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Items: 1 to 50 of 123

1.

Epigenetic profiling for the molecular classification of metastatic brain tumors.

Orozco JIJ, Knijnenburg TA, Manughian-Peter AO, Salomon MP, Barkhoudarian G, Jalas JR, Wilmott JS, Hothi P, Wang X, Takasumi Y, Buckland ME, Thompson JF, Long GV, Cobbs CS, Shmulevich I, Kelly DF, Scolyer RA, Hoon DSB, Marzese DM.

Nat Commun. 2018 Nov 6;9(1):4627. doi: 10.1038/s41467-018-06715-y.

2.

Emergence of diversity in homogeneous coupled Boolean networks.

Kang C, Aguilar B, Shmulevich I.

Phys Rev E. 2018 May;97(5-1):052415. doi: 10.1103/PhysRevE.97.052415.

PMID:
29906914
3.

Pathogenic Germline Variants in 10,389 Adult Cancers.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L.

Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.

4.

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M; Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N.

Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035.

5.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

6.

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I; Cancer Genome Atlas Research Network, Monnat RJ Jr, Xiao Y, Wang C.

Cell Rep. 2018 Apr 3;23(1):239-254.e6. doi: 10.1016/j.celrep.2018.03.076.

7.

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L.

Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050.

8.

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J; Cancer Genome Atlas Research Network, Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V.

Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086.

9.

Cell death as a trigger for morphogenesis.

Aguilar B, Ghaffarizadeh A, Johnson CD, Podgorski GJ, Shmulevich I, Flann NS.

PLoS One. 2018 Mar 22;13(3):e0191089. doi: 10.1371/journal.pone.0191089. eCollection 2018.

10.

The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.

Reynolds SM, Miller M, Lee P, Leinonen K, Paquette SM, Rodebaugh Z, Hahn A, Gibbs DL, Slagel J, Longabaugh WJ, Dhankani V, Reyes M, Pihl T, Backus M, Bookman M, Deflaux N, Bingham J, Pot D, Shmulevich I.

Cancer Res. 2017 Nov 1;77(21):e7-e10. doi: 10.1158/0008-5472.CAN-17-0617.

11.

Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center.

Kytola V, Topaloglu U, Miller LD, Bitting RL, Goodman MM, D Agostino RB Jr, Desnoyers RJ, Albright C, Yacoub G, Qasem SA, DeYoung B, Thorsson V, Shmulevich I, Yang M, Shcherban A, Pagni M, Liu L, Nykter M, Chen K, Hawkins GA, Grant SC, Petty WJ, Alistar AT, Levine EA, Staren ED, Langefeld CD, Miller V, Singal G, Petro RM, Robinson M, Blackstock W, Powell BL, Wagner LI, Foley KL, Abraham E, Pasche B, Zhang W.

Theranostics. 2017 Jul 12;7(11):2914-2923. doi: 10.7150/thno.20355. eCollection 2017.

12.

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.

Gibbs DL, Shmulevich I.

PLoS Comput Biol. 2017 Jun 19;13(6):e1005591. doi: 10.1371/journal.pcbi.1005591. eCollection 2017 Jun. Erratum in: PLoS Comput Biol. 2018 May 23;14(5):e1006190.

13.

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.

Poole W, Leinonen K, Shmulevich I, Knijnenburg TA, Bernard B.

PLoS Comput Biol. 2017 Feb 7;13(2):e1005347. doi: 10.1371/journal.pcbi.1005347. eCollection 2017 Feb. Erratum in: PLoS Comput Biol. 2017 Apr 6;13(4):e1005472.

14.

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF.

Sci Rep. 2016 Nov 23;6:36812. doi: 10.1038/srep36812.

15.

MIIP haploinsufficiency induces chromosomal instability and promotes tumour progression in colorectal cancer.

Sun Y, Ji P, Chen T, Zhou X, Yang D, Guo Y, Liu Y, Hu L, Xia D, Liu Y, Multani AS, Shmulevich I, Kucherlapati R, Kopetz S, Sood AK, Hamilton SR, Sun B, Zhang W.

J Pathol. 2017 Jan;241(1):67-79. doi: 10.1002/path.4823. Epub 2016 Nov 24.

16.

Combining dependent P-values with an empirical adaptation of Brown's method.

Poole W, Gibbs DL, Shmulevich I, Bernard B, Knijnenburg TA.

Bioinformatics. 2016 Sep 1;32(17):i430-i436. doi: 10.1093/bioinformatics/btw438.

17.

Literature-based discovery of new candidates for drug repurposing.

Yang HT, Ju JH, Wong YT, Shmulevich I, Chiang JH.

