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Items: 18

1.

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.

2.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC.

BMC Bioinformatics. 2018 Jan 31;19(1):28. doi: 10.1186/s12859-018-2046-0.

3.

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.

4.

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.

5.

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.

6.

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.

7.

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.

Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL.

Sci Transl Med. 2013 Apr 17;5(181):181re1. doi: 10.1126/scitranslmed.3006112.

8.

Metcalfe's law and the biology information commons.

Friend SH, Norman TC.

Nat Biotechnol. 2013 Apr;31(4):297-303. doi: 10.1038/nbt.2555. No abstract available.

PMID:
23563423
9.

FGF21 analogs of sustained action enabled by orthogonal biosynthesis demonstrate enhanced antidiabetic pharmacology in rodents.

Mu J, Pinkstaff J, Li Z, Skidmore L, Li N, Myler H, Dallas-Yang Q, Putnam AM, Yao J, Bussell S, Wu M, Norman TC, Rodriguez CG, Kimmel B, Metzger JM, Manibusan A, Lee D, Zaller DM, Zhang BB, DiMarchi RD, Berger JP, Axelrod DW.

Diabetes. 2012 Feb;61(2):505-12. doi: 10.2337/db11-0838. Epub 2011 Dec 30.

10.

Leveraging crowdsourcing to facilitate the discovery of new medicines.

Norman TC, Bountra C, Edwards AM, Yamamoto KR, Friend SH.

Sci Transl Med. 2011 Jun 22;3(88):88mr1. doi: 10.1126/scitranslmed.3002678.

PMID:
21697527
11.

Optimized clinical performance of growth hormone with an expanded genetic code.

Cho H, Daniel T, Buechler YJ, Litzinger DC, Maio Z, Putnam AM, Kraynov VS, Sim BC, Bussell S, Javahishvili T, Kaphle S, Viramontes G, Ong M, Chu S, Becky GC, Lieu R, Knudsen N, Castiglioni P, Norman TC, Axelrod DW, Hoffman AR, Schultz PG, DiMarchi RD, Kimmel BE.

Proc Natl Acad Sci U S A. 2011 May 31;108(22):9060-5. doi: 10.1073/pnas.1100387108. Epub 2011 May 16.

12.

Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains.

Askenazi M, Driggers EM, Holtzman DA, Norman TC, Iverson S, Zimmer DP, Boers ME, Blomquist PR, Martinez EJ, Monreal AW, Feibelman TP, Mayorga ME, Maxon ME, Sykes K, Tobin JV, Cordero E, Salama SR, Trueheart J, Royer JC, Madden KT.

Nat Biotechnol. 2003 Feb;21(2):150-6. Epub 2003 Jan 21.

PMID:
12536215
13.

Genetic selection of peptide inhibitors of biological pathways.

Norman TC, Smith DL, Sorger PK, Drees BL, O'Rourke SM, Hughes TR, Roberts CJ, Friend SH, Fields S, Murray AW.

Science. 1999 Jul 23;285(5427):591-5.

14.

Synthesis and application of functionally diverse 2,6,9-trisubstituted purine libraries as CDK inhibitors.

Chang YT, Gray NS, Rosania GR, Sutherlin DP, Kwon S, Norman TC, Sarohia R, Leost M, Meijer L, Schultz PG.

Chem Biol. 1999 Jun;6(6):361-75.

15.

Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors.

Gray NS, Wodicka L, Thunnissen AM, Norman TC, Kwon S, Espinoza FH, Morgan DO, Barnes G, LeClerc S, Meijer L, Kim SH, Lockhart DJ, Schultz PG.

Science. 1998 Jul 24;281(5376):533-8.

16.

CVT-313, a specific and potent inhibitor of CDK2 that prevents neointimal proliferation.

Brooks EE, Gray NS, Joly A, Kerwar SS, Lum R, Mackman RL, Norman TC, Rosete J, Rowe M, Schow SR, Schultz PG, Wang X, Wick MM, Shiffman D.

J Biol Chem. 1997 Nov 14;272(46):29207-11.

17.

Prevention of HIV-1 infection and preservation of CD4 function by the binding of CPFs to gp120.

Finberg RW, Diamond DC, Mitchell DB, Rosenstein Y, Soman G, Norman TC, Schreiber SL, Burakoff SJ.

Science. 1990 Jul 20;249(4966):287-91.

PMID:
2115689
18.

A case study on the effects of strenuous exercise on serum lithium levels.

Norman TC, Mathews W, Yohe CD.

Nebr Med J. 1987 Jul;72(7):224-5. No abstract available.

PMID:
3614447

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