Profile
My lab is interested in the potential application of ML to medical oncology problems in the areas of population screening, diagnosis and prognosis the the domain of breast cancer. The following are representative studies from such collaborations with Dr. Greiner (i) We published works and built an online tool on the use of single nucleotide polymorphisms (SNPs) to identify ethnic ancestry of populations and this is an area of importance in population based association studies to identify populations who are at risk for disease predisposition. Association statistics tend to be inflated if the samples (cases or controls) are of mixed ancestry. (ii) We used SNPs to build predictive models for breast cancer risk. (iii) Traditionally used survival curves (Kaplan-Meier) represent population statistics and are not ideal to assess individual's prognosis (an area of emphasis in personalized medicine and genomics driven science). Patient Specific Survival Prediction curves were attempted to improve on the prognostication (disease free survival or overall survival) in breast cancer patients taking in to account clinical characteristics and genomics data. Similar patient based studies for identifying individual's risk for adverse drug reactions to chemotherapy treatments is also underway.
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Authors
Projects
Identifying the Best Surface Topography Parameters for Detecting Idiopathic Scoliosis Curve Progression University of Alberta Publication 2010-01-01 Fine-mapping of a novel premenopausal breast cancer susceptibility locus at Chr4q31.22 in Caucasian women and validation in African and Chinese women University of Alberta Publication 2019-05-01 Oncogenic activity of poly (ADP -ribose) glycohydrolase University of Alberta Publication 2018-11-01 Maud Marques, Maika Jangal, Li-Chun Wang, Anna Kazanets, Sabrina Daniela da Silva, Tiejun Zhao, Amanda Lovato, Henry Yu, Su Jie, Sonia del Rincon,
John Mackey ,
Sambasivarao Damaraju , Moulay Alaoui-Jamali, Michael Witcher
Germline copy number variations are associated with breast cancer risk and prognosis University of Alberta Publication 2017-11-01 High Myc expression and transcription activity underlies intra-tumoral heterogeneity in triple-negative breast cancer University of Alberta Publication 2017-03-01 Nidhi Gupta, Karen Jung, Chengsheng Wu, Abdulraheem Alshareef, Hind Alqahtani,
Sambasivarao Damaraju ,
John Mackey , Sunita Ghosh, Siham Sabri, Bassam S. Abdulkarim, Gilbert Bigras, Raymond Lai
Insights into a novel nuclear function for Fascin in the regulation of the amino-acid transporter SLC 3A2 University of Alberta Publication 2016-11-01 Amine Saad, Krikor Bijian, Dinghong Qiu, Sabrina Daniela da Silva, Maud Marques, Chia-Hao Chang, Hassan Nassour, Dindial Ramotar,
Sambasivarao Damaraju ,
John Mackey , Tarek Bismar, Michael Witcher, Moulay A. Alaoui-Jamali
Genome-wide profiling of transfer RNAs and their role as novel prognostic markers for breast cancer University of Alberta Publication 2016-09-01 Profiling of Small Nucleolar RNAs by Next Generation Sequencing: Potential New Players for Breast Cancer Prognosis University of Alberta Publication 2016-09-01 The pro-apoptotic paradox: the BH 3-only protein Bcl-2 interacting killer (Bik) is prognostic for unfavorable outcomes in breast cancer University of Alberta Publication 2016-04-01 A Uridine Glucuronosyltransferase 2B7 Polymorphism Predicts Epirubicin Clearance and Outcomes in Early-Stage Breast Cancer University of Alberta Publication 2016-04-01 Michael B. Sawyer, Edith Pituskin,
Sambasivarao Damaraju , Robert R. Bies, Larissa J. Vos, Carla. M.M. Prado, Michelle Kuzma, Andrew G. Scarfe, Mark Clemons, Katia Tonkin, Heather-Jane Au, Sheryl Koski, Anil A. Joy, Michael Smylie, Karen King, Diana Carandang, Vijaya L. Damaraju, John Hanson, Carol E. Cass,
