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TransMed COSI Track Presentations

KEYNOTE: Metavariable based genome-phenome integrative analysis to facilitate personalized cancer medicine
Date: Tuesday, July 25
Time: 8:40 a.m.-9:15 a.m.
Room: Hall 4
  • Anguraj Sadanandam, The Institute of Cancer Research, United Kingdom

Presentation Overview: Show

Heterogeneity in treatment responses and prognosis (phenotypes) in cancers can be attributed to differences in genome, transcriptome, proteome and metabolome (multi-omics) profiles of individual patient tumours. Previously, we discretely integrated gene expression, microRNA, mutation and metabolome profiles from tumour samples and associated them with the clinical variables. However, integrating multi-omics data profiles simultaneously is not straight-forward since the biological system is dynamic and subject to multiple levels of regulations associated with phenotypes. In addition, integrating multi-omics data (with different units and scales/magnitudes) from different platforms can introduce bias that need to be taken into account. Hence, an efficient approach to data integration needs capturing all the information from genome and phenome for a comprehensive subtype discovery. Along this line, we have developed a data integration framework that can simultaneously integrate multiple high-throughput omics datasets from different platforms to discover functional subtypes (i.e. subtypes whose biological meaning is known) and their associated multi-omics biomarkers and clinical variables. This integrative analysis improves the power of capturing different levels of heterogeneity in tumours and interactions between genome and phenome profiles.

Short Profile: Sadanandam completed his interdisciplinary (wet-lab and computational biology) Ph.D. from the USA, and continued postdoc under Professors Joe Gray and Douglas Hanahan (USA and Switzerland). Briefly worked at Swiss Institute of Bioinformatics. Currently leading Systems and Precision Medicine team at the Institute of Cancer Research (ICR) with Honarary Appointment from Royal Marsden Hospital (RMH). His team uses cutting-edge wet-lab and computational biology to focus on inter- and intra-tumoral heterogeneity at the genetic, epigenetic, molecular and metabolic levels and to understand how they contribute to variations in metastatic potential, prognosis and therapeutic responses in patients. To this end, Sadanandam and colleagues have classified different tumor types including breast cancer cell lines, and pancreatic and colorectal tumours and cell lines into distinct molecular and/or drug response subtypes (Heiser and Sadanandam et al. PNAS 2012, Collisson and Sadanandam et al. Nature Medicine 2011, Sadanandam et al. Nature Medicine 2013, Sadanandam et al. Cancer Discovery 2015, and Colorectal Cancer Subtyping Consortium based Nature Medicine, 2015). In addition, they have identified subtype-specific cellular origin and molecular mechanisms and suggested possible precise therapies using combined (systems biology) wet-lab and bioinformatics approaches. These subtypes are being explored by clinicians for potential applications in the clinic. Currently, their goal is to identify and refine tumor subtype-specific robust biomarkers using integrated genome and phenome analysis, develop and validate biomarker-based companion diagnostic assays, screen for targeted therapies and understand their mechanisms of action using pre-clinical (both in vitro and in vivo) studies.

