelson JD, Cheng S, Feller MB, Datwani A, Shatz CJ.Nature. 2014 May 8;509(7499):195-200. doi: 10.1038/nature13154. Epub 2014 Mar 30. PMID: 24695230

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. Nature Genetics 46, 318–319 (March 27, 2014) doi:10.1038/ng.2932

Coupled dimensionality reduction and classification for supervised and semi-supervised multi label learning. Gönen, M. Pattern Recognition Letters, Volume 38, 1 March 2014, Pages 132-141, ISSN 0167-8655, http://dx.doi.org/10.1016/j.patrec.2013.11.021.

Synthetic lethal screens as a means to understand and treat MYC-driven cancers. Cermelli S, Jang IS, Bernard B, Grandori C. . 2014 Mar 1;4(3). pii: a014209. doi: 10.1101/cshperspect.a014209. PMID: 24591535

ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma. Eckel-Passow JE, Serie DJ, Bot BM, Joseph RW, Cheville JC, Parker AS. BMC Urol. 2014 Jan 31;14:14. doi: 10.1186/1471-2490-14-14. PMID: 24479813

Discriminating survival outcomes in patients with glioblastoma using a simulation-based, patient-specific response metric Neal ML, Trister AD, Cloke T, Sodt R, Ahn S, Baldock AL, Bridge CA, Lai A, Cloughest T, Mrugala MM, Rockhill JK, Rockne RC, Swanson, KR. PLoS One. 2013;8(1):e51951. doi: 10.1371/journal.pone.0051951. Epub 2013 Jan 23.

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data. In Sock Jang, Elias Chaibub Neto, Justin Guinney, Stephen Friend, Adam Margolin. Pac Symp Biocomput. January, 2014;19:63-74.

Bayesian Multiview Dimensionality Reduction for Learning Predictive Subspaces.Gönen M, Gönen GB, and Gürgen F. European Conference on Artificial Intelligence. (2014). doi:10.3233/978-1-61499-419-0-387

Embedding Heterogeneous Data by Preserving Multiple Kernels. Gönen M. European Conference on Artificial Intelligence. (2014) doi:10.3233/978-1-61499-419-0-381

The evolution of our molecular understanding of colorectal cancer: what we are doing now, what the future holds, and how tumor profiling is just the beginning. Dienstmann R, Salazar R, Tabernero J. Am Soc Clin Oncol Educ Book. 2014:91-9. doi: 10.14694/EdBook_AM.2014.34.91

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data. Jang IS, Neto EC, Guinney J, Friend SH, Margolin AA. Pac Symp Biocomput. 2014;19:63-74. PMC399554

Somatic Expression of ENRAGE is Associated with Obesity Status among Patients with Clear Cell Renal Cell Carcinoma Jeanette E. Eckel-Passow, Daniel J. Serie, Brian M. Bot, Richard W. Joseph, Steven N. Hart, John C. Cheville, Alexander S. Parker. Carcinogenesis (2013) doi: 10.1093/carcin/bgt485

Modeling RAS Phenotype in Colorectal Cancer Uncovers Novel Molecular Traits of RAS Dependency and Improves Prediction of Response to Targeted Agents in Patients. Guinney J, Ferté C, Dry J, McEwen R, Manceau G, Kao K, Chang KM, Bendtsen C, Hudson K, Huang E, Dougherty B, Ducreux M, Soria JC, Friend S, Derry J, Laurent-Puig P. Clin Cancer Res. 2013 Dec 12

Cancer, Potential of the synthetic lethality principle Sebastian M.B. Nijman and Stephen H. Friend. Science. 2013 Nov 15;342(6160):809-11. doi: 10.1126/science.1244669.

MyoD is a tumor suppressor gene in medulloblastoma Dey J, Dubuc AM, Pedro KD, Thirstrup D, Mecham B, Northcott PA, Wu X, Shih D, Tapscott SJ, Leblanc M, Taylor MD, Olson JM. Cancer Res. 2013 Nov 15;73(22):6828-37. doi: 10.1158/0008-5472.CAN-13-0730-T

Tumor Growth Rate is an early indicator of anti-tumor drug activity in phase I trials Charles Ferté, Marianna Fernandez, Antoine Hollebecque, Serge Koscielny, Antonin Levy, Christophe Massard, Rastislav Balheda, Brian Bot, Carlos Gomez-Roca, Clarisse Dromain, Samy Ammari, Jean-Charles Soria. Clin Cancer Res. 2013 Dec 12.