John Mackey Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer University of Alberta Publication 2016-05-01 Next generation sequencing profiling identifies miR -574-3p and miR-660-5p as potential novel prognostic markers for breast cancer University of Alberta Publication 2015-09-01 Quantitative proteomic analysis of HER 2 normal and overexpressing MCF-7 breast cancer cells revealed proteomic changes accompanied with HER2 gene amplification University of Alberta Publication 2013-10-01 Breast cancer prediction using genome wide single nucleotide polymorphism data University of Alberta Publication 2013-01-01 Assessing SNP -SNP Interactions among DNA Repair, Modification and Metabolism Related Pathway Genes in Breast Cancer Susceptibility University of Alberta Publication 2013-06-01 Identification of a Breast Cancer Susceptibility Locus at 4q31.22 Using a Genome-Wide Association Study Paradigm University of Alberta Publication 2013-05-01 ETHNOPRED : a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction University of Alberta Publication 2013-01-01 Germline DNA Copy Number Aberrations Identified as Potential Prognostic Factors for Breast Cancer Recurrence University of Alberta Publication 2013-01-01 Considerations on Dealing with Tissues and Cell Samples (Include Tissue Banking) University of Alberta Publication 2012-01-01 The clonal and mutational evolution spectrum of primary triple-negative breast cancers University of Alberta Publication 2012-04-01 Sohrab P. Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, Yongjun Zhao, Gulisa Turashvili, Jiarui Ding, Kane Tse, Gholamreza Haffari, Ali Bashashati, Leah M. Prentice, Jaswinder Khattra, Angela Burleigh, Damian Yap, Virginie Bernard, Andrew McPherson, Karey Shumansky, Anamaria Crisan, Ryan Giuliany, Alireza Heravi-Moussavi, Jamie Rosner, Daniel Lai, Inanc Birol, Richard Varhol, Angela Tam, Noreen Dhalla, Thomas Zeng, Kevin Ma, Simon K. Chan, Malachi Griffith, Annie Moradian, S.-W. Grace Cheng, Gregg B. Morin, Peter Watson, Karen Gelmon, Stephen Chia, Suet-Feung Chin, Christina Curtis, Oscar M. Rueda, Paul D. Pharoah,
Sambasivarao Damaraju ,
John Mackey , Kelly Hoon, Timothy Harkins, Vasisht Tadigotla, Mahvash Sigaroudinia, Philippe Gascard, Thea Tlsty, Joseph F. Costello, Irmtraud M. Meyer, Connie J. Eaves, Wyeth W. Wasserman, Steven Jones, David Huntsman, Martin Hirst, Carlos Caldas, Marco A. Marra, Samuel Aparicio
Analysis of Fc~ Receptor IIIa and IIa Polymorphisms: Lack of Correlation with Outcome in Trastuzumab-Treated Breast Cancer Patients University of Alberta Publication 2012-04-01 S. A. Hurvitz, D. J. Betting, H. M. Stern, E. Quinaux, J. Stinson, S. Seshagiri, Y. Zhao, M. Buyse,
John Mackey , A. Driga,
Sambasivarao Damaraju , M. X. Sliwkowski, N. J. Robert, V. Valero, J. Crown, C. Falkson, A. Brufsky, T. Pienkowski, W. Eiermann, M. Martin, V. Bee, O. Marathe, D. J. Slamon, J. M. Timmerman
A two-stage association study identifies methyl-CpG -binding domain protein 2 gene polymorphisms as candidates for breast cancer susceptibility University of Alberta Publication 2012-01-01 Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility University of Alberta Publication 2011-03-01 The BH 3-only protein Bad confers breast cancer taxane sensitivity through a nonapoptotic mechanism University of Alberta Publication 2010-07-01 A C Craik, R A Veldhoen, M Czernick, T W Buckland, K Kyselytzia, S Ghosh, R Lai,
Sambasivarao Damaraju , D A Underhill,
John Mackey , I S Goping
Evidence for copurification of micronuclei in sucrose density gradient-enriched plasma membranes from cell lines University of Alberta Publication 2010-01-01 Sambasivarao Damaraju , Nancy Zhang, Nan Li, Lidan Tao, Vijaya L. Damaraju, Jennifer Dufour, Cheryl Santos, Xue-Jun Sun,
John Mackey , David S. Wishart, Carol E. Cass, Liang Li
