Publications

Kancherla J, Rao S, Bhuvaneshwar K, Riggins RB, Beckman RA, Madhavan S, Corrada Bravo H, Boca SM. “Evidence-Based Network Approach to Recommending Targeted Cancer Therapies.” (2020) JCO Clin Cancer Inform. 4:71-88. 

Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. “A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.” (2020) Nat Genetics 52(4):448-457

Pishvaian MJ, Blais EM, Brody JR, Lyons E, DeArbeloa P, Hendifar A, Mikhail S, Chung V, Sahai V, Sohal DPS, Bellakbira S, Thach D, Rahib L, Madhavan S, Matrisian LM, Petricoin EF 3rd. “Overall survival in patients with pancreatic cancer receiving matched therapies following molecular profiling: a retrospective analysis of the Know Your Tumor registry trial.” (2020) Lancet Oncol ;21(4):508-518. 

Dhiraj Kumar, Ala Lisok, Elyes Dahmane, Matthew D McCoy, Sagar Shelake, Samit Chatterjee, Viola Allaj, Polina Sysa-Shah, Bryan Wharram, Wojciech G Lesniak, Ellen Tully, Edward Gabrielson, Elizabeth M Jaffee, John T Poirier, Charles M Rudin, Jogarao VS Gobburu, Martin G Pomper, Sridhar Nimmagadda. Peptide-based PET quantifies target engagement of PD-L1 therapeutics. Journal of Clinical Investigation. Feb 2019. PMID: 30457978

McCoy MD, Shivakumar V, Nimmagadda S, Jafri MS, Madhavan S. “SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants.” (2019) BMC Bioinformatics. 20(1):171. 

Pishvaian MJ, Blais EM, Bender RJ, Rao S, Boca SM, Chung V, Hendifar AE, Mikhail S, Sohal DPS, Pohlmann PR, Moore KN, He K, Monk BJ, Coleman RL, Herzog TJ, Halverson DD, DeArbeloa P, Petricoin EF 3rd, Madhavan S. “A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients” (2019) JAMIA Open (4):505-515. 

Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL. “Standard operating procedure for curation and clinical interpretation of variants in cancer”. (2019) Genome Med. 11(1):76. 

Bhuvaneshwar K, Harris M, Gusev Y, Madhavan S, Iyer R, Vilboux T, Deeken J, Yang E, Shankar S. (2019) “Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients” BMC Cancer 16;19(1):357

Ren J, Li G, Ross K, Arighi C, McGarvey P, Rao S, Cowart J, Madhavan S, Vijay-Shanker, Wu CH. iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. Database. 2018 

Beckman R A., Chen C, Posch M, and Zohar S, Trial Designs for Rare Diseases and Small Samples in Oncology (Book Chapter), Textbook of Clinical Trials in Oncology, S. Michaels, ed., Taylor & Francis Group. 2018

Chen C, Li XN, Li W, Beckman RA. Adaptive Expansions of Biomarker Populations in Phase 3 Clinical Trials. Contemporary Clinical Trials. 2018. PMID 29981858.

Dillon M, Grove L, Newbold K, Shaw H, Brown N, Mendell J, Chen S, Beckman R A, Jennings A, Ricamara M, Greenberg J, Forster M and Harrington K J. Patritumab with Cetuximab Plus Platinum-Containing Therapy in Recurrent or Metastatic Squamous. Clinical Cancer Reserach. PMID 30327312.

Antonijevic Z, Beckman RA. Basket Trials at the Confirmatory Stage (Book chapter). Platform Trials in Drug Development: Umbrella Trials and Basket Trials. Chapman & Hall/CRC Biostatistics Series, Taylor & Francis Group. 2018

Boca SM, Leek JT. A direct approach to estimating false discovery rates conditional on covariates. PeerJ. PMID 30581661

UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Research. PMID 30395287

Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A; Clinical Genome (ClinGen) Resource. ClinGen Allele Registry links information about genetic variants. Human Mutation. PMID 30311374

Chen D, Zhao Z, Huang Z, Chen DC, Zhu XX, Wang YZ, Yan YW, Tang S, Madhavan S, Ni W, Huang ZP, Li W, Ji W, Shen H, Lin S, Jiang YZ. Super enhancer inhibitors suppress MYC driven transcriptional amplification and tumor progression in osteosarcoma. Bone Research. 2018 PMID 29644114

Peran I, Madhavan S, Byers SW, McCoy MD. Curation of the Pancreatic Ductal Adenocarcinoma Subset of the Cancer Genome Atlas Is Essential for Accurate Conclusions about Survival-Related Molecular Mechanisms. Clinical Cancer Research. 2018. PMID 29739787

