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Items: 16

1.

Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers.

Wang Y, Li L, Douville C, Cohen JD, Yen TT, Kinde I, Sundfelt K, Kjær SK, Hruban RH, Shih IM, Wang TL, Kurman RJ, Springer S, Ptak J, Popoli M, Schaefer J, Silliman N, Dobbyn L, Tanner EJ, Angarita A, Lycke M, Jochumsen K, Afsari B, Danilova L, Levine DA, Jardon K, Zeng X, Arseneau J, Fu L, Diaz LA Jr, Karchin R, Tomasetti C, Kinzler KW, Vogelstein B, Fader AN, Gilbert L, Papadopoulos N.

Sci Transl Med. 2018 Mar 21;10(433). pii: eaap8793. doi: 10.1126/scitranslmed.aap8793.

PMID:
29563323
2.

Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy.

Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ.

Elife. 2018 Mar 20;7. pii: e32143. doi: 10.7554/eLife.32143.

3.

Detection and localization of surgically resectable cancers with a multi-analyte blood test.

Cohen JD, Li L, Wang Y, Thoburn C, Afsari B, Danilova L, Douville C, Javed AA, Wong F, Mattox A, Hruban RH, Wolfgang CL, Goggins MG, Dal Molin M, Wang TL, Roden R, Klein AP, Ptak J, Dobbyn L, Schaefer J, Silliman N, Popoli M, Vogelstein JT, Browne JD, Schoen RE, Brand RE, Tie J, Gibbs P, Wong HL, Mansfield AS, Jen J, Hanash SM, Falconi M, Allen PJ, Zhou S, Bettegowda C, Diaz LA Jr, Tomasetti C, Kinzler KW, Vogelstein B, Lennon AM, Papadopoulos N.

Science. 2018 Feb 23;359(6378):926-930. doi: 10.1126/science.aar3247. Epub 2018 Jan 18.

PMID:
29348365
4.

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.

Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ.

Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004.

PMID:
29342249
5.

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks.

Kelley DZ, Flam EL, Izumchenko E, Danilova LV, Wulf HA, Guo T, Singman DA, Afsari B, Skaist AM, Considine M, Welch JA, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan SJ, Califano JA, Favorov AV, Fertig EJ, Gaykalova DA.

Cancer Res. 2017 Dec 1;77(23):6538-6550. doi: 10.1158/0008-5472.CAN-17-0833. Epub 2017 Sep 25.

PMID:
28947419
6.

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers.

Guo T, Sakai A, Afsari B, Considine M, Danilova L, Favorov AV, Yegnasubramanian S, Kelley DZ, Flam E, Ha PK, Khan Z, Wheelan SJ, Gutkind JS, Fertig EJ, Gaykalova DA, Califano J.

Cancer Res. 2017 Oct 1;77(19):5248-5258. doi: 10.1158/0008-5472.CAN-16-3106. Epub 2017 Jul 21.

PMID:
28733453
7.

Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy.

Kim JS, Afsari B, Chirikjian GS.

J Comput Biol. 2017 Jan;24(1):13-30. doi: 10.1089/cmb.2016.0139. Epub 2016 Oct 6.

8.

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.

9.

Approximate joint diagonalization and geometric mean of symmetric positive definite matrices.

Congedo M, Afsari B, Barachant A, Moakher M.

PLoS One. 2015 Apr 28;10(4):e0121423. doi: 10.1371/journal.pone.0121423. eCollection 2014.

10.

Learning dysregulated pathways in cancers from differential variability analysis.

Afsari B, Geman D, Fertig EJ.

Cancer Inform. 2014 Oct 23;13(Suppl 5):61-7. doi: 10.4137/CIN.S14066. eCollection 2014. Review.

11.

switchBox: an R package for k-Top Scoring Pairs classifier development.

Afsari B, Fertig EJ, Geman D, Marchionni L.

Bioinformatics. 2015 Jan 15;31(2):273-4. doi: 10.1093/bioinformatics/btu622. Epub 2014 Sep 26.

12.

A simple and reproducible breast cancer prognostic test.

Marchionni L, Afsari B, Geman D, Leek JT.

BMC Genomics. 2013 May 17;14:336. doi: 10.1186/1471-2164-14-336.

13.

Estimation of non-negative ODFs using the eigenvalue distribution of spherical functions.

Schwab E, Afsari B, Vidal R.

Med Image Comput Comput Assist Interv. 2012;15(Pt 2):322-30.

PMID:
23286064
14.

Rotation invariant features for HARDI.

Schwab E, Cetingül HE, Afsari B, Vidal R.

Inf Process Med Imaging. 2013;23:705-17.

15.

GROUP ACTION INDUCED AVERAGING FOR HARDI PROCESSING.

Cetingül HE, Afsari B, Wright MJ, Thompson PM, Vidal R.

Proc IEEE Int Symp Biomed Imaging. 2012:1389-1392.

16.

The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.

Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D.

BMC Bioinformatics. 2009 Aug 20;10:256. doi: 10.1186/1471-2105-10-256.

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