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On statistical modeling of sequencing noise in high depth data to assess tumor evolution.

Rabadan R, Bhanot G, Marsilio S, Chiorazzi N, Pasqualucci L, Khiabanian H.

J Stat Phys. 2018 Jul;172(1):143-155. doi: 10.1007/s10955-017-1945-1. Epub 2017 Dec 21.


Immune Activation and Benefit From Avelumab in EBV-Positive Gastric Cancer.

Panda A, Mehnert JM, Hirshfield KM, Riedlinger G, Damare S, Saunders T, Kane M, Sokol L, Stein MN, Poplin E, Rodriguez-Rodriguez L, Silk AW, Aisner J, Chan N, Malhotra J, Frankel M, Kaufman HL, Ali S, Ross JS, White EP, Bhanot G, Ganesan S.

J Natl Cancer Inst. 2018 Mar 1;110(3):316-320. doi: 10.1093/jnci/djx213.


Using Cluster Analysis to Group Countries for Cost-effectiveness Analysis: An Application to Sub-Saharan Africa.

Russell LB, Bhanot G, Kim SY, Sinha A.

Med Decis Making. 2018 Feb;38(2):139-149. doi: 10.1177/0272989X17724773. Epub 2017 Aug 19.


Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma.

Bjørklund SS, Panda A, Kumar S, Seiler M, Robinson D, Gheeya J, Yao M, Alnæs GIG, Toppmeyer D, Riis M, Naume B, Børresen-Dale AL, Kristensen VN, Ganesan S, Bhanot G.

Sci Rep. 2017 Jul 17;7(1):5568. doi: 10.1038/s41598-017-05537-0.


Identifying a Clinically Applicable Mutational Burden Threshold as a Potential Biomarker of Response to Immune Checkpoint Therapy in Solid Tumors.

Panda A, Betigeri A, Subramanian K, Ross JS, Pavlick DC, Ali S, Markowski P, Silk A, Kaufman HL, Lattime E, Mehnert JM, Sullivan R, Lovly CM, Sosman J, Johnson DB, Bhanot G, Ganesan S.

JCO Precis Oncol. 2017;2017. doi: 10.1200/PO.17.00146. Epub 2017 Dec 7.


The Modular Adaptive Ribosome.

Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H, Bhanot G.

PLoS One. 2016 Nov 3;11(11):e0166021. doi: 10.1371/journal.pone.0166021. eCollection 2016.


Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer.

Mehnert JM, Panda A, Zhong H, Hirshfield K, Damare S, Lane K, Sokol L, Stein MN, Rodriguez-Rodriquez L, Kaufman HL, Ali S, Ross JS, Pavlick DC, Bhanot G, White EP, DiPaola RS, Lovell A, Cheng J, Ganesan S.

J Clin Invest. 2016 Jun 1;126(6):2334-40. doi: 10.1172/JCI84940. Epub 2016 May 9.


Glutaminase 2 is a novel negative regulator of small GTPase Rac1 and mediates p53 function in suppressing metastasis.

Zhang C, Liu J, Zhao Y, Yue X, Zhu Y, Wang X, Wu H, Blanco F, Li S, Bhanot G, Haffty BG, Hu W, Feng Z.

Elife. 2016 Jan 11;5:e10727. doi: 10.7554/eLife.10727.


Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas.

Bjørklund SS, Kristensen VN, Seiler M, Kumar S, Alnæs GI, Ming Y, Kerrigan J, Naume B, Sachidanandam R, Bhanot G, Børresen-Dale AL, Ganesan S.

BMC Cancer. 2015 Jul 17;15:524. doi: 10.1186/s12885-015-1510-8.


Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation.

Yadav A, Radhakrishnan A, Bhanot G, Sinha H.

G3 (Bethesda). 2015 Feb 23;5(5):699-709. doi: 10.1534/g3.115.017020.


IRF5 is a novel regulator of CXCL13 expression in breast cancer that regulates CXCR5(+) B- and T-cell trafficking to tumor-conditioned media.

Pimenta EM, De S, Weiss R, Feng D, Hall K, Kilic S, Bhanot G, Ganesan S, Ran S, Barnes BJ.

Immunol Cell Biol. 2015 May-Jun;93(5):486-99. doi: 10.1038/icb.2014.110. Epub 2014 Dec 23.


