Papers
- "KPP: KEGG Pathway Painter", Ganiraju Manyam, Vikas Chandhoke and Ancha Baranova. (In Submission)
- "Access to the nucleus and functional association with c-Myc is required for the full oncogenic potential of δEGFR/EGFRvIII", Anupama Gururaj, Laura Gibson, Sonali Panchabai, MingHui Bai, Ganiraju Manyam, Yue Lu, Khatri Latha, Marta Rojas, Yeohyeon Hwang, Shoudan Liang and Oliver Bogler. (Journal of Biological Chemistry, in Revision)
- "Integrative Bayesian Analysis of High-Dimensional Multi-platform Genomics Data”, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey Morris, Bradley Broom, Ganiraju Manyam, and Kim-Anh Do. (Bioinformatics, In Revision)
- "Temporal transcriptional response during infection of Type II alveolar epithelial cells with Francisella tularensis LVS supports a general host suppression and bacterial uptake by macropinocytosis", Christopher Bradburne, Anne Verhoeven, Ganiraju Manyam, Saira Chaudhry, Eddie Chang, Dzung Thach, Charles Bailey and Monique van Hoek. (Journal of Biological Chemistry, in Revision)
- "Bayesian hierarchical structured variable selection methods with application to MIP studies in breast cancer", Lin Zhang, Veerabhadran Baladandayuthapani, Bani K. Mallick, Ganiraju Manyam, Patricia A. Thompson, Melissa L. Bondy and Kim-Anh Do. (Biometrics, in Revision)
- "Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics", Ganiraju Manyam, Michelle Payton, Jack Roth, Lynne Abruzzo and Kevin Coombes. (Genomics, 2012)
- "A Tree-based Algorithm for systematic analysis of siRNA Sequences", Ancha Baranova, Jonathan Bode, Ganiraju Manyam and Maria Emelianenko. (BMC Research Notes, 2011)
- "Proteomic Characterization and Functional Analysis of Outer Membrane Vesicles of Francisella novicida Suggests Possible Role in Virulence and Use as a Vaccine.", Pierson T, Matrakas DV, Taylor YU, Manyam G, Morozov VN, Zhou W and van Hoek M. (Journal of Proteome Research, 2011)
- "Pro-apoptotic and anti-proliferative activity of human KCNRG, a putative tumor suppressor for CLL and multiple myeloma", Aybike Birerdinc, Elizabeth Nohelty, Andrey Marakhonov, Ganiraju Manyam, Ivan Panov, Stephanie Coon, Eugene Nikitin, Mikhail Skoblov, Vikas Chandhoke and Ancha Baranova. (Tumor Biology, 2010)
- "Functional pathway analysis of genes associated with response to treatment for chronic Hepatitis C", Aybike Birerdinc, Arian Afendy, Maria Stepanova, Issah Younossi, Ganiraju Manyam, Ancha Baranova and Zobair Younossi. (Journal of Viral Hepatitis, 2010)
- "SnS-Align: A graphic tool for alignment of distantly related proteins", Ganiraju Manyam, Ancha Baranova, Mikhail Skoblov and Rakesh Mishra. (IJBRA, 2009)
- "Early gene expression profiles of patients with chronic hepatitis C treated with pegylated interferon-alfa and ribavirin", Zobair Younossi, Ancha Baranova, Arian Afendy, Rochelle Collantes, Maria Stepanova, Ganiraju Manyam, Anita Bakshi, Christopher Sigua, Joanne Chan, Ayuko Iverson, Christopher Santini and Sheng-Yung Chang. (Hepatology, 2009)
Books
"Gene expression during carcinogenesis: A bioinformatics perspective (An analysis of the global patterns of changes in the gene expression associated with genesis of cancer)", Ganiraju Manyam and Ancha Baranova (Book at Amazon).
Patents
"Tumor Discriminator"Ancha Baranova, Ganiraju Manyam and Giuliani Alessandro. (US Patent Application No: 20110301853)
Posters
- "Integrative Bayesian Analysis of High-Dimensional Multi-Platform Genomics Data”, Kim-Anh Do, Wenting Wang, Bradley M Broom, Jeffrey S Morris and Ganiraju Manyam. Joint Statistical Meetings(JSM) - American Statistical Association at San Diego, CA in July 2012.
- "Bayesian Hierarchical Structured Variable Selection Methods with Application to MIP Studies in Breast Cancer", Lin Zhang, Veera Baladandayuthapani, Bani K Mallick, Ganiraju Manyam, Patricia Thompson, Melissa Bondy and Kim-Anh Do. Joint Statistical Meetings(JSM) - American Statistical Association at San Diego, CA in July 2012.
- "GeneSmash: A RESTful web service for gene annotations", Ganiraju Manyam, Michelle Payton, Chris Wakefield, Jack Roth, Lynne Abruzzo and Kevin Coombes. 9th Annual Rocky Mountain Bioinformatics Conference at Aspen, CO in December 2011.