McCoy MD, Madhavan S. A Computational Approach for Prioritizing Selection of Therapies Targeting Drug Resistant Variation in Anaplastic Lymphoma Kinase. AMIA Joint Summits Translational Science Proceedings. 2019. PMID 29888064

Kumar D, Ala Lisok, Elyes Dahmane, Matthew D McCoy, Sagar Shelake, Samit Chatterjee, Viola Allaj, Polina Sysa-Shah, Bryan Wharram, Wojciech G Lesniak, Ellen Tully, Edward Gabrielson, Elizabeth M Jaffee, John T Poirier, Charles M Rudin, Jogarao VS Gobburu, Martin G Pomper, Sridhar Nimmagadda. Peptide-based PET quantifies target engagement of PD-L1 therapeutics. Journal of Clinical Investigation. 2018. PMID 30457978

Madhavan S, Subramaniam S, Brown TD, Chen JL. Art and Challenges of Precision Medicine: Interpreting and Integrating Genomic Data into Clinical Practice. American Society of Clinical Oncology. 2018. PMID 30231369

Pishvaian MJ, Bender RJ, Halverson D, Rahib L, Hendifar AE, Mikhail S, Chung V, Picozzi VJ, Sohal D, Blais EM, Mason K, Lyons EE, Matrisian LM, Brody JR, Madhavan S, Petricoin EF 3rd. Molecular Profiling of Patients with Pancreatic Cancer: Initial Results from the Know Your Tumor Initiative. Clinical Cancer Research. 2018. PMID 29954777

Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL; Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members. Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. Human Mutation. 2018. PMID 30311370

Gusev Y, Bhuvaneshwar K, Song L, Zenklusen J, Fine H, Madhavan S. The REMBRANDT study – a large collection of genomic data from brain cancer patients. Nature Scientific Data. 2018. PMID 30106394

Bhuvaneshwar K, Song L, Madhavan S and Gusev Y. viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors. Frontiers in Microbiology. PMID 29922260

Sharma V, Fong A, Beckman RA, Rao S, Boca SM, McGarvey PB, Ratwani RM, and Madhavan S. An Eye-tracking Study to Enhance Usability of Molecular Diagnostics Reports in Cancer Precision Medicine. JCO Precision Oncology. 2018. http://ascopubs.org/doi/10.1200/PO.17.00296

Pollmann SE, Calvert VS, Rao S, Boca SM, Madhavan S, Horak ID, Kjær A, Petricoin EF, Kragh M, and Poulsen TT. Acquired resistance to a MET antibody in vivo can be overcome by the MET antibody mixtureSym015. Molecular Cancer Therapeutics. 2018. PMID 29545332

Ching T, et al. Opportunities and obstacles for deep learning in biology and medicine. J. R. Soc. Interface 15 (141). 2018. PMC5938574

Sampson J, Boca SM, Moore SC, Heller R. FWER and FDR control when testing multiple mediators. Bioinformatics. 2018. PMID 29420693

Boca SM, Panagiotou OA, Rao S, McGarvey PB, Madhavan S. The future of evidence synthesis in precision oncology: Between systematic reviews and biocuration. JCO Precision Oncology. 2018.

Ahn J, Conkright B, Boca SM and Madhavan S. POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations. Journal of Computational Biology. 2018. PMID 29293371

Madhavan S, Ritter D, Micheel C, Rao S, Roy A, Sonkin D, McCoy M, Griffith M, Griffith OL, McGarvey PB, Kulkarni S on behalf of the ClinGen Somatic Working Group. ClinGen Cancer Somatic Working Group – standardizing and democratizing access to cancer molecular diagnostic data to drive translational research. Pacific Symposium on Biocomputing. 2018. PMID 29218886

A. S. M. Ashique Mahmood, Shruti Rao, Peter McGarvey, Cathy Wu, Subha Madhavan, K. Vijay-Shanker. eGARD: Extracting associations between genomic anomalies and drug responses from text. PLoS One. 2017. PMID 29261751

Lei Song,* Krithika Bhuvaneshwar,* Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, and Yuriy Gusev. CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data. Cancer Informatics. 2017. PMID 29343938

Jessica D Tenenbaum, Krithika Bhuvaneshwar, Jane P Gagliardi, Kate Fultz Hollis, Peilin Jia, Liang Ma, Radhakrishnan Nagarajan, Gopalkumar Rakesh,  Vignesh Subbian,  Shyam Visweswaran,  Zhongming Zhao, Leon Rozenblit. Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. Briefings in Bioinformatics. 2017. PMID 29186302

