RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges
POSTER PRESENTATIONS
Updated November 07, 2013
Links within this page: Systems Biology (SB) | Regulatory Genomics (RG)
| --> DREAM Challenges: Friday, November 8 | ||
| Poster Number |
Authors (Presenter's name is in bold) |
Title |
| DREAM01 | Vincenzo Belcastro, Erhan Bilal, Jean Binder, Stéphanie Boué, Nveed Chaudhary, Brett Fields, William Hayes, Julia Hoeng, Anita Iskandar, Robin Kleiman, Raquel Norel, Jennifer Park, Manuel Peitsch, Kahn Rhrissorrakrai, John J Rice, Pablo M Rojas, Jörg Sprengel, Gustavo Stolovitzky and Marja Talikka | Verification of Systems Biology Research in the Age of Collaborative Competition |
| DREAM02 | Jonathan R. Karr, Christian D. Basile, Alejandro F. Villaverde, Po-Ru Loh, Brandon A. Allgood, Simon Wilkinson, Brian M. Bot, Bruce R. Hoff, Jay Hodgson, Dream Parameter Estimation Consortium, Mike R. Kellen, Thea C. Norman, Markus W. Covert, Gustavo A. Stolovitzky and Pablo Meyer | A Crowdsourced Approach to Whole-Cell Model Parameter Estimation |
| DREAM03 | Nki-Ohsu-Mdacc-Ebi-Eth-Dream Consortium (Steven Hill, Laura Heiser, Thomas Cokelaer) | HPN-DREAM Breast Cancer Network Inference Challenge: Inferring Causal Signaling Networks and Predicting Protein Phosphorylation Dynamics in Cancer |
| DREAM04 | Niehs-Ncats-Unc-Dream Consortium (Federica Eduati) | Predicting Cytotoxicity in Individuals and Populations Using Genetics and Genomics Data |
| DREAM05 | Kevin Emmett, Sakellarios Zairis |
HPN-DREAM8: Network Inference of RTK Signaling Using Gradient Boosted Regression Trees |
| DREAM06 | Brian M. Bot, Chris Bare, Bruce Hoff, Jay Hodgson, Thea Norman, Gustavo Stolovitzky, Stephen Friend, Michael Kellen | Synapse: Enabling a Collaborative Future |
| DREAM07 | Bahman Afsari, Ludmila V. Danilova, Alexander V. Favorov, Wai-shing Lee, Dane Taylor, and Elana J. Fertig | Prediction for Time-Course Proteomics In Vitro |
| DREAM08 | Ying Hu, Chunhua Yan, Chih-Hao Hsu, Yu Liu, George Komatsoulis and Daoud Meerzaman | Time-series Data Prediction with Consensus Networks and the Generalized Linear Model |
| DREAM09 | Yang Zhang, Haizhou Wang, and Joe Song | FUNCHISQ: Deciphering Interactions in Causal Networks |
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| -->Systems Biology (SB): Saturday, November 9 and Sunday, November 10 |
||
| Poster Number |
Authors (Presenter's name is in bold) | Title |
| SB01 | S. M. Minhaz Ud-Dean and Rudiyanto Gunawan | Ensemble Inference and Inferability of Gene Regulatory Networks |
| SB02 | David Knowles, Alexis Battle and Daphne Koller | Discovering Latent Cancer Characteristics Predictive of Drug Sensitivity |
| SB03 | Stephen Rowley, James Watters and Laurent Debussche | Integrated Profiling of p53 Wild-type Cell Lines Identifies Differentially Responsive Populations and a Gene Expression Signature that Predicts Sensitivity to SAR299155, a Potent and Selective Disruptor of the p53-MDM2 Interaction |
| SB04 | Louis-Francois Handfield and Alan Moses | Quantification of Cell-to-cell Variability in Protein Spatial Spread from Fluorescence Microscopy of Unsynchronized Budding Yeast |
| SB05 | Bahram Samanfar, Katayoun Omidi and Ashkan Golshani | Utilizing Yeast Genetics to Identify Novel Genes Involved in Oxygen Responding Pathway |
| SB06 | Lun Yang | Prediction of Novel Drug co-Prescription or Fix-dose Drug Combination based only on Three Clinical Side-Effects |
| SB07 | Roberto Pagliarini, Raffaele Castello, Nicola Brunetti-Pierri and Diego Di Bernardo | A Large-scale Computational Model of Inborn Error of Liver Metabolism Unravels Previously Unrecognized Metabolic Derangements and Novel Therapeutic Options |
| SB08 | Yayoi Natsume-Kitatani and Hiroshi Mamitsuka | Detection of Timing-differences in Histone Modification at Ash1 Target Genes |