The somatic genomic landscape of chromophobe renal cell carcinoma.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ.

Cancer Cell. 2014 Sep 8;26(3):319-330. doi: 10.1016/j.ccr.2014.07.014. Epub 2014 Aug 21.


Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets.

Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A.

Bioinformatics. 2015 Feb 15;31(4):492-500. doi: 10.1093/bioinformatics/btu569. Epub 2014 Aug 24.


Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge.

Dayarian A, Romero R, Wang Z, Biehl M, Bilal E, Hormoz S, Meyer P, Norel R, Rhrissorrakrai K, Bhanot G, Luo F, Tarca AL.

Bioinformatics. 2015 Feb 15;31(4):462-70. doi: 10.1093/bioinformatics/btu490. Epub 2014 Jul 23.


Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.

Biehl M, Sadowski P, Bhanot G, Bilal E, Dayarian A, Meyer P, Norel R, Rhrissorrakrai K, Zeller MD, Hormoz S.

Bioinformatics. 2015 Feb 15;31(4):453-61. doi: 10.1093/bioinformatics/btu407. Epub 2014 Jul 3.


Bird to human transmission biases and vaccine escape mutants in H5N1 infections.

Wagh K, Bhatia A, Greenbaum BD, Bhanot G.

PLoS One. 2014 Jul 2;9(7):e100754. doi: 10.1371/journal.pone.0100754. eCollection 2014.


ERBB2 overexpression suppresses stress-induced autophagy and renders ERBB2-induced mammary tumorigenesis independent of monoallelic Becn1 loss.

Lozy F, Cai-McRae X, Teplova I, Price S, Reddy A, Bhanot G, Ganesan S, Vazquez A, Karantza V.

Autophagy. 2014 Apr;10(4):662-76. doi: 10.4161/auto.27867. Epub 2014 Jan 30.


Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

Bhatia A, Yadav A, Zhu C, Gagneur J, Radhakrishnan A, Steinmetz LM, Bhanot G, Sinha H.

G3 (Bethesda). 2014 Jan 28;4(5):769-77. doi: 10.1534/g3.113.009142.


Sporulation genes associated with sporulation efficiency in natural isolates of yeast.

Tomar P, Bhatia A, Ramdas S, Diao L, Bhanot G, Sinha H.

PLoS One. 2013 Jul 17;8(7):e69765. doi: 10.1371/journal.pone.0069765. Print 2013.


Potential tumorigenic programs associated with TP53 mutation status reveal role of VEGF pathway.

Joshi H, Bhanot G, Børresen-Dale AL, Kristensen V.

Br J Cancer. 2012 Nov 6;107(10):1722-8. doi: 10.1038/bjc.2012.461. Epub 2012 Oct 18.


Lactase persistence and lipid pathway selection in the Maasai.

Wagh K, Bhatia A, Alexe G, Reddy A, Ravikumar V, Seiler M, Boemo M, Yao M, Cronk L, Naqvi A, Ganesan S, Levine AJ, Bhanot G.

PLoS One. 2012;7(9):e44751. doi: 10.1371/journal.pone.0044751. Epub 2012 Sep 28.


Occupational stress and social support in naval personnel.

Pawar AA, Chikkanna CB, Rote MS, Singh RJ, Bhanot G, Pillai A, Pisharody RR.

Med J Armed Forces India. 2012 Oct;68(4):360-5. doi: 10.1016/j.mjafi.2012.04.026. Epub 2012 Sep 28.


Automated reconstruction algorithm for identification of 3D architectures of cribriform ductal carcinoma in situ.

Norton KA, Namazi S, Barnard N, Fujibayashi M, Bhanot G, Ganesan S, Iyatomi H, Ogawa K, Shinbrot T.

PLoS One. 2012;7(9):e44011. doi: 10.1371/journal.pone.0044011. Epub 2012 Sep 6.


Neurite sprouting and synapse deterioration in the aging Caenorhabditis elegans nervous system.

Toth ML, Melentijevic I, Shah L, Bhatia A, Lu K, Talwar A, Naji H, Ibanez-Ventoso C, Ghose P, Jevince A, Xue J, Herndon LA, Bhanot G, Rongo C, Hall DH, Driscoll M.