Brief Bioinform. 2017 May 1;18(3):488-497. doi: 10.1093/bib/bbw030.

PMID:
27113728
18.

Using Incomplete Trios to Boost Confidence in Family Based Association Studies.

Dhankani V, Gibbs DL, Knijnenburg T, Kramer R, Vockley J, Niederhuber J, Shmulevich I, Bernard B.

Front Genet. 2016 Mar 18;7:34. doi: 10.3389/fgene.2016.00034. eCollection 2016.

19.

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.

Bressler R, Kreisberg RB, Bernard B, Niederhuber JE, Vockley JG, Shmulevich I, Knijnenburg TA.

PLoS One. 2015 Dec 17;10(12):e0144820. doi: 10.1371/journal.pone.0144820. eCollection 2015.

20.

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Knijnenburg TA, Bismeijer T, Wessels LF, Shmulevich I.

Chin J Cancer. 2015 Sep 14;34(10):439-49. doi: 10.1186/s40880-015-0050-6.

21.

Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma.

Liu Y, Yasukawa M, Chen K, Hu L, Broaddus RR, Ding L, Mardis ER, Spellman P, Levine DA, Mills GB, Shmulevich I, Sood AK, Zhang W.

JAMA Oncol. 2015 Jul;1(4):486-94. doi: 10.1001/jamaoncol.2015.1432.

22.

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J.

N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10.

23.

Augmentation of response to chemotherapy by microRNA-506 through regulation of RAD51 in serous ovarian cancers.

Liu G, Yang D, Rupaimoole R, Pecot CV, Sun Y, Mangala LS, Li X, Ji P, Cogdell D, Hu L, Wang Y, Rodriguez-Aguayo C, Lopez-Berestein G, Shmulevich I, De Cecco L, Chen K, Mezzanzanica D, Xue F, Sood AK, Zhang W.

J Natl Cancer Inst. 2015 May 20;107(7). pii: djv108. doi: 10.1093/jnci/djv108. Print 2015 Jul.

24.

Identification of copy number variants in whole-genome data using Reference Coverage Profiles.

Glusman G, Severson A, Dhankani V, Robinson M, Farrah T, Mauldin DE, Stittrich AB, Ament SA, Roach JC, Brunkow ME, Bodian DL, Vockley JG, Shmulevich I, Niederhuber JE, Hood L.

Front Genet. 2015 Feb 17;6:45. doi: 10.3389/fgene.2015.00045. eCollection 2015.

25.

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression.

Turner KM, Sun Y, Ji P, Granberg KJ, Bernard B, Hu L, Cogdell DE, Zhou X, Yli-Harja O, Nykter M, Shmulevich I, Yung WK, Fuller GN, Zhang W.

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3421-6. doi: 10.1073/pnas.1414573112. Epub 2015 Mar 3.

26.

Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer.

Sun Y, Guo F, Bagnoli M, Xue FX, Sun BC, Shmulevich I, Mezzanzanica D, Chen KX, Sood AK, Yang D, Zhang W.

Chin J Cancer. 2015 Jan;34(1):28-40. doi: 10.5732/cjc.014.10284. Review.

27.

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers.

Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga NS.

Nucleic Acids Res. 2014 Dec 1;42(21):12973-83. doi: 10.1093/nar/gku1031. Epub 2014 Nov 5.

28.

Large-scale molecular characterization and analysis of gastric cancer.

Shmulevich I.

Chin J Cancer. 2014 Aug;33(8):369-70. No abstract available.

29.

Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma.

Liu Y, Patel L, Mills GB, Lu KH, Sood AK, Ding L, Kucherlapati R, Mardis ER, Levine DA, Shmulevich I, Broaddus RR, Zhang W.

J Natl Cancer Inst. 2014 Sep 10;106(9). pii: dju245. doi: 10.1093/jnci/dju245. Print 2014 Sep.

30.

Biocellion: accelerating computer simulation of multicellular biological system models.

Kang S, Kahan S, McDermott J, Flann N, Shmulevich I.

Bioinformatics. 2014 Nov 1;30(21):3101-8. doi: 10.1093/bioinformatics/btu498. Epub 2014 Jul 26.

31.

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.

32.

Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma.

Li X, Liu Y, Granberg KJ, Wang Q, Moore LM, Ji P, Gumin J, Sulman EP, Calin GA, Haapasalo H, Nykter M, Shmulevich I, Fuller GN, Lang FF, Zhang W.

Oncogene. 2015 Mar 26;34(13):1619-1628. doi: 10.1038/onc.2014.98. Epub 2014 Apr 21.