Proteome Profile of Human Breast Cancer Tissue Generated by LC -ESI-MS/MS Combined with Sequential Protein Precipitation and Solubilization University of Alberta Publication 2008-08-01 Nucleoside anticancer drugs: the role of nucleoside transporters in resistance to cancer chemotherapy University of Alberta Publication 2003-10-01 PolySearch : a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites University of Alberta Publication 2008-05-01 Differentially expressed alternatively spliced genes in skeletal muscle from cancer patients with cachexia University of Alberta Publication 2017-10-01 Small RNAome profiling from human skeletal muscle: novel miRNAs and their targets associated with cancer cachexia University of Alberta Publication 2017-01-01 Effects of Sample Size on Differential Gene Expression, Rank Order and Prediction Accuracy of a Gene Signature University of Alberta Publication 2013-06-01 Cynthia Stretch, Sheehan Khan, Nasimeh Asgarian, Roman Eisner, Saman Vaisipour,
Sambasivarao Damaraju , Kathryn Graham, Oliver F. Bathe, Helen Steed,
Russell Greiner , Vickie E. Baracos
Prediction of Skeletal Muscle and Fat Mass in Patients with Advanced Cancer Using a Metabolomic Approach University of Alberta Publication 2011-12-01 Cynthia Stretch, Thomas Eastman, Rupasri Mandal, Roman Eisner, David S. Wishart, Marina Mourtzakis, Carla M. M. Prado,
Sambasivarao Damaraju , Ronald O. Ball,
Russell Greiner , Vickie E. Baracos
Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites University of Alberta Publication 2010-08-01 Association of DNA Repair and Steroid Metabolism Gene Polymorphisms with Clinical Late Toxicity in Patients Treated with Conformal Radiotherapy for Prostate Cancer University of Alberta Publication 2006-04-01 Clinical and biological characterization of skeletal muscle tissue biopsies of surgical cancer patients University of Alberta Publication 2019-07-01 Ana Anoveros-Barrera, Amritpal S. Bhullar, Cynthia Stretch, Nina Esfandiari, Abha R. Dunichand-Hoedl, Karen J.B. Martins, David Bigam, Rachel G. Khadaroo, Todd McMullen, Oliver F. Bathe,
Sambasivarao Damaraju , Richard J. Skipworth, Charles T. Putman, Vickie E. Baracos, Vera C. Mazurak
Breast cancer associated germline structural variants harboring small noncoding RNAs impact post-transcriptional gene regulation University of Alberta Publication 2018-05-01 Single-Nucleotide Polymorphisms in TAOK 3 Are Associated With High Opioid Requirement for Pain Management in Patients With Advanced Cancer Admitted to a Tertiary Palliative Care Unit University of Alberta Publication 2018-10-01 Timothy Gutteridge, Mahalakshmi Kumaran, Sunita Ghosh, Robin Fainsinger, På l Klepstad, Yoko Tarumi,
Sambasivarao Damaraju , Vickie E. Baracos
Taxane acute pain syndrome (TAPS ) in patients receiving chemotherapy for breast or prostate cancer: a prospective multi-center study University of Alberta Publication 2018-03-01 R. Fernandes, S. Mazzarello, A. A. Joy, G. R. Pond, J. Hilton, M. F. K. Ibrahim, C. Canil, M. Ong, C. Stober, L. Vandermeer, B. Hutton, M. da Costa,
Sambasivarao Damaraju , Mark Clemons
Sarcopenia and myosteatosis are accompanied by distinct biological profiles in patients with pancreatic and periampullary adenocarcinomas University of Alberta Publication 2018-05-01 Cynthia Stretch, Jean-Michel Aubin, Beata Mickiewicz, Derek Leugner, Tariq Al-manasra, Elizabeth Tobola, Santiago Salazar, Francis R. Sutherland, Chad G. Ball, Elijah Dixon, Hans J. Vogel,
Sambasivarao Damaraju , Vickie E. Baracos, Oliver F. Bathe
The Challenges and Opportunities in the Clinical Application of Noncoding RNAs : The Road Map for miRNAs and piRNAs in Cancer Diagnostics and Prognostics University of Alberta Publication 2018-01-01 Determination of the Relative Efficacy of Eicosapentaenoic Acid and Docosahexaenoic Acid for Anti-Cancer Effects in Human Breast Cancer Models University of Alberta Publication 2017-12-01 New genetic signatures associated with cancer cachexia as defined by low skeletal muscle index and weight loss University of Alberta Publication 2016-08-01 Neil Johns, Cynthia Stretch, Benjamin H.L. Tan, Tora S. Solheim, Sveinung Sø rhaug, Nathan A. Stephens, Ioannis Gioulbasanis, Richard J.E. Skipworth, D.A. Christopher Deans, Antonio Vigano, James A. Ross, Oliver F. Bathe, Michel L. Tremblay, Stein Kaasa, Florian Strasser, Bruno Gagnon, Vickie E. Baracos,
