Publications

Year 2016

Guy Tal, Simina M. Boca, Jay Mittenthal, Gustavo Caetano-Anollés. A dynamic model for the evolution of protein structure. Journal of Molecular Evolution, Accepted 2016

Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M Johnson, Lei Song, Adil Alaoui, Michael A Harris, Robert Clarke, Louis M Weiner, Yuriy Gusev, Subha Madhavan. G-DOC Plus - an integrative bioinformatics platform for precision medicine. BMC Bioinformatics, in press 2016

Chen, Cong, Li, Nicole, Shentu, Yue, Pang, Lei, and Robert A. Beckman. Adaptive Informational Design of Confirmatory Phase III Trials with an Uncertain Biomarker Effect to Improve the Probability of Success. Statistics in Biopharmaceutical Research, in press 2016

Simina M. Boca, Maki Nishida, Michael Harris, Shruti Rao, Amrita K. Cheema, Kirandeep Gill, Haeri Seol, Lauren P. Morgenroth, Erik Henricson, Craig McDonald, Jean K. Mah, Paula R. Clemens, Eric P Hoffman, Yetrib Hathout and Subha Madhavan. Discovery of metabolic biomarkers for Duchenne Muscular Dystrophy within a natural history study. PLOS ONE, April 15, 2016 Full text   

Linlin Luo, Peter McGarvey, Subha Madhavan, Rakesh Kumar, Yuriy Gusev, Geeta Upadhyay. Distinct lymphocyte antigens 6 (Ly6) family members Ly6D, Ly6E, Ly6K and Ly6H drive tumorigenesis and clinical outcome. Oncotarget. 2016. Pubmed

Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan and Yuriy Gusev. CINdex: Chromosome Instability Index. R package version 0.99.9. (2016) Link

Midrar Al Hossiny, Linlin Luo, William R Frazier, Noriko Steiner, Yuriy Gusev, Bhaskar Kallakury, Eric Glasgow, Karen Creswell, Subha Madhavan, Rakesh Kumar and Geeta Upadhyay. Ly6E/K signaling to TGF-ß promotes breast cancer progression, immune escape and drug resistance. Cancer Research . April 2016 Full Text

Year 2015

Sampson JN., ... et al. Boca SM., Cerhan JR., Ferri GM., Hartge P., Hsiung CA., Magnani C., Miligi L., Morton LM., Smedby KE., Teras LR., Vijai J., Wang SS., Brennan P., Caporaso NE., Hunter DJ., Kraft P., Rothman N., Silverman DT., Slager SL., Chanock SJ., and Chatterjee N.  Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types.  JNCI.  2015 Sep 3.  Full Text

Marika Ciprotti, Niall Tebbutt, Robert A. Beckman, Andrew M. Scott, et al. Phase I and Pharmacodynamic Study of CS-1008 in Patients with Metastatic Colorectal Cancer.  Journal of Clinical Oncology. 2015 June 29.  PubMed

Ann-Li Cheng, Yoon-Koo Kang, Aiwu Ruth He, Robert A. Beckman, Masatoshi Kudo, et al.  Safety and Efficacy of Tigatuzumab Plus Sorafenib as First-Line Therapy in Subjects with Advanced Hepatocellular Carcinoma: A Phase 2 Randomized Study.  Journal of Hepatology.  2015 June 10; 63: 896-904.  PubMed

James N. Baraniuk, Begona Casado, Lewis K. Pannell, Peter McGarvey, Piera Boschetto,  Maurizio Luisetti, and Paolo Iadarola.  Protein Networks in Induced Sputum from Smokers and COPD Patients.  International Journal of Chronic Obstructive Pulmonary Disease.  2015 May 31.  PubMed  

Subha Madhavan, Yuriy Gusev,  Salendra Singh and Rebecca B. Riggins.  ERRγ target genes are poor prognostic factors in Tamoxifen-treated breast cancer.  Journal of Experimental & Clinical Cancer Research.  2015 May 15; 34(1):45.  PubMed