| SB09 | Dries De Maeyer, Joris Renkens, Luc De Raedt and Kathleen Marchal | "Omics" Result Interpretation Using Interaction Networks |
| SB10 | Syed Haider, Michal Grzadkowski, Maud H.W. Starmans, Cindy Q. Yao, Jianxin Wang, Francis Nguyen, Nathalie C. Moon, Arek Kasprzyk, Philippe Lambin, Pietro Lio and Paul C. Boutros | SIMMS: A Generalized Subnetwork-Approach to Multimodal Biomarker Discovery |
| SB11 | Alexey Porollo, Margaret Collins and Melanie Cushion |
Toward Deciphering Metabolic Strategies of the Obligate Fungal Pathogen Pneumocystis Carinii |
| SB12 | Barbara Di Camillo, Francesco Sambo, Toffolo Gianna and Claudio Cobelli |
A Pathway Cumulative SNP Association analysis Robust to Rare Variants and Different Direction of Genotype Effect |
| SB13 | Weijun Luo and Cory Brouwer | Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization |
| SB14 | Beatriz Penalver Bernabe, Huge Galdones, Anaar Siletz, Teresa K. Woodruff, Linda J. Broadbelt and Lonnie D. Shea | A Systems Biology Approach to Ovarian Folliculogenesis |
| SB15 | Youlian Pan, Alain Tchagang, Sieu Phan, Yunli Wang, Jitao Zou, Jinxiong Shen and Yi Huang | Systems Biology Association Mining in Crop Plants |
| SB16 | Katayoun Omidi and Ashkan Golshani |
Kat1/Pak2 Complex is Involved in Regulation of Efficient Non-Homologous End-Joining Pathway Dependent to Cell Cycle in the Yeast Saccharomyces Cerevisiae |
| SB17 | Bhaskar Dutta, Yongjian Guo, Jing Sun, Ronald Germain and Iain Fraser | CARD: Comprehensive Analysis of RNAi-screen Data |
| SB18 | Rahul and Brian Ingalls |
Optimal Parameter Estimation of Kinetic Models using the Surrogate Modeling Framework |
| SB19 | Petri Pölönen, Hanna Leinonen, Henna-Kaisa Jyrkkänen, Antti Ylipää, Matti Nykter, Merja Heinäniemi and Anna-Liisa Levonen | Identification of Cancer Types with Nrf2 Hyperactivity |
| SB20 | Maria Nicoletta Moretti, Stefania Criscuolo, Andrea Ballabio and Diego Di Bernardo | Reverse Engineering Transcriptional Regulation of Lysosomal and Autophagic Pathways: an Experimental and Computational Approach |
| SB21 | Francesco Napolitano, Diego Carrella, Dario Righelli, Luis J.V. Galietta and Diego Di Bernardo |
Elucidation of the Mode of Action of Correctors for the Cystic Fibrosis Mutant Gene (DF508-CFTR): an Integrated Experimental and Computational Approach |
| SB22 | Zichen Wang, Neil Clark and Avi Ma'Ayan | Identifying and Correcting Gene Occurrence Biases in High Content Experiments and Biomedical Literature |
| SB23 | Thomas Cokelaer, Federica Eduati, Emanuel Goncalves, Carito Guziolowski, David Henriques, Aidan MacNamara, Melody Morris, Camille Terfve, Sven Thiele, Martijn van Iersel, Santiago Videla, Anne Siegel, Douglas A. Lauffenburger and Julio Saez-Rodriguez | Analysing and Understanding Complex Signalling Networks Using CellNOpt Software |
| SB24 | Oren Kraus, Erin Styles, Lei Jimmy Ba, Brenda Andrews, Charlie Boone and Brendan J. Frey | Global Analysis of Subcellular Morphology in Saccharomyces Cerevisiae |
| SB25 | Christoph Müssel, Markus Maucher and Hans Kestler | Guided Evolution Links Knowledge from Diverse Sources for Regulatory Network Inference |
| SB26 | Sweta Sharma, Desmond Lun, Jean-Camille Birget, Dawei Hong and Anthony Wirth | A Theoretical Approach to Gene Network Identification |
| SB27 | Lieven Verbeke, Ana Carolina Fierro, Jimmy Van Den Eynden, Piet Demeester, Jan Fostier and Kathleen Marchal |
Identifying Relevant Pathways for Different Breast Cancer Subtypes Using Network Based Data Integration |
| SB28 | Daniela Boernigen, Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Andrew Taylor, Sheng Wang, Paul Dave, Jinbo Xu, Conrad Gilliam and Natalia Maltsev | Systems Analysis Of Complex Disorders Using Lynx |
| SB29 | Gabriela Alexe, Pablo Tamayo, Nicholas W. Haining, Kimberly Stegmaier and Jill P. Mesirov |