33.

Multiscale representation of genomic signals.

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.

Nat Methods. 2014 Jun;11(6):689-94. doi: 10.1038/nmeth.2924. Epub 2014 Apr 13.

34.

MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer.

Liu G, Sun Y, Ji P, Li X, Cogdell D, Yang D, Parker Kerrigan BC, Shmulevich I, Chen K, Sood AK, Xue F, Zhang W.

J Pathol. 2014 Jul;233(3):308-18. doi: 10.1002/path.4348. Epub 2014 May 21.

35.

Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions.

Guo F, Parker Kerrigan BC, Yang D, Hu L, Shmulevich I, Sood AK, Xue F, Zhang W.

J Hematol Oncol. 2014 Mar 5;7:19. doi: 10.1186/1756-8722-7-19. Review.

36.

Quantitative analysis of colony morphology in yeast.

Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.

Biotechniques. 2014 Jan;56(1):18-27. doi: 10.2144/000114123.

37.

POMO--Plotting Omics analysis results for Multiple Organisms.

Lin J, Kreisberg R, Kallio A, Dudley AM, Nykter M, Shmulevich I, May P, Autio R.

BMC Genomics. 2013 Dec 24;14:918. doi: 10.1186/1471-2164-14-918.

38.

The somatic genomic landscape of glioblastoma.

Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network.

Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. Erratum in: Cell. 2014 Apr 24;157(3):753.

39.

The Cancer Genome Atlas Pan-Cancer analysis project.

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM.

Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764.

40.

On the limitations of biological knowledge.

Dougherty ER, Shmulevich I.

Curr Genomics. 2012 Nov;13(7):574-87. doi: 10.2174/138920212803251445.

41.

Gene-pair expression signatures reveal lineage control.

Heinäniemi M, Nykter M, Kramer R, Wienecke-Baldacchino A, Sinkkonen L, Zhou JX, Kreisberg R, Kauffman SA, Huang S, Shmulevich I.

Nat Methods. 2013 Jun;10(6):577-83. doi: 10.1038/nmeth.2445. Epub 2013 Apr 21.

42.

Information-theoretic analysis of the dynamics of an executable biological model.

Sadot A, Sarbu S, Kesseli J, Amir-Kroll H, Zhang W, Nykter M, Shmulevich I.

PLoS One. 2013;8(3):e59303. doi: 10.1371/journal.pone.0059303. Epub 2013 Mar 19.

43.

Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer.

Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R, Cogdell D, Nykter M, Broaddus R, Rodriguez-Aguayo C, Lopez-Berestein G, Liu J, Shmulevich I, Sood AK, Chen K, Zhang W.

Cancer Cell. 2013 Feb 11;23(2):186-99. doi: 10.1016/j.ccr.2012.12.020. Erratum in: Cancer Cell. 2013 May 13;23(5):705.

44.

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3645-50. doi: 10.1073/pnas.1216918110. Epub 2013 Feb 6.

45.

Structure learning for Bayesian networks as models of biological networks.

Larjo A, Shmulevich I, Lähdesmäki H.

Methods Mol Biol. 2013;939:35-45. doi: 10.1007/978-1-62703-107-3_4.

PMID:
23192539
46.

Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer.

Liu G, Yang D, Sun Y, Shmulevich I, Xue F, Sood AK, Zhang W.

Pharmacogenomics. 2012 Oct;13(13):1523-35. doi: 10.2217/pgs.12.137. Review.

47.

Fastbreak: a tool for analysis and visualization of structural variations in genomic data.

Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, Rovira H, Knijnenburg T, Boyle J, Shmulevich I.

EURASIP J Bioinform Syst Biol. 2012 Oct 9;2012(1):15. doi: 10.1186/1687-4153-2012-15.

48.

Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma.

Moore LM, Kivinen V, Liu Y, Annala M, Cogdell D, Liu X, Liu CG, Sawaya R, Yli-Harja O, Shmulevich I, Fuller GN, Zhang W, Nykter M.

J Pathol. 2013 Feb;229(3):449-59. doi: 10.1002/path.4109.

49.

Increasing coverage of transcription factor position weight matrices through domain-level homology.

Bernard B, Thorsson V, Rovira H, Shmulevich I.

PLoS One. 2012;7(8):e42779. doi: 10.1371/journal.pone.0042779. Epub 2012 Aug 27.

50.

Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma.

Liu Y, Sun Y, Broaddus R, Liu J, Sood AK, Shmulevich I, Zhang W.

PLoS One. 2012;7(5):e36383. doi: 10.1371/journal.pone.0036383. Epub 2012 May 8.

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