Edwards, Nathan; Oberti, Mauricio; Thangudu, Ratna; Cai, Shuang; McGarvey, Peter; Jacob, Shine; Madhavan, Subha; Ketchum, Karen.  The CPTAC Data Portal: A Resource for Cancer Proteomics Research.  Journal of Proteome Research.  2015 Apr. 15.  PubMed

Guertin KA, Loftfield E, Boca SM, Sampson JN, Moore SC, Xiao Q, Huang WY, Xiong X, Freedman ND, Cross AJ, Sinha R.  Serum biomarkers of habitual coffee consumption may provide insight into the mechanism underlying the association between coffee consumption and colorectal cancer.  American Journal of Clinical Nutrition.  2015 March 11.  Full Text

Mendell, Jeanne; Freeman, Daniel J; Feng, Wenqin; Hettmann, Thore; Schneider, Matthias; Blum, Sabine; Ruhe, Jens; Bange, Johannes; Nakamaru, Kenji; Chen, Shuquan; Tsuchihashi, Zenta; von Pawel, Joachim; Copigneaux, Catherine; Robert A. Beckman.  Clinical Translation and Validation of a Predictive Biomarker for Patritumab, an Anti- Human Epidermal Growth Factor Receptor 3 (HER3) Monoclonal Antibody, in Patients With Advanced Non–Small Cell Lung Cancer.  Ebiomedicine.  2015 Feb. 12; 2:264-271.  PubMed

Aiwu Ruth He, Krithika Bhuvaneshwar, and Yuriy Gusev.  Role of SPTBN1 in Hepatocellular Carcinoma.  Hepatology.  2015 Feb. 1.

Xiuling Zhi, Ling Lin, Shaoxian Yang, Krithika Bhuvaneshwar, Hongkun Wang, Yuriy Gusev, Mi‐Hye Lee, Bhaskar Kallakury, Narayan Shivapurkar, Katherine Cahn, Xuefei Tian, John L Marshall, Stephen W. Byers and Aiwu R. He.  βII-spectrin (SPTBN1) suppresses progression of hepatocellular carcinoma and Wnt signaling via regulation of Wnt inhibitor kallistatin.  Hepatology.  2015 Feb. 1.  PubMed    

Rupak Pathak, Amrita Cheema, Simina Boca, Kimberly Krager, Martin Hauer-Jensen, and Nukhet Aykin-Burns.  Modulation of radiation response.  Antioxidants.  2015 Jan. 12.     

Wang D., Song L., Singh V., Rao S., An L., and Madhavan S.  SNP2Structure: A public and versatile resource for mapping and three-dimensional modeling of missense SNPs on human protein structuresComputational and Structural Biotechnology Journal.  2015.  (In Press) 

Ciprotti M., Tebbutt NC., Lee F., Lee S., Gan HK., McKee DC., O’Keefe GJ., Gong SJ., Chong G., Hopkins W., Scott FE., Brechbiel MW., Tse AN., Jansen M., Matsumura M., Kotsuma M., Watanabe R., Venhaus R., Beckman RA., Greenberg J., and Scott AM.  Phase I Imaging and Pharmacodynamic Trial in Patients with Metastatic Colorectal Cancer.  Journal of Clinical Oncology.  2015; 33: 2609-2616. 