- "Integrative Bayesian Analysis of Genomics with Application to Analyze Gene Expression and Methylation Data for TCGA Glioblastoma Study", Wenting Wang, Veera Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju Manyam, Kenneth D Aldape and Kim-Anh Do. Biotechnology and Bioinformatics Symposium (BIOT) at Houston TX in October 2011.
- "Access to the nucleus is required for the full oncogenic potential of EGFR/EGFRvIII", Anupama E. Gururaj, Laura Gibson, Sonali Panchabai, MingHui Bai, Ganiraju Manyam, Yue Lu, Khatri Latha, Marta L. Rojas, Yeohyeon Hwang, Shoudan Liang and Oliver Bogler. Symposia on Cancer Research (New Roles for the EGFR Family in Cancer), at Houston, TX in September 2011.
- "Gene expression profile of the tumor as a composite biomarker", Ancha Baranova, Wang Lei, Alessandro Giuliani and Ganiraju Manyam. Moscow conference on computational molecular biology at Moscow, Russia in July 2011.
- "Antigen processing and proteasome degradation pathways are involved in patients with chronic Hepatitis-C with negative predictors of response to pegylated interferon and ribavrin (PEG-IFN/RBV)", Aybike Birerdinc, Arian Afendy, Maria Stepanova, Issah Younossi, Ganiraju Manyam, Ancha Baranova and Zobair Younossi. The International Liver CongressTM at Berlin, Germany in March 2011.
- "Up-Regulation of Matrix Metalloproteinase 9 (MMP-9) and Interleukin-8 (IL-8) in African American Patients with Chronic Hepatitis C", Aybike Birerdinc, Maria Stepanova, Ganiraju Manyam, Arian Afendy, T Gramlich, and Ancha Baranova. Disease Digestive Week, at New Orleans, LA in May 2010.
- "Genome-wide expression pattern as a composite biomarker of cancer", Ganiraju Manyam, Giuliani Alessandro, and Ancha Baranova. AACR 101st Annual Meeting, at Washington DC in April 2010.
- "Functional Pathway analysis of Gene Expression in Patients with Non-alcoholic Fatty Liver Disease (NAFLD) and Non-alcoholic Steatohepatitis (NASH)", Zobair Younossi, Ganiraju Manyam, Maria Stepanova, Ancha Baranova, Noreen Hossain, Zachary Goodman, and Vikas Chandhoke. The International Liver Congress, at Vienna, Austria in April 2010.
- "Tumor as an attractor: Toward the use of global patterns of gene expression in the predictive diagnostics of tumorigenesis", Ganiraju Manyam, Giuliani Alessandro, and Ancha Baranova. Circulating Tumor Cells meeting of NCI-NIH, at Bethesda in September 2009.
- "Gene expression biomarkers predicting response to pegylated interferon alpha and ribavirin in the peripheral blood of patients with chronic hepatitis C, non-responder to previous treatment", Zobair Younossi, Rochelle Collantes, Ancha Baranova, Amy Kim, Ganiraju Manyam, Maria Stepanova, Chris Santini, Chris Sigua, Joanne Chan and Ayuko I. Annual meeting of AASLD, at Boston in November 2008.
- "Gene Expression Biomarkers Predicting Response to Pegylated Interferon alpha (PEG-IFN) and Ribavirin (RBV) in Treatment-Naive Patients with Chronic Hepatitis C (CH-C)", Zobair Younossi, Rochelle Collantes, Ancha Baranova, Anita Bakshi, Maria Stepanova, Ganiraju Manyam, Chris Santini, Chris Sigua, Joanne Chan, Ayuko L. Annual meeting of AASLD, at Boston in November 2007.
- "SNS-Align: A tool to align evolutionarily distant proteins", Ganiraju Manyam, Andrey Marakhonov, Ancha Baranova and Rakesh Mishra. MCCMB me eting, at Moscow (Russia) in July 2007.
- "Effects of the tumor-specific telomere elongation on the adjacent gene expression", Ganiraju Manyam, Bagrat Kapanadze, Galina Glazko, Maria Stepanova, Vikas Chandhoke and Ancha Baranova. HUGO Meeting, at Montreal (Canada) in May 2007.
- "Comparative Genomics of the Vertebrate HOX Clusters", Ganiraju Manyam, Venu Madhav, S Krishnan, Navneet Mathur and Rakesh Mishra. EMBO Workshop, at Hyderabad (India) in December 2005.
- "The Fab-7 boundary in the Bithorax Complex requires Trl-GAGA", Ganiraju Manyam, Ram P Kumar and Rakesh K Mishra. ISDB conference, at Bangalore (India) in December 2004.
Talks
- "GeneSmash: A RESTful web service for gene annotations",presented at the 9th Annual Rocky Mountain Bioinformatics Conference in 2011 held at Aspen, CO.
- "KPP: KEGG pathway painter", presented at the Annual Meeting of Virginia Academy of Science in 2009 held at Virginia Commonwealth University, VA.
- "Tumor as an attractor. Toward the use of the global patterns of gene expression in the predictive diagnostics of tumorigenesis", presented at the 2nd Systems Biology Research Panel in 2009, held at George Mason University, VA.