Metabolic Hallmarks of Cancer Revealed through Metagene Projection and Information Theoretic Strategies |
| SB30 | Jining Huang, Andrei L. Turinsky, Shuye Pu, Marc Fiume, Huayun Hou, Jennifer A. Mitchell, Michael D. Wilson, Michael Brudno and Shoshana J. Wodak | PinGem: Genome-wide Consolidation of Protein-DNA and Protein-Protein Interactions |
| SB31 | Albert Xue, Mark Ciaccio and Neda Bagheri |
Integrated Bayesian Genetic Algorithm Accurately Infers Networks from Large-scale Phosphoproteomic Data |
| SB32 | Andrew Yates, Raghu Machiraju and Kun Huang |
Inferring Directed Gene Transcription Networks Using Logical Dependency Classes in C. Elegans Embryonic Development |
| SB33 | Brandon Barker, Jason Locasale, Zhenglong Gu and Yiping Wang | Estimating Fluxes in the Human Metabolic Network with Expression Data |
| SB34 | Georgios Kararigas, Elke Dworatzek, George Petrov, Holger Summer, Tabea Marie Schulze, Istvan Baczko, Christoph Knosalla, Stefan Golz, Roland Hetzer and Vera Regitz-Zagrosek | Sex-specific Molecular Signature of Human Left Ventricular Remodeling Under Pressure Overload |
| SB35 | Hazem Ahmed and Janice Glasgow |
3PI: A Novel Method for Predicting High-Confidence Protein-Protein Interactions using Particle Swarm-based Network Alignment |
| SB36 | Elana J Fertig, Ana Markovic, Ludmila V Danilova, Daria A Gaykalova, Leslie Cope, Christine H Chung, Joseph A Califano and Michael F Ochs |
Integrated meta-pathway algorithm infers epigenetic modulations that distinguish HNSCC clinical subtypes and hedgehog signaling specific to HPV-negative HNSCC |
| SB37 | Yingzhou Wu and Frederick P. Roth | Evaluating the Correspondence Between Masking and Suppression Genetic Interactions and the Order of Action of Genes in S. Cerevisiae |
| SB38 | Fan Yang, Jochen Weile, Song Sun, Marta Verby, Frederick P. Roth | Cancer-Type-Specific Landscapes Of Human Somatic Mutations |
| SB39 | Frank Honti and Caleb Webber | A Phenotypic-linkage Gene Network for Unbiased Functional Clustering of Gene Variants |
| SB40 | Mark Ciaccio, Vincent Chen, Richard Jones and Neda Bagheri | A Systems-level, Multitarget Anti-cancer Strategy Integrates PLSR-based Network Inference with a Broad-range Microwestern Array Phosphoprotein Dataset |
| SB41 | Heba Sailem, Julia Sero and Chris Bakal | Integration of Multi-level Cellular Phenotypic Data Reveals a Relationship Between NF-κB Signaling and Cell Context |
| SB42 | Maria Liivrand, Merja Heinäniemi, Elisabeth John, Jochen G. Schneider,Thomas Sauter and Lasse Sinkkonen | Combinatorial Regulation of Lipoprotein Lipase by MicroRNAs During Mouse Adipogenesis |
| SB43 | Juri Reimand, Omar Wagih and Gary Bader | The Mutational landscape of Phosphorylation Signaling in Cancer |
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| -->Regulatory Genomics (RG): Monday, November 11 and Tuesday, November 12 |
||
| Poster Number |
Authors (Presenter's name is in bold) | Title |
| RG01 | Jingyi Jessica Li, Peter Bickel and Mark Biggin |
System Wide Analyses Have Underestimated Transcriptional Importance in Animals |
| RG02 | David Akavia, Carla Danussi, Antonio Iavarone and Dana Pe'Er | Integrative and Parallel Approaches to Uncover Drivers of Cancer |
| RG03 | Brad Gulko, Ilan Gronau, Leonardo Arbiza, Melissa Hubisz and Adam Siepel | The Functional Potential Score: Integrating Comparative, Population and Functional Genomic Data to Identify Recent Selective pressure in Noncoding Human DNA |
| RG04 | Sofia Kyriazopoulou-Panagiotopoulou, Anshul Kundaje, Marco Cusumano-Towner and Serafim Batzoglou | Integrating Gene Expression and Sequence Data with Existing Biological Knowledge to Model Context-specific Gene Regulation |