Molecular signatures that can be transferred across different omics platforms
Date: Tuesday, July 25
Time: 9:15 a.m.-9:30 a.m.
Room: Hall 4
  • Rainer Spang, University of Regensburg, Germany
  • Peter J. Oefner, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany, Germany
  • Wolfram Klapper, Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
  • Neus Masqué-Soler, Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
  • Monika Szczepanowski, Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
  • Julia Richter, Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
  • Wolfram Gronwald, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany, Germany
  • Christian W. Kohler, Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany, Germany
  • Jörg Reinders, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany, Germany
  • Thorsten Rehberg, Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany, Germany
  • Philipp Schwarzfischer, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany, Germany
  • Michael Altenbuchinger, University of Regensburg, Germany
Topic TBD
Date: Tuesday, July 25
Time: 10:00 a.m.-10:35 a.m.
Room: Hall 4
  • Tim Hubbard, King's College London, United Kingdom
Association testing of bisulfite sequencing methylation data via a Laplace approximation
Date: Tuesday, July 25
Time: 10:35 a.m.-10:50 a.m.
Room: Hall 4
  • Omer Weissbrod, ,
Identification of Associations between Genotypes and Longitudinal Phenotypes via Temporally-constrained Group Sparse Canonical Correlation Analysis
Date: Tuesday, July 25
Time: 10:50 a.m.-11:05 a.m.
Room: Hall 4
  • Daoqiang Zhang, Nanjing University of Aeronautics and Astronautics, China
  • Andrew Saykin, Indiana University, United States
  • Li Shen, Indiana University, United States
  • Shannon Risacher, Indiana University, United States
  • Jingwen Yan, Indiana University, United States
  • Xiaohui Yao, Indiana University, United States
  • Chanxiu Li, Nanjing University of Aeronautics and Astronautics, China
  • Xiaoke Hao, Nanjing University of Aeronautics and Astronautics, China
Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression
Date: Tuesday, July 25
Time: 11:05 a.m.-11:20 a.m.
Room: Hall 4
  • Daniel Mcdonald, Indiana University, United States
  • Lei Ding, Indiana University Bloomington, United States
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
Date: Tuesday, July 25
Time: 11:20 a.m.-11:35 a.m.
Room: Hall 4
  • Tero Aittokallio, Institute of Molecular Medicine Finland, University of Helsinki, Finland
  • Krister Wennerberg, Institute of Molecular Medicine Finland, University of Helsinki, Finland
  • Suleiman Ali Khan, Institute of Molecular Medicine Finland, University of Helsinki, Finland
  • Muhammad Ammad-Ud-Din, Institute of Molecular Medicine Finland, University of Helsinki, Finland
Epigenomic profiling of glioblastoma through treatment and progression
Date: Tuesday, July 25
Time: 11:35 a.m.-11:45 a.m.
Room: Hall 4
  • Johanna Klughammer, CeMM, Austria
Predicting cancer sequential treatments and drug repurposing with SATIE
Date: Tuesday, July 25
Time: 11:45 a.m.-12:00 p.m.
Room: Hall 4
  • Fatima Al-Shahrour, Spanish National Research Cancer Centre, CNIO, Spain
  • Gonzalo Gómez-López, Spanish National Research Cancer Centre, CNIO, Spain
  • Julián Carretero, Departament de Fisiologia, Facultat de Farmacia, Universitat de Valencia, Spain
  • Inés Pulido, Departament de Fisiologia, Facultat de Farmacia, Universitat de Valencia, Spain
  • Kevin Troulé, Spanish National Research Cancer Centre, CNIO, Spain
  • Coral Fustero-Torre, Spanish National Research Cancer Centre, CNIO, Spain
  • Andres Cañada, Spanish National Research Cancer Centre, CNIO, Spain
  • Miriam Rubio-Camarillo, Spanish National Research Cancer Centre, CNIO, Spain
  • Javier Perales-Patón, Spanish National Research Cancer Centre, CNIO, Spain
  • Héctor Tejero, Spanish National Research Cancer Centre, CNIO, Spain
canSAR: an integrated knowledgebase for cancer research and drug discovery
Date: Tuesday, July 25
Time: 12:00 p.m.-12:15 p.m.
Room: Hall 4
  • Bissan Al-Lazikani, The Institute of Cancer Research, United Kingdom
  • Patrizio Di Micco, The Institute of Cancer Research, United Kingdom
  • Albert Antolin, The Institute of Cancer Research, United Kingdom
  • Costas Mitsopoulos, The Institute of Cancer Research, United Kingdom
  • Joe Tym, The Institute of Cancer Research, United Kingdom
  • Elizabeth Coker, The Institute of Cancer Research, United Kingdom
Integrative analysis of personalized, multidimensional datasets of glioblastoma patients
Date: Tuesday, July 25
Time: 12:15 p.m.-12:30 p.m.
Room: Hall 4
  • Nikolaus Fortelny, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Austria
Topic TBD
Date: Tuesday, July 25
Time: 2:00 p.m.-2:35 p.m.
Room: Hall 4
  • Speaker TBD, ,
Using Multi-Scale Genetic, Protein, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms
Date: Tuesday, July 25
Time: 2:35 p.m.-2:50 p.m.
Room: Hall 4
  • Holger Fröhlich, University of Bonn, UCB Biosciences GmbH, Germany
  • Martin Hofmann-Apitius, Fraunhofer SCAI, University of Bonn, Germany
  • Anandhi Iyappan, Fraunhofer SCAI, University of Bonn, Germany
  • Shashank Khanna, Fraunhofer SCAI, University of Bonn, Germany
Understanding human disease relationships through integrated molecular and clinical analysis
Date: Tuesday, July 25
Time: 2:50 p.m.-3:05 p.m.
Room: Hall 4
  • Purvesh Khatri, Stanford University, United States
  • Nigam Shah, Stanford University, United States
  • Timothy Sweeney, Stanford University, United States
  • Paul J. Utz, Stanford University, United States
  • Shane Lofgren, Stanford University, United States
  • Erika Bongen, Stanford University, United States
  • Charles Liu, Stanford University, United States
  • Greg Gaskins, Stanford University, United States
  • Francesco Vallania, Stanford University, United States
  • Rohit Vashisht, Stanford University, United States
  • Winston Haynes, Stanford University, United States
Integrating personalized gene expression profiles into predictive disease-associated gene pools
Date: Tuesday, July 25
Time: 3:05 p.m.-3:20 p.m.
Room: Hall 4
  • Emre Guney, Institute for Research in Biomedicine (IRB Barcelona), Spain
Translational elastic compute and knowledge Integration environment for quantitative systems pharmacology and disease progression modelling
Date: Tuesday, July 25
Time: 3:20 p.m.-3:35 p.m.
Room: Hall 4
  • Jeffrey Barrett, Sanofi Pharmaceuticals, United States
  • Justin Lee, Sanofi Pharmaceuticals, United States
  • Karim Azer, Sanofi Pharmaceuticals, United States
  • Liming Shen, Sanofi Pharmaceuticals, United States
  • Raj Bandaru, Sanofi, United States
Pseudotemporal disease trajectories from cross-sectional data
Date: Tuesday, July 25
Time: 3:35 p.m.-3:50 p.m.
Room: Hall 4
  • Christopher Yau, University of Birmingham, United Kingdom
  • Kieran Campbell, University of Oxford, United Kingdom
Integrating genomics and transcriptomics to dissect the pathogenic mechanism of X-Linked Dystonia-Parkinsonism
Date: Tuesday, July 25
Time: 3:50 p.m.-4:00 p.m.
Room: Hall 4
  • Jyotsna Dhakal, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Ashok Ragavendran, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Criscely Go, Department of Behavorial Medicine, Jose Reyes Memorial Medical Center, Manila, Philippines
  • Marisela Elizabeth Dy, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Carrie Hanscom, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Harrison Brand, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Benjamin Currall, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Alexei Stortchevoi, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Christine A. Vaine, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Ryan L. Collins, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Dadi Gao, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • David Shin, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • William T. Hendriks, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Tatsiana Aneichyk, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Rachita Yadav, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
  • Naoto Ito, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Nutan Sharma, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Xandra Breakefield, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Laurie Ozelius, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • D. Cristopher Bragg, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
  • Michael Talkowski, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
Classification of Paediatric Inflammatory Bowel Disease using Machine Learning
Date: Tuesday, July 25
Time: 4:00 p.m.-4:10 p.m.
Room: Hall 4
  • Enrico Mossotto, University of Southampton, United Kingdom
  • James Ashton, University of Southampton, United Kingdom
  • Tracy Coelho, University of Southampton, United Kingdom
  • Mark Beattie, Southampton Children’s Hospital, United Kingdom
  • Benjamin MacArthur, University of Southampton, United Kingdom
  • Sarah Ennis, University of Southampton, United Kingdom
Understanding human knockouts
Date: Tuesday, July 25
Time: 4:10 p.m.-4:20 p.m.
Room: Hall 4
  • Suganthi Balasubramanian, Regeneron Genetics Center, Regeneron Pharmaceuticals, United States
  • Yao Fu, Bina Technologies, Part of Roche Sequencing, United States
  • Mayur Pawashe, Yale University, United States
  • Patrick McGillivray, Yale University, United States
  • Mike Jin, Yale University, United States
  • Jeremy Liu, Yale University, United States
  • Konrad  Karczewski, Massachusetts General Hospital, United States
  • Daniel MacArthur, Massachusetts General Hospital, United States
  • Mark Gerstein, Yale University, United States