Akanksha S. Mahajan, Bruna M. Sugita, Anju N. Duttargi, Francisco Saenz, Ewa Krawczyk, Justine N. McCutcheon, Aline S. Fonseca, Bhaskar Kallakury, Paula Pohlmann, Yuriy Gusev, Luciane R. Cavalli. Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors. PLoS One. 2017. PMID 29049316

Janice L. Krupnick, Bonnie L. Green, Richard Amdur, Adil Alaoui, Anas Belouali, Erika Roberge, David Cueva, Miguel Roberts, Elizabeth Melnikoff, Mary Ann Dutton. An Internet-based writing intervention for PTSD in veterans: A feasibility and pilot effectiveness trial. Psychological Trauma. 2017. PMID 27607767

Rao, Shruti*, Beckman, Robert A.*, Riazi, Shahla, Yabar, Cinthya S., Boca, Simina M. Marshall, John L., Pishvaian, Michael J., Brody, Jonathan R., and Subha Madhavan. Quantification and Expert Evaluation of Evidence for Chemopredictive Biomarkers to Personalize Cancer Treatment. Oncotarget. 2017. PMID 27888622

Thomas Ondra, Sebastian Jobjörnsson, Robert A Beckman, Carl-Fredrik Burman, Franz König, Nigel Stallard, Martin Posch. Optimized adaptive enrichment designs. Statistical methods in Medical Research. 2017. PMID 29254436

Beckman, Robert A., and Loeb, Lawrence A. Evolutionary Dynamics and Significance of Multiple Subclonal Mutations in Cancer. DNA Repair (Amst). 2017 Aug;56:7-15. doi: 10.1016/j.dnarep.2017.06.002. Epub 2017 Jun 9.

Chen, Cong, Deng, Qiqi, He, Linchen, Mehrotra, Devan V, Rubin, Eric H, and Beckman, Robert A.  How Many Tumor Indications Should Be Initially Studied in Clinical Development of Next Generation Immunotherapies? Contemporary Clinical Trials. 2017

Li, Wen, Chen, Cong, Li, Xiaojun, and Beckman, Robert A. Estimation of treatment effect in two-stage confirmatory oncology trials of personalized medicines. Statistics in Medicine. 2017

Orcutt, Kelly D, Adams, Gregory P., Wu, Anna M., Silva, Matthew, Harwell, Catey, Hoppin, Jack, Matsumura, Manabu, Kotsuma, Masakatsu, Greenberg, Jonathan, Scott, Andrew M., and Beckman, Robert A. Molecular simulation of receptor occupancy and tumor penetration of an antibody and smaller scaffolds: Application to molecular imaging. Molecular Imaging and Biology. 2017

Kristof, Jessica, Sakrison Kellen, Jin, Xiaoping, Nakamaru, Kenji, Schneider, Matthias, Beckman, Robert A., Freeman, Daniel, Spittle, Cindy, and Feng, Wenqin. Real-time reverse-transcription quantitative polymerase chain reaction assay is a feasible method for the relative quantification of heregulin expression in non-small cell lung cancer tissue. Biomarker Insights, 12: 1-14. 2017

Ayesha N. Shajahan-Haq, Simina M. Boca*, Lu Jin*, Krithika Bhuvaneshwar,*, Yuriy Gusev, Amrita K. Cheema, Diane D. Demas, Kristopher S. Raghavan, Ryan Michalek, Subha Madhavan and Robert Clarke. EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer. Oncotarget, 2017. https://doi.org/10.18632/oncotarget.18292

Boca SM, Pfeiffer RM, Sampson JN. Multivariate meta-analysis with an increasing number of parameters. Biom J. 2017 May;59(3):496-510. doi: 10.1002/bimj.201600013. Epub 2017 Feb 14.

Zhu XX, Yan YW, Ai CZ, Jiang S, Xu SS, Niu M, Wang XZ, Zhong GS, Lu XF, Xue Y, Tian S, Li G, Tang S, Jiang YZ. Jarid2 is essential for the maintenance of tumor initiating cells in bladder cancer. Oncotarget. 2017 Apr 11;8(15):24483-24490. doi: 10.18632/oncotarget.15522

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

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. 

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)

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 structures. Computational 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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.

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.

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.

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

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.

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)

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).

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.

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) 

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.

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) 

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) 

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.

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.

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)

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).

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