Selected Publications

Unsupervised cancer driver detection with parsimony-guided learning.

Nature Genetics

Kumar RD, Swamidass SJ, and Bose R.  Nature Genetics. 48(10):1288-94 (Oct 2016).


Kavuri SM, Jain N, Galimi F, Cottino F, Leto SM, Migliardi G, Searleman AC,Shen W, Monsey J, Trusolino L, Jacobs SA, Bertotti A, Bose R.
Cancer Discovery, 5(8):832-41 (Aug. 2015).


Biophysical Evidence for Intrinsic Disorder in the C-terminal Tails of the EGFR and HER3 Receptor Tyrosine Kinases.

Keppel TR, Sarpong K, Murray EM, Monsey J, Zhu J, and Bose R.
Journal of Biological Chemistry. 292(2):597-610 (Jan. 2017).

Genomic Characterization of Primary Invasive Lobular Breast Cancer.

Desmedt C, Zoppoli G, Gundem G, Pruneri G, Larsimont D, Fornili M, Fumagalli D, Brown D, Rothé F, Vincent D, Kheddoumi N, Rouas G, Majjaj S, Brohée S, Van Loo P, Maisonneuve P, Salgado R, Van Brussel T, Lambrechts D, Bose R, Metzger O, Galant C, Bertucci F, Piccart-Gebhart M, Viale G, Biganzoli E, Campbell PJ, Sotiriou C.
Journal of Clinical Oncology. 34(16):1872-81 (Jun 1, 2016)

Nonamplification ERBB2 genomic alterations in 5605 cases of recurrent and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies.

Ross JS, Gay LM, Wang K, Ali SM, Chumsri S, Elvin JA, Bose R, Vergilio JA, Suh J, Yelensky R, Lipson D, Chmielecki J, Waintraub S, Leyland-Jones B, Miller VA, Stephens PJ.
Cancer. 122(17):2654-62 (2016).


Kumar RD, Searleman AC, Swamidass SJ, Griffith OL, and Bose R.
Bioinformatics. 31(22):3561-8, (Nov. 15, 2015). doi: 10.1093/bioinformatics/btv430.

Activating HER2 mutations in HER2 gene amplification negative breast cancer.

Bose R, Kavuri SM, Searleman AC, Shen W, Shen D, Koboldt DC, Monsey J, Goel N, Aronson AB, Li S, Ma CX, Ding L, Mardis ER, Ellis MJ.
Cancer Discovery, 3(2):224-37 (2013).

This paper is one of the most highly-cited Cancer Discovery articles published in 2013. This was announced at the April 2015, AACR Annual Meeting.


Tissue Phosphoproteomics with PolyMAC Identifies Potential Therapeutic Targets in a Transgenic Mouse Model of HER2 Positive Breast Cancer.

Searleman AC, Iliuk AB, Collier TS, Chodosh LA, Tao WA, Bose R.
Electrophoresis, 35(24): 3463-9 (2014).

DGIdb – Mining the druggable genome.

Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK.
Nature Methods, 10(12):1209-10 (2013).

Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data.

Kumar RD, Chang LW, Ellis MJ, Bose R.
PLOS One, 8(6):e67980, Jun 27, 2013.

Carboxyl Group Footprinting Mass Spectrometry and Molecular Dynamics Identify Key Interactions in the HER2-HER3 Receptor Tyrosine Kinase Interface.

Collier TS, Diraviyam K, Monsey J, Shen W, Sept D, Bose R.
Journal of Biological Chemistry, 288: 25254-25264 (2013).

Quantitative Proteomics with siRNA Screening Identifies Novel Mechanisms of Trastuzumab Resistance in HER2 Amplified Breast Cancers.

Boyer AP, Collier TS, Vidavsky I, Bose R.
Molecular & Cellular Proteomics, 12(1):180-93 (2013).

Whole Genome Sequencing to Characterise Breast Cancer Response to Aromatase Inhibition.

Ellis MJ, Ding L, Shen D, Luo J, SumanVJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider, J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LF, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER.
Nature, 486: 353-360 (2012).

Comprehensive molecular portraits of human breast tumors.

The Cancer Genome Atlas Research Network (author list includes Bose R).
Nature, 490: 61-70 (2012).

Comprehensive genomic characterization of squamous cell lung cancers.

The Cancer Genome Atlas Research Network, Hammerman PS, Hayes DN, Wilkerson MD, Schultz N, Bose R, Chu A, Collisson EA, Cope L, Creighton CJ, Getz G, Herman JG, Johnson BE, Kucherlapati R, Ladanyi M, Maher CA, Robertson G, Sander C, Shen R, Sinha R, Sivachenko A, Thomas RK, Travis WD, Tsao MS, Weinstein JN, Wigle DA, Baylin SB, Govindan R, Meyerson M.
Nature, 489:519-25 (2012).

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers.

Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK.
Cell, 150(6): 1121-1134 (2012).

Carboxyl-group Footprinting Mass Spectrometry Maps the Dimerization Interface and Phosphorylation-induced Conformational Changes of a Membrane-associated Tyrosine Kinase.

Zhang H, Shen W, Rempel D, Monsey J, Vidavsky I, Gross ML, Bose R.
Molecular & Cellular Proteomics, 10(6):M110.005678 (2011).

Her4 and Her2/neu Tyrosine Kinase Domains Dimerize and Activate in a Reconstituted in vitro System.

Monsey J, Shen W, Schlesinger P, Bose R.
Journal of Biological Chemistry, 285 (10):7035–7044 (2010).


last updated on 3/10/17.