Sambasivarao Damaraju , Kenneth C.H. Fearon
A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility University of Alberta Publication 2016-01-01 Designing and Testing of Novel Taxanes to Probe the Highly Complex Mechanisms by Which Taxanes Bind to Microtubules and Cause Cytotoxicity to Cancer Cells University of Alberta Publication 2015-06-01 Marc St. George, Ahmed T. Ayoub, Asok Banerjee, Cassandra D. M. Churchill,
Philip Winter , Mariusz Klobukowski, Carol E. Cass, Richard F. Ludueñ a, Jack A. Tuszynski,
Sambasivarao Damaraju Genetic basis of interindividual susceptibility to cancer cachexia: selection of potential candidate gene polymorphisms for association studies University of Alberta Publication 2014-12-01 N. JOHNS, B. H. TAN, M. MACMILLAN, T. S. SOLHEIM, J. A. ROSS, V. E. BARACOS,
Sambasivarao Damaraju , K. C. H. FEARON
A Practical Tool for Modeling Biospecimen User Fees University of Alberta Publication 2014-08-01 Lise Matzke, Simon Dee, John Bartlett,
Sambasivarao Damaraju , Kathryn Graham, Randal Johnston, Anne-Marie Mes-Masson, Leigh Murphy, Lois Shepherd, Brent Schacter, Peter H. Watson
Generating a Comprehensive Set of Standard Operating Procedures for a Biorepository Network\textemdash The CTRNet Experience University of Alberta Publication 2013-12-01 Rebecca Barnes, Monique Albert,
Sambasivarao Damaraju , Jean de Sousa-Hitzler, Sugy Kodeeswaran, Anne-Marie Mes-Masson, Peter Watson, Brent Schacter
Molecular characterization of mucinous ovarian tumours supports a stratified treatment approach with HER 2 targeting in 19\% of carcinomas University of Alberta Publication 2012-12-01 Michael S Anglesio, Stefan Kommoss, Mary C Tolcher, Blaise Clarke, Laura Galletta, Henry Porter,
Sambasivarao Damaraju , Sian Fereday, Boris J Winterhoff, Steve E Kalloger, Janine Senz, Winnie Yang, Helen Steed, Ghassan Allo, Sarah Ferguson, Patricia Shaw, Attila Teoman, Joaquin J Garcia, John K Schoolmeester, Jamie Bakkum-Gamez, Anna V Tinker, David D Bowtell, David G Huntsman, C Blake Gilks, Jessica N McAlpine
Specimen Quality Evaluation in Canadian Biobanks Participating in the COEUR Repository University of Alberta Publication 2013-04-01 Cé cile Le Page, Martin Köbel, Manon de Ladurantaye, Kurosh Rahimi, Jason Madore, Sindy Babinszky, Dimcho R. Bachvarov, Magdalena Bachvarova, Marie-Claude Beauchamp, Carol E Cass, Dianne Chadwick, Crane Colleen,
Sambasivarao Damaraju , Jennifer Dufour, Walter H. Gotlieb, Steve E. Kalloger, Lise Portelance, Jessica N. McAlpine, Isabelle Matte, Alain Piché, Patricia Shaw, Michael H.A. Roehrl, Barbara C. Vanderhyden, Peter H. Watson, David G. Huntsman, Diane M. Provencher, Anne-Marie Mes-Masson
Computational Predictions of Volatile Anesthetic Interactions with the Microtubule Cytoskeleton: Implications for Side Effects of General Anesthesia University of Alberta Publication 2012-06-01 Travis J. A. Craddock, Marc St. George, Holly Freedman, Khaled H. Barakat,
Sambasivarao Damaraju , Stuart Hameroff, Jack A. Tuszynski
P-selectin genotype is associated with the development of cancer cachexia University of Alberta Publication 2012-04-01 Benjamin H. L. Tan, Torill Fladvad, Theodore P. Braun, Antonio Vigano, Florian Strasser, D. A. Christopher Deans, Richard J. E. Skipworth, Tora S. Solheim,
Sambasivarao Damaraju , James A. Ross, Stein Kaasa, Daniel L. Marks, Vickie E. Baracos, Frank Skorpen, Kenneth C. H. Fearon and
Central nervous system inflammation induces muscle atrophy via activation of the hypothalamic\textendash pituitary\textendashadrenal axis University of Alberta Publication 2011-11-01 Theodore P. Braun, Xinxia Zhu, Marek Szumowski, Gregory D. Scott, Aaron J. Grossberg, Peter R. Levasseur, Kathryn Graham, Sheehan Khan,