| RG05 | Hatice Osmanbeyoglu, Raphael Pelossof, Jacqueline Bromberg and Christina Leslie | Linking Signaling Pathways to Transcriptional Response in Breast Cancer |
| RG06 | Roger Pique-Regi, Gregory Moyerbrailean, Chris Harvey, Xiaoquan Wen and Francesca Luca | Analysis of Non-coding Genetic Variants Impact on Gene Regulation and Complex Traits |
| RG07 | Michael D. Wilson, Benoit Ballestar, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzalez-Porta, Matthew Carlucci, Kyle Chessman, Andre J. Faure, Angela Goncalves, Claudia Kutter, Margus Lukk, Suraj Menon, William M. McLaren, Klara Stefflova, Stephen Watt, Merlin Crossley, John C. Marioni, Duncan T. Odom and Paul Flicek | Conserved Combinatorial Transcription Factor Binding Identifies Regulatory Variants in Human Disease Pathways |
| RG08 | Yaron Orenstein and Ron Shamir |
A Comparative Analysis of TF Binding Models Learned from PBM, HT-SELEX and ChIP Data |
| RG09 | Daniel Gusenleitner, Scott Auerbach, David Sherr and Stefano Monti | Rodent-based Toxicogenomic Models of Hepatocarcinogenicity |
| RG10 | Seungyeul Yoo, Tao Huang, Joshua Campbell, Sachiko Takikawa, Carmen Argmann, Zhidong Tu, Avrum Spira, Eric Schadt, Charles Powell and Jun Zhu | Integrative Analysis of DNA Methylation and Gene Expression Data Reveals Complex Regulation of COPD |
| RG11 | Robin Friedman, Benno Schwikowski and Philippe Sansonetti | Design Principles of the Intestinal Epithelial Response to the Microbiome |
| RG12 | Kate Cook, Debashish Ray, Ally Yang, Hong Zheng, Quaid Morris and Timothy Hughes | Simultaneous Determination of Sequence and Secondary Structure Requirements of RNA-binding Proteins |
| RG13 | Liming Lai, Wei Wang, Jason Hennessey, Yuguang Ban, Jianli Qi, Gaixin Jiang, Ye Kang and Steven Ge | Detecting Regulatory Modules and Pathways with a Comprehensive Knowledge Base for Mouse |
| RG14 | Samuel Lambert, Kamesh Narasimhan, Ally Yang, Hong Zheng, Carl de Boer, Matthew T. Weirauch and Timothy R. Hughes | Creating a Model of C. Elegans Cis-regulation |
| RG15 | Anthony Mathelier and Wyeth Wasserman | The Next Generation of Transcription Factor Binding Site Prediction |
| RG16 | Kristina Shostak, Bahram Samanfar and Ashkan Golshani |
Systematic Analysis of Saccharomyces Cerevisiae Genome for Novel Genes Involved in Internal Translation Initiation |
| RG17 | Nicolas Fernandez, Peter Hornbeck and Avi Ma'Ayan | Phosphorylation-site Enrichment Analysis |
| RG18 | Aleksander Jankowski, Shyam Prabhakar and Jerzy Tiuryn | General-purpose Tool for Predicting Transcription Factor Dimers Reveals a Structural Principle of Transcriptional Regulation |
| RG19 | Sofie Demeyer and Tom Michoel | Identification of Open Chromatin Regions Responsible for Gene Expression Variation |
| RG20 | Michelle Lacey, Carl Baribault and Melanie Ehrlich |
Modeling, Simulation and Analysis of Methylation Profiles from Reduced Representation Bisulfite Sequencing Experiments |
| RG21 | Florian Halbritter and Simon R. Tomlinson |
Instant Access to High-Throughput Genomics for Translational Systems Biology via the GeneProf Database |
| RG22 | Tomoshige Ohno, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka and Hideo Matsuda | Integrative Prediction of miRNA-mRNA Interactions from High-Throughput Sequencing Data |
| RG23 | Azzurra Carlon, Barbara Di Camillo and Gianna Toffolo |
Key network motifs of insulin signaling pathway identified by local parametric sensitivity analysis |
| RG24 | Wendy Ashlock and Suprakash Datta |
Finding Motifs In Regulatory Sequences Using Side Effect Machines |
| RG25 | Tao Wang, Beibei Chen, Mins Kim, Yang Xie and Guanghua Xiao | A Model-based Approach to Identify Binding Sites in CLIP-Seq Data |
| RG26 | Irene Kaplow, Sarah Mah, Yiqi Zhou, Michael Kobor and Hunter Fraser | Understanding the Relationship between Genetic Variation and Differential DNA Methylation |