Robert A. Beckman, Cong Chen.  Efficient, Adaptive Clinical Validation of Predictive Biomarkers in Cancer Therapeutic Development.  Advances in Cancer Biomarkers.  2015.  PubMed

Robert A. Beckman, Cong Chen.  Translating Predictive Biomarkers within Oncology Clinical Development Programs.  Biomarkers in Medicine.  2015; 9:851-862.  PubMed  

Year 2014

Peter B McGarvey ,  Baris E Suzek, James N Baraniuk, Shruti Rao, Brian Conkright, Samir Lababidi, Andrea Sutherland, Richard Forshee and Subha Madhavan.  In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases.  BMC Immunology.  9 Dec. 2014.  PubMed

Krithika Bhuvaneshwar, Dinanath Sulakhe, R. Gauba, A. Rodrigues, R. Madduri, U. Dave, L, Lacinski, I. Foster, Y. Gusev, and S. Madhavan.  A case study for cloud based high throughput analysis of NGS data using the globus genomics system.  Computational and Structural Biotechnology.  13 Nov. 2014.    

Baris E. Suzek, Yuqi Wang,  Hongzhan Huang, Peter B. McGarvey, Cathy H. Wu and the UniProt Consortium.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.  Bioinformatics.  13 Nov. 2014.  PubMed 

The Uniprot Consortium.  UniProt: a hub for protein information.  Nucleic Acids Research.  28 Oct. 2014.  PubMed  

Zhi X, Lin L, Yang S, Bhuvaneshwar K, Wang H, Gusev Y, Lee MH, Kallakury B, Shivapurkar N, Cahn K, Tian X, Marshall JL, Byers SW, He AR.  βII-Spectrin (SPTBN1) suppresses progression of hepatocellular carcinoma and Wnt signaling by regulation of Wnt inhibitor kallistatin.  Hepatology.  Oct. 2014.  PubMed    

Yantian Zhang, Rivka Colen; Ian Foster; Robert Gatenby; Mary Ellen Giger; Robert Gillies; Matthew Heller; Anant Madabhushi; Subha Madhavan; Sandy Napel; Arvind Rao; Joel Saltz; James Tatum; Roeland Verhaak; Gary Whitman. NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures. Translational Oncology . 10 Oct. 2014.  PubMed  

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC4; the NCI CPTAC; National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC).  Proteogenomic characterization of human colon and rectal cancer. Nature. 2014 Jul 20. PubMed

UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014;42(11):7486. doi: 10.1093/nar/gku469. Epub 2014 Jun 2. PubMed

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-Ud-Din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S1, Gray JW, Stolovitzky G. A community effort to assess and improve drug sensitivity prediction algorithms.  Nat Biotechnol. 2014 Jun 1. doi: 10.1038/nbt.2877.  PubMed

He, Aiwu Ruth;  Lin, Ling; Yao, Zhixing; Bhuvaneshwar, Krithika; Gusev, Yuriy; Kallakury, Bhaskar; Yang, Shaoxian; Shetty, Kirti.  Transcriptional Regulation of STAT3.  Carcinogenesis.  16 May 2014. 

Torresan C, Oliveira MM, Pereira SR, Ribeiro EM, Marian C, Gusev Y, Lima RS, Urban CA, Berg PE, Haddad BR, Cavalli IJ, Cavalli LR. Increased copy number of the DLX4 homeobox gene in breast axillary lymph node metastasis.  Cancer Genet. 2014 May 2. PubMed

Mary M. Heckler, Hemang Thakor, Cara C. Schafer and Rebecca B. Riggins.  ERK/MAPK regulates ERRc expression, transcriptional activity and receptor-mediated tamoxifen resistance in ER+ breast cancer. FEBS J. 2014 May; 281(10):2431-42. Epub 2014 Apr 28.  PubMed

Mandeep Gill,  Bruna Sugita, Silma R Pereira, Catalin Marian, Xi Li, Yuriy Gusev, Enilze MSF Ribeiro, Iglenir J Cavalli, Luciane R Cavalli.  Identification of microRNA targets in triple-negative breast cancer.  Cancer Research.  5 April 2014.  

Shivapurkar N, Weiner LM, Marshall JL, Madhavan S, Deslattes Mays A, et al. (2014) Recurrence of Early Stage Colon Cancer Predicted by Expression Pattern of Circulating microRNAs. PLoS ONE 9(1): e84686.  2014.  PubMed

Robinder Gauba, S Madhavan,  R Clarke, Y Gusev.  Integrative Analysis Workflow for Untargeted Metabolomics in Translational Research.  Metabolomics.  2 March 2014. 