Sambasivarao Damaraju , William F. Colmers, Vickie E. Baracos, Daniel L. Marks
First report on the patient database for the identification of the genetic pathways involved in patients over-reacting to radiotherapy: GENEPI -II University of Alberta Publication 2010-10-01 Dirk De Ruysscher, Diane Severin, Elizabeth Barnes, Michael Baumann, Rob Bristow, Vincent Gré goire, Tobias Hölscher, Theo Veninga, Andrzej Pola\'nski, Evert-Ben van Veen, Christine Verfaillie, Germaine Heeren,
Sambasivarao Damaraju , Uwe Just, Karin Haustermans
Computational Design and Biological Testing of Highly Cytotoxic Colchicine Ring A Modifications University of Alberta Publication 2010-04-01 Cytotoxic activity of gemcitabine in cultured cell lines derived from histologically different types of bladder cancer: Role of thymidine kinase 2 University of Alberta Publication 2010-01-01 Swathi Damaraju, Vijaya L. Damaraju, Delores Mowles, Michael B. Sawyer,
Sambasivarao Damaraju , Carol E. Cass
Predicting node positivity in gastric cancer from gene expression profiles University of Alberta Publication 2009-05-01 A study of reproducibility of guanidination\textendash dimethylation labeling and liquid chromatography matrix-assisted laser desorption ionization mass spectrometry for relative proteome quantification University of Alberta Publication 2007-03-01 Chengjie Ji, Nan Zhang,
Sambasivarao Damaraju , Vijaya L. Damaraju, Pat Carpenter, Carol E. Cass, Liang Li
Lymphovascular Invasion Is Associated With Poor Survival in Gastric Cancer University of Alberta Publication 2006-01-01 Bryan J. Dicken, Kathryn Graham, Stewart M. Hamilton, Sam Andrews, Raymond Lai, Jennifer Listgarten, Gian S. Jhangri, L Duncan Saunders,
Sambasivarao Damaraju , Carol Cass
Identification and functional characterization of variants in human concentrative nucleoside transporter 3, hCNT 3 (SLC28A3), arising from single nucleotide polymorphisms in coding regions of the hCNT3 gene University of Alberta Publication 2005-03-01 Sambasivarao Damaraju , Jing Zhang, Frank Visser, Tracey Tackaberry, Jennifer Dufour, Kyla M. Smith, Melissa Slugoski, Mabel W.L. Ritzel, Stephen A. Baldwin, James D. Young, Carol E. Cass
Differential effects of a molybdopterin synthase sulfurylase (moeB ) mutation on Escherichia coli molybdoenzyme maturation University of Alberta Publication 2002-08-01 Investigation ofEscherichia coliDimethyl Sulfoxide Reductase Assembly and Processing in Strains Defective for thesec-Independent Protein Translocation System Membrane Targeting and Translocation University of Alberta Publication 2001-02-01 Multiple Roles for the Twin Arginine Leader Sequence of Dimethyl Sulfoxide Reductase ofEscherichia coli University of Alberta Publication 2000-05-01 Interactions of a Transcriptional Activator in theenvGene of the Mouse Mammary Tumor Virus with Activation-dependent, T Cell-specific Transacting Factors University of Alberta Publication 1996-04-01 A novel immunosuppressive factor in bovine colostrum blocks activation of the interleukin 2 gene enhancer at the NFAT site University of Alberta Publication 1996-07-01 Molecular analysis of dimethylsulfoxide reductase: a complex iron-sulfur molybdoenzyme of Escherichia coli University of Alberta Publication 1992-08-01 Differentiation of the multiple S- and N-oxide-reducing activities ofEscherichia coli University of Alberta Publication 1991-08-01 Dimethyl sulfoxide reductase of Escherichia coli: an investigation of function and assembly by use of in vivo complementation. University of Alberta Publication 1991-01-01 Organization of dimethyl sulfoxide reductase in the plasma membrane of Escherichia coli. University of Alberta Publication 1990-01-01 Role of calcium in synaptosomal substrate oxidation University of Alberta Publication 1988-08-01