J Neurosci. 2012 Jun 27;32(26):8778-90. doi: 10.1523/JNEUROSCI.1494-11.2012.


Amplified loci on chromosomes 8 and 17 predict early relapse in ER-positive breast cancers.

Bilal E, Vassallo K, Toppmeyer D, Barnard N, Rye IH, Almendro V, Russnes H, Børresen-Dale AL, Levine AJ, Bhanot G, Ganesan S.

PLoS One. 2012;7(6):e38575. doi: 10.1371/journal.pone.0038575. Epub 2012 Jun 13.


Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines.

Powell AA, Talasaz AH, Zhang H, Coram MA, Reddy A, Deng G, Telli ML, Advani RH, Carlson RW, Mollick JA, Sheth S, Kurian AW, Ford JM, Stockdale FE, Quake SR, Pease RF, Mindrinos MN, Bhanot G, Dairkee SH, Davis RW, Jeffrey SS.

PLoS One. 2012;7(5):e33788. doi: 10.1371/journal.pone.0033788. Epub 2012 May 7.


Age-dependent sex bias in clinical malarial disease in hypoendemic regions.

Pathak S, Rege M, Gogtay NJ, Aigal U, Sharma SK, Valecha N, Bhanot G, Kshirsagar NA, Sharma S.

PLoS One. 2012;7(4):e35592. doi: 10.1371/journal.pone.0035592. Epub 2012 Apr 25.


Identifying microRNA/mRNA dysregulations in ovarian cancer.

Miles GD, Seiler M, Rodriguez L, Rajagopal G, Bhanot G.

BMC Res Notes. 2012 Mar 27;5:164. doi: 10.1186/1756-0500-5-164.


ErbB2, EphrinB1, Src kinase and PTPN13 signaling complex regulates MAP kinase signaling in human cancers.

Vermeer PD, Bell M, Lee K, Vermeer DW, Wieking BG, Bilal E, Bhanot G, Drapkin RI, Ganesan S, Klingelhutz AJ, Hendriks WJ, Lee JH.

PLoS One. 2012;7(1):e30447. doi: 10.1371/journal.pone.0030447. Epub 2012 Jan 18.


Identification of the YES1 Kinase as a Therapeutic Target in Basal-Like Breast Cancers.

Bilal E, Alexe G, Yao M, Cong L, Kulkarni A, Ginjala V, Toppmeyer D, Ganesan S, Bhanot G.

Genes Cancer. 2010 Oct;1(10):1063-73. doi: 10.1177/1947601910395583.


Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns.

Brannon AR, Reddy A, Seiler M, Arreola A, Moore DT, Pruthi RS, Wallen EM, Nielsen ME, Liu H, Nathanson KL, Ljungberg B, Zhao H, Brooks JD, Ganesan S, Bhanot G, Rathmell WK.

Genes Cancer. 2010 Feb 1;1(2):152-163.


Robust gene network analysis reveals alteration of the STAT5a network as a hallmark of prostate cancer.

Reddy A, Huang CC, Liu H, Delisi C, Nevalainen MT, Szalma S, Bhanot G.

Genome Inform. 2010;24:139-53.


Robust multi-tissue gene panel for cancer detection.

Irgon J, Huang CC, Zhang Y, Talantov D, Bhanot G, Szalma S.

BMC Cancer. 2010 Jun 22;10:319. doi: 10.1186/1471-2407-10-319.


Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma.

Liu H, Brannon AR, Reddy AR, Alexe G, Seiler MW, Arreola A, Oza JH, Yao M, Juan D, Liou LS, Ganesan S, Levine AJ, Rathmell WK, Bhanot GV.

BMC Syst Biol. 2010 Apr 27;4:51. doi: 10.1186/1752-0509-4-51.


Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology.

Fatakdawala H, Xu J, Basavanhally A, Bhanot G, Ganesan S, Feldman M, Tomaszewski JE, Madabhushi A.

IEEE Trans Biomed Eng. 2010 Jul;57(7):1676-89. doi: 10.1109/TBME.2010.2041232. Epub 2010 Feb 17.


ConsensusCluster: a software tool for unsupervised cluster discovery in numerical data.

Seiler M, Huang CC, Szalma S, Bhanot G.

OMICS. 2010 Feb;14(1):109-13. doi: 10.1089/omi.2009.0083.