| RG27 | Tisha Melia and David Waxman | Elucidation of growth hormone (GH)-dependent gene regulation involving long intergenic noncoding RNA (lincRNA) in mouse liver. |
| RG28 | Corey Hudson and Kelly Williams |
LearnedIslands: Genomic Island Finding using Random Forests on Phylogenetic Profiles |
| RG29 | Fereydoon Bondarian, Mansour Omidi, Sepideh Torabi and Fereshteh Nemat Allahi | Virtual analysis of salutaridinol 7-O-acetyltransferase (SAT) in Iranian Poppy |
| RG30 | Ning Shen, John Horton and Raluca Gordan |
In Vitro Genomic-context PBM Data Explain Differences in the In Vivo Binding Profiles of C-Myc and its Antagonist Mxi1 |
| RG31 | Jia Wu, Mark Duncan, Seungjin Shin, William Miller, Lonnie Shea and Neda Bagheri |
Dynamic Models of Transcription Factor Activity Profiles Reveal Key Regulatory Interactions During Hematopoietic Differentiation |
| RG32 | Justin Finkle, Mark Ciaccio, Grace Yu, Kevin White and Neda Bagheri | Dynamic LASSO Regression Identifies RNA Transcripts Regulated by Transcription Factors in Breast Cancer Cells |
| RG33 | Ernest Radovani, Frank W. Schmitges, Shuye Pu, Hua Tong, Guoqing Zhong, Hongbo Guo, Peter Young, Shoshana Wodak, Andrew Emili, Timothy R. Hughes and Jack Greenblatt | Generation of Protein-Protein Interaction Networks for Human Transcription Factors |
| RG34 | Michael R. Brent, Ezekial Maier, Stacey Gish, Zhou Wang Wang and Tamara Doering | Validated Methods for Predictive Genetics |
| RG35 | Federico Giorgi, Mariano Alvarez, Yao Shen, Yishai Shimoni and Andrea Califano |
Combinatorial Identification of TUmor Subtypes (CITrUS): a pipeline for integrating genetic and phenotypic data to define patient-centric tumor subtype classification |
| RG36 | Yuheng Lu, Steve Lianoglou and Christina Leslie |
A Novel Predictive Model for MicroRNA-mRNA Interactions |
| RG37 | Bobak Kechavarzi and Sarath Chandra Janga |
Dissecting the Expression Landscape of RNA-Binding Proteins Implicated In Human Cancers |
| RG38 | Nirmala Arul Rayan, Ricardo Del Rosario and Shyam Prabhakar |
Massive Contribution of Repeats to Primate Origins |
| RG39 | Pradipta Ray, Aaron Kotamarti and Michael Zhang | Integrative Computational Prediction of DNA 5-hydroxymethylcytosine Modifications at Individual CpG Site Resolution Using Genomic, Epigenomic and Spatial Features in a Max-margin Framework |
| RG40 | Matthew T. Maurano, Eric Haugen, Eric Rynes, Richard Sandstrom, Jeff Vierstra and John A. Stamatoyannopoulos | A Catalog of Functional Regulatory Variation from Massive In Vivo Regulatory Profiling |
| RG41 | Jason Ernst and Manolis Kellis |
ChromImpute: A Method for Imputation of Chromatin Datasets Leveraging a Compendium of Reference Human Epigenomes |
| RG42 | Sefa Kilic, Elliot White, Dinara Sagitova and Ivan Erill |
CollecTF: a database of experimentally-validated bacterial transcription factor-binding sites |
| RG43 | Christopher Fiore, Jamie Kwasnieski, Hemangi Chaudhari, Barak Cohen | Massively parallel tests of ENCODE enhancer predictions |
| RG44 | Melina Claussnitzer, Simon N. Dankel, Bernward Klocke, Harald Grallert, Viktoria Glunk, Tea Berulava, Heekyoung Lee Bernhard Horsthemke, DIAGRAM+ Consortium, Ola Hansson, Stefanie M. Hauck, Matthias Blüher, Peter Arner, Leif Groop, Thomas Illig, Karsten Suhre, Yi-Hsiang Hsu, Gunnar Mellgren, Hans Hauner, Helmut Laumen | Leveraging Cross-species Transcription Factor Binding Site Patterns: from Diabetes Risk Loci to Disease Mechanisms |
| RG45 | Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Melinda Aldrich, Hua Xu, Joshua Denny and Zhongming Zhao |
A Novel Computational Framework to Explore Signaling Pathway Networks for Understanding Drug Action |
| RG46 | Adrian Heilbut, Myriam Heiman, Eric Kolaczyk and Jill P. Mesirov |
FACTOTUM (FACTOTUM Analyzes Contextual Transcripts