Michael Harris, Krithika Bhuvaneshwar, Thanemozhi Natarajan, Laura Sheahan, Difei Wang, Mahlet G. Tadesse, Ira Shoulson, Ross Filice, Kenneth Steadman, Subha Madhavan, and John Deeken. Pharmacogenomic characterization of gemcitabine response – a framework for data integration to enable personalized medicine.  Pharmacogenet Genomics. 2014 Feb;24(2):81-93. PubMed 

Year 2013

Zhang B, Hou X, Yuan X, Shih IM, Zhang Z, Clarke, Wang RR, Fu Y, Madhavan S, Wang Y, Yu G, "AISAIC: a software suite for accurate identification of significant aberrations in cancers," Bioinformatics, Dec. 13, 2013.  PubMed

Madhavan S, Gusev Y, Natarajan T, Song L, Bhuvaneshwar K, Gauba R, Pandey A, Haddad B,  Goerlitz D, Cheema A, Juhl H, Kallakury B, Marshall J, Byers S, Weiner L. Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse.  Frontiers in Genetics. Nov, 2013. doi: 10.3389/fgene.2013.00236

Elgamal OA, Park JK, Gusev Y, Azevedo-Pouly AC, Jiang J, Roopra A, Schmittgen  TD.  Tumor suppressive function of mir-205 in breast cancer is linked to HMGB3 regulation.  PLoS One. 2013 Oct 2;8(10):e76402. PubMed

Wang N, Meng F, Chen L, Madhavan S, Clarke R, Hoffman EP, Xuan J, and Wang Y. The CAM Software for Nonnegative Blind Source Separation in R-Java.  Journal of Machine Learning Research. 14 (2013) 2899-2903. 

Nikitina T, Wang D, Gomberg M, Grigoryev SA, Zhurkin VB. Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping. J Mol Biol. 2013 Jun 12;425(11):1946-60.  PubMed

Madhavan S, Gauba R, Song L, Bhuvaneshwar K, Gusev Y, Byers S, Juhl H, Weiner L.  Platform for Personalized Oncology: Integrative analyses reveal novel molecular signatures associated with colorectal cancer relapse. AMIA Summits Transl Sci Proc. 2013 Mar 18; 2013:118. PubMed

Madhavan S. The Development of Informatics Platforms to Help Drive Systems Medicine. Handbook of Personalized Medicine: Advances in Nanotechnology, Drug Delivery and Therapy. Pan Stanford Publishing (2013).

Gusev Y, Riggins RB, Bhuvaneshwar K, Gauba R, Sheahan L, Clarke R, and Madhavan S.  In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers. Cancer Informatics 2013:12 31-51 PubMed 

Year 2012

Albanese C, Rodriguez OC, Vanmeter J, Fricke ST, Rood BR, Lee Y, Wang SS, Madhavan S, Gusev Y, Petricoin EF 3rd, Wang Y. Preclinical Magnetic Resonance Imaging and Systems Biology in Cancer Research: Current Applications and Challenges. Am J. Pathology. 2012 Dec 4. PubMed

McGarvey P, Dharia S, Oberti M, Dragomir A, Hedlund E, Tanenbaum D, Suzek B, Madhavan S. Informatics and Data Quality at Collaborative Multicenter Breast and Colon Cancer Family Registries. JAMIA , Feb 10;10.1136. EPub. (2012) PubMed

Gauba R, Natarajan TG, Song L, Bhuvaneshwar K, Madhavan S, and Gusev Y. Metabolomic and exome sequence analysis reveal novel molecular signatures associated with colorectal cancer relapse.  BMC Proceedings 6 (Suppl 6), P41, 2012.