Identification of a microRNA panel for clear-cell kidney cancer.

Juan D, Alexe G, Antes T, Liu H, Madabhushi A, Delisi C, Ganesan S, Bhanot G, Liou LS.

Urology. 2010 Apr;75(4):835-41. doi: 10.1016/j.urology.2009.10.033. Epub 2009 Dec 29.


A 2D mechanistic model of breast ductal carcinoma in situ (DCIS) morphology and progression.

Norton KA, Wininger M, Bhanot G, Ganesan S, Barnard N, Shinbrot T.

J Theor Biol. 2010 Apr 21;263(4):393-406. doi: 10.1016/j.jtbi.2009.11.024. Epub 2009 Dec 16.


Computerized image-based detection and grading of lymphocytic infiltration in HER2+ breast cancer histopathology.

Basavanhally AN, Ganesan S, Agner S, Monaco JP, Feldman MD, Tomaszewski JE, Bhanot G, Madabhushi A.

IEEE Trans Biomed Eng. 2010 Mar;57(3):642-53. doi: 10.1109/TBME.2009.2035305. Epub 2009 Oct 30.


Autophagy suppresses tumorigenesis through elimination of p62.

Mathew R, Karp CM, Beaudoin B, Vuong N, Chen G, Chen HY, Bray K, Reddy A, Bhanot G, Gelinas C, Dipaola RS, Karantza-Wadsworth V, White E.

Cell. 2009 Jun 12;137(6):1062-75. doi: 10.1016/j.cell.2009.03.048. Erratum in: Cell. 2011 Apr 15;145(2):322.


Towards improved cancer diagnosis and prognosis using analysis of gene expression data and computer aided imaging.

Lexe G, Monaco J, Doyle S, Basavanhally A, Reddy A, Seiler M, Ganesan S, Bhanot G, Madabhushi A.

Exp Biol Med (Maywood). 2009 Aug;234(8):860-79. doi: 10.3181/0902-MR-89. Epub 2009 Jun 2. Review.


PCA and clustering reveal alternate mtDNA phylogeny of N and M clades.

Alexe G, Satya RV, Seiler M, Platt D, Bhanot T, Hui S, Tanaka M, Levine AJ, Bhanot G.

J Mol Evol. 2008 Nov;67(5):465-87. doi: 10.1007/s00239-008-9148-7. Epub 2008 Oct 15.


Breast cancer stratification from analysis of micro-array data of micro-dissected specimens.

Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, Delisi C, Bhanot G.

Genome Inform. 2007;18:130-40.


Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan.

Bilal E, Rabadan R, Alexe G, Fuku N, Ueno H, Nishigaki Y, Fujita Y, Ito M, Arai Y, Hirose N, Ruckenstein A, Bhanot G, Tanaka M.

PLoS One. 2008 Jun 11;3(6):e2421. doi: 10.1371/journal.pone.0002421.


Patterns of evolution and host gene mimicry in influenza and other RNA viruses.

Greenbaum BD, Levine AJ, Bhanot G, Rabadan R.

PLoS Pathog. 2008 Jun 6;4(6):e1000079. doi: 10.1371/journal.ppat.1000079.


High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates.

Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, DeLisi C, Harris L, Barnard N, Martel M, Levine AJ, Ganesan S, Bhanot G.

Cancer Res. 2007 Nov 15;67(22):10669-76.


Analysis of breast cancer progression using principal component analysis and clustering.

Alexe G, Dalgin GS, Ganesan S, Delisi C, Bhanot G.

J Biosci. 2007 Aug;32(5):1027-39.


Portraits of breast cancer progression.

Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, DeLisi C, Bhanot G.

BMC Bioinformatics. 2007 Aug 6;8:291.


Enrichment of longevity phenotype in mtDNA haplogroups D4b2b, D4a, and D5 in the Japanese population.

Alexe G, Fuku N, Bilal E, Ueno H, Nishigaki Y, Fujita Y, Ito M, Arai Y, Hirose N, Bhanot G, Tanaka M.

Hum Genet. 2007 May;121(3-4):347-56. Epub 2007 Feb 17.


Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns.

Alexe G, Dalgin GS, Ramaswamy R, Delisi C, Bhanot G.

Cancer Inform. 2007 Feb 19;2:243-74.

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