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Items: 13

1.

Intratumoral heterogeneity and clonal evolution in liver cancer.

Losic B, Craig AJ, Villacorta-Martin C, Martins-Filho SN, Akers N, Chen X, Ahsen ME, von Felden J, Labgaa I, DʹAvola D, Allette K, Lira SA, Furtado GC, Garcia-Lezana T, Restrepo P, Stueck A, Ward SC, Fiel MI, Hiotis SP, Gunasekaran G, Sia D, Schadt EE, Sebra R, Schwartz M, Llovet JM, Thung S, Stolovitzky G, Villanueva A.

Nat Commun. 2020 Jan 15;11(1):291. doi: 10.1038/s41467-019-14050-z.

2.

R/PY-SUMMA: An R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics.

Ahsen ME, Vogel R, Stolovitzky GA.

J Comput Biol. 2020 Jan 3. doi: 10.1089/cmb.2019.0348. [Epub ahead of print]

PMID:
31905016
3.

NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers.

Ahsen ME, Chun Y, Grishin A, Grishina G, Stolovitzky G, Pandey G, Bunyavanich S.

Sci Rep. 2019 Sep 10;9(1):12970. doi: 10.1038/s41598-019-49498-y.

4.

Assessment of network module identification across complex diseases.

Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D.

Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30.

5.

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.

6.

Radiogenomics Consortium Genome-Wide Association Study Meta-analysis of Late Toxicity after Prostate Cancer Radiotherapy.

Kerns SL, Fachal L, Dorling L, Barnett GC, Baran A, Peterson DR, Hollenberg M, Hao K, Narzo AD, Ahsen ME, Pandey G, Bentzen SM, Janelsins M, Elliott RM, Pharoah PDP, Burnet NG, Dearnaley DP, Gulliford SL, Hall E, Sydes MR, Aguado-Barrera ME, Gómez-Caamaño A, Carballo AM, Peleteiro P, Lobato-Busto R, Stock R, Stone NN, Ostrer H, Usmani N, Singhal S, Tsuji H, Imai T, Saito S, Eeles R, DeRuyck K, Parliament M, Dunning AM, Vega A, Rosenstein BS, West CML.

J Natl Cancer Inst. 2019 May 16. pii: djz075. doi: 10.1093/jnci/djz075. [Epub ahead of print]

PMID:
31095341
7.

Preference-Sensitive Management of Post-Mammography Decisions in Breast Cancer Diagnosis.

Ayvaci MUS, Alagoz O, Ahsen ME, Burnside ES.

Prod Oper Manag. 2018 Dec;27(12):2313-2338. doi: 10.1111/poms.12897. Epub 2018 May 22.

8.

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.

9.

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
10.

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.

Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R; Respiratory Viral DREAM Challenge Consortium, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK.

Nat Commun. 2018 Oct 24;9(1):4418. doi: 10.1038/s41467-018-06735-8.

11.

A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data.

Pandey G, Pandey OP, Rogers AJ, Ahsen ME, Hoffman GE, Raby BA, Weiss ST, Schadt EE, Bunyavanich S.

Sci Rep. 2018 Jun 11;8(1):8826. doi: 10.1038/s41598-018-27189-4.

12.

Sparse feature selection for classification and prediction of metastasis in endometrial cancer.

Ahsen ME, Boren TP, Singh NK, Misganaw B, Mutch DG, Moore KN, Backes FJ, McCourt CK, Lea JS, Miller DS, White MA, Vidyasagar M.

BMC Genomics. 2017 Mar 27;18(Suppl 3):233. doi: 10.1186/s12864-017-3604-y.

13.

Estimating Waiting Time for Deceased Donor Renal Transplantion in the Era of New Kidney Allocation System.

Torlak F, Ayvaci MU, Ahsen ME, Arce C, Vazquez MA, Tanriover B.

Transplant Proc. 2016 Jul-Aug;48(6):1916-9. doi: 10.1016/j.transproceed.2016.03.041.

PMID:
27569922

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