Mercado RC, Hampel H, Kastrinos F, Steyerberg E, Balmana J, Stoffel E, Cohn DE, Backes FJ, Hopper JL, Jenkins MA, Lindor NM, Casey G, Haile R, Madhavan S, de la Chapelle A, Syngal S. Performance of PREMM(1,2,6), MMRpredict, and MMRpro in detecting Lynch syndrome among endometrial cancer cases. Genet Med., Jul;14(7):670-80 (2012). PubMed

Dakshanamurthy S, Issa NT, Assefnia S, Seshasayee A, Peters OJ, Madhavan S, Uren A, Brown ML, and Byers SW. Predicting New Indications for Approved Drugs Using a Proteochemometric Method. J. Med. Chem., 2012, 55 (15), pp 6832–6848.  PubMed 

Year 2011

Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet L, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM.  G-DOC®: A Systems Medicine Platform for Personalized Oncology Neoplasia 13:9. (2011) PubMed

Madhavan S, Gusev Y, Harris MA, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, and Weiner LM.   G-CODE: enabling systems medicine through innovative informatics. Genome Biology, 12 (Suppl 1):P38, September 2011.  PubMed

Madhavan S, Sander A, Chou W-Y, Shuster A, Boone K, Dente M, Shad A, Hesse B.  Pediatric Palliative Care in the Age of eHealth: Opportunities for Advances in HIT to Improve Patient-Centered Communication. Am J Prev Medicine 40 (5) Supplement 2: S208 – S216. (2011) PubMed

Yu G, Li H, Ha S, Shih I, Clarke R, Hoffman EP, Madhavan S, Xuan J, Wang Y. PUGSVM: A caBIG-TM analytical tool for multiclass gene selection and predictive classification. Bioinformatics, Mar 1;27(5):736-738. (2011) PubMed

Zhang B, Li H, Jin J, Tian Y, Xuan J, Shih I, Madhavan S, Clarke R, Wang Y. DDN: A caBIG-TM analytical tool for comparative network analysis. Bioinformatics (2011) 27 (7):1036-1038. PubMed

Semenuk MA, Veenstra TD, Georgevich G, Rochman M, Gusev Y, Haanes EJ, Bogunovic BM, Lebowitz M, Daraselia N, Schwartz EI. Translating Cancer Biomarker Discoveries to Clinical Tests: What should be Considered? Recent Patents on Biomarkers, 2011, 1: 222-240.

Park JK, Henry JC, Jiang J; Esau C., Gusev Y, Lerner MR, Postier RG, Brackett DJ, Schmittgen TD. miR-132 and miR-212 are increased in pancreatic cancer and target the retinoblastoma tumor suppressor. Biochemical and Biophysical Research Communications. Vol 406, Issue 4, 25 March 2011, pg 518–523. PubMed 

Year 2010

Narayanan R, Jiang J, Gusev Y, Jones A, Kearbey, JD, Miller DD, Schmittgen TD, and Dalton JT. MicroRNAs are mediators of androgen action in prostate and muscle. PLoS One, 5 (10): e13637, 2010.  PubMed 

Year 2008

Saltz J., Kurc T., Hastings S., Langella S., Oster S., Ervin D., Sharma A., Pan T., Gurcan M., Permar J., Ferreira R., Payne P., Catalyurek U., Caserta E., Leone G., Ostrowski M. C., Madduri R., Foster I.,Madhavan S., Buetow K. H., Shanbhag K., Siegel E.  e-Science, caGrid, and Translational Biomedical Research Computer (Long Beach Calif). Nov; 41(11):58-66. (2008) PubMed

Madhavan S., Zenklusen J. C., Kotliarov Y., Sahni H., Fine H., and Buetow K. Rembrandt: Helping Personalized Medicine Become a Reality Through Integrative Translational Research.  Molecular Cancer Research 7(2): 157-167. (2008).  PubMed

Cancer Genome Atlas Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8. (2008). PubMed