The Cancer Genome Atlas Pan-Cancer analysis project Cancer Genome Atlas Research Network; Genome Characterization Center, Chang K, Creighton CJ, Davis C, Donehower L, Drummond J, Wheeler D, Ally A, Balasundaram M, Birol I, Butterfield YS, Chu A, Chuah E, Chun HJ, et. al. Nature Genetics 45, 1113–1120 (2013) doi:10.1038/ng.2764

Enabling Transparent and Collaborative Computational Analysis of 12 tumor types within The Cancer Genome Atlas Larsson Omberg, Kyle Ellrott, Yuan Yuan, Cyriac Kandoth, Chris Wong, Stephen H Friend, Josh Stuart, Han Liang & Adam A Margolin. Nat Genet. 2013 Sep 26;45(10):1121-6

HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism Chi-Yi Yu, Elizabeth Theusch, Kathleen Lo, Lara M. Mangravite, Devesh Naidoo, Mariya Kutilova, and Marisa W. Medina. Hum Mol Genet. 2014 Jan 15;23(2):319-32. doi: 10.1093/hmg/ddt422. Epub 2013 Sep 2

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy Lara M. Mangravite, Barbara E. Engelhardt, Marisa W. Medina, Brigham H. Mecham, Bryan Howie, Heejung Shim, Devesh Naidoo, Josh D. Smith, Mark J. Rieder, Deborah A. Nickerson, Matthew Stephens, Ronald M. Krauss. Nature. 2013 Oct 17;502(7471):377-80

Comparison of Outcomes After Fluorouracil-Based Adjuvant Therapy for Stage II and III Colon Cancer Between 1978-1995 and 1996-2007: Findings from the ACCENT Database. Shi Q, Andre T, Grothey A, Yothers G, Hamilton S, Bot B, Haller D, Van Cutsem E, Twelves C, Benedetti J, O’Connell M, Sargent D. J Clin Oncol. 2013 Oct 10;31(29):3656-63. doi: 10.1200/JCO.2013.49.4344. Epub 2013 Aug 26.

Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in clinical oncology Ferte C, Trister AD, Huang E, Bot BM, Guinney J, Commo F, Sieberts S, Andre F, Besse B, Soria JC, Friend SH. Clin Cancer Res August 15, 2013 19:4315-4325

Parallel globally optimal structure learning of Bayesian networks Olga Nikolova, Jaroslaw Zola, Srinivas Aluru. Journal of Parallel and Distributed Computing, Volume 73, Issue 8, August 2013, Pages 1039-1048

Tumor Growth Rate Provides Useful Information to Evaluate Sorafenib and Everolimus Treatment in Metastatic Renal Cell Carcinoma Patients: An Integrated Analysis of the TARGET and RECORD Phase 3 Trial Data. Ferté C, Koscielny S, Albiges L, Rocher L, Soria JC, Iacovelli R, Loriot Y, Fizazi K, Escudier B. European Urology, http://dx.doi.org/10.1016/j.eururo.2013.08.010

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs Christopher D. Brown, Lara M. Mangravite, and Barbara E. Engelhardt. PLoS Genet. 2013 August; 9(8): e1003649.

A phase II flexible screening design allowing for interim analysis and comparison with historical control Wenting Wu, Brian M. Bot, Yan Hu, Susan Geyer, Daniel Sargent. Contemporary Clinical Trials, Volume 35, Issue 2, July 2013, Pages 128-137

Genome-wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination Iana Haralambieva, Ann Oberg, Inna Ovsyannikova, Richard Kennedy, Diane Grill, Sumit Middha, Brian Bot, Vivian Wang, David Smith, Robert Jacobson, Gregory Poland. PLoS ONE 8(5): e62149

Improving Breast Cancer Survival Analysis Through Competition-Based Multidimensional Modeling Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. PLoS Comput Biol 9(5): e1003047

IGF-1R targeting increases the antitumor effects of DNA damaging agents in SCLC model: an opportunity to increase the efficacy of standard therapy Charles Ferté, Yohann Loriot, Céline Clémenson, Frederic Commo Andrea Gombos Jean-Emmanuel Bibault, Ingrid Fumagalli, Saad Hamama, Nathalie Auger6, Benoit Lahon, Cyrus Chargari, Julien Calderaro6, Jean-Charles Soria5 and Eric Deutsch. Mol Cancer Ther. 2013 May 2.

Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer A. A. Margolin, E. Bilal, E. Huang, T. C. Norman, L. Ottestad, B. H. Mecham, B. Sauerwine, M. R. Kellen, L. M. Mangravite, M. D. Furia, H. K. M. Vollan, O. M. Rueda, J. Guinney, N. A. Deflaux, B. Hoff, X. Schildwachter, H. G. Russnes, D. Park, V. O. Vang, T. Pirtle, L. Youseff, C. Citro, C. Curtis, The Sage DREAM Breast Cancer Challenge Consortium, V. N. Kristensen, J. Hellerstein, S. H. Friend, G. Stolovitzky, S. Aparicio, C. Caldas, A.-L. Borresen-Dale,. Sci. Transl. Med. 5, 181re1 (2013)- doi: 10.1126/scitranslmed.3006112

Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge Plenge RM, Greenberg JD, Mangravite LM, Derry JM, Stahl EA, Coenen MJ, Barton A, Padyukov L, Klareskog L, Gregersen PK, Mariette X, Moreland LW, Bridges SL Jr, de Vries N, Huizinga TW, Guchelaar HJ; International Rheumatoid Arthritis Consortium (INTERACT), Friend SH, Stolovitzky G. Nat Genet. 2013 Apr 26;45(5):468-9. doi: 10.1038/ng.2623

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease Bin Zhang, Chris Gaiteri, Liviu-Gabriel Bodea, Zhi Wang, Joshua McElwee, Alexei A. Podtelezhnikov, Chunsheng Zhang, Tao Xie, Linh Tran, Radu Dobrin, Eugene Fluder, Bruce Clurman, Stacey Melquist, Manikandan Narayanan, Christine Suver, Hardik Shah, Milind Mahajan, Tammy Gillis, Jayalakshmi Mysore, Marcy E. MacDonald, John R. Lamb, David A. Bennett, Cliona Molony, David J. Stone, Vilmundur Gudnason, Amanda J. Myers, Eric E. Schadt, Harald Neumann, Jun Zhu, Valur Emilsson. Cell – 25 April 2013 (Vol. 153, Issue 3, pp. 707-720)

A network-heuristic approach to improve the impact of genomic data on drug discovery Trister AD, Huang ES., Clin Pharmacol Ther. 2013 Apr;93(4):295-7. doi: 10.1038/clpt.2012.246

Variants in triggering receptor expressed on myeloid cells 2 are associated with both behavioral variant frontotemporal lobar degeneration and Alzheimer’s disease. Giraldo M, Lopera F, Siniard AL, Corneveaux JJ, Schrauwen I, Carvajal J, Muñoz C, Ramirez-Restrepo M, Gaiteri C, Myers AJ, Caselli RJ, Kosik KS, Reiman EM, Huentelman MJ. Neurobiol Aging. 2013 Apr 9. doi:pii: S0197-4580(13)00095-X.

Metcalfe’s law and the biology information commons Stephen H Friend and Thea C Norman, Nature Biotechnology 31, 297–303 (2013) doi:10.1038/nbt.2555

A Fool’s Errand John Wilbanks. Nature. 2013 Mar 28;495(7442):440-1. doi: 10.1038/495440a.

A system biology framework identifies molecular underpinings of coronary heart disease Huan T, Zhang B, Wang Z, Joehanes R, Zhu J, Johnson AD, Ying S, Munson PJ, Raghavachari N, Wang R, Liu P, Courchesne P, Hwang SJ, Assimes TL, McPherson R, Samani NJ, Schunkert H; Coronary ARteryDIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium, International Consortium for Blood Pressure GWAS (ICBP), Meng Q, Suver C, O’Donnell CJ, Derry J, Yang X, Levy D. Arterioscler Thromb Vasc Biol. 2013 Jun;33(6):1427-34. doi: 10.1161/ATVBAHA.112.300112. Epub 2013 Mar 28

Modeling causality for pairs of phenotypes in systems genetics Neto EC, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS. Genetics. 2013 Mar;193(3):1003-13. doi: 10.1534/genetics.112.147124., 10.1534/genetics.112.147124

clearScience: Infrastructure for communicating Data-intensive science Bot BM, Burdick D, Kellen M, Huang ES. AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:27

US-EU Scientific Research Collaborations: Sage Bionetworks’ Experience Navigating the Complex Regulatory Landscape. Suver, Christine, Wilbanks, John and Friend, Stephen H. http://ssrn.com/abstract=2234133 or http://dx.doi.org/10.2139/ssrn.2234133

Response classification based on a minimal model of glioblastoma growth is prognostic for clinical outcomes and distinguishes progression from pseudoprogression Neal ML, Trister AD, Ahn S, Baldock A, Bridge CA, Guyman L, Lange J, Sodt R, Cloke T, Lai A, Cloughesy TF, Mrugala MM, Rockhill JK, Rockne RC, Swanson KR. Cancer Res. 2013 Feb 11.

GSVA: Gene Set Variation Analysis Haenzelmann S, Castelo R, Guinney J. BMC Bioinformatics. 2013 Jan 16;14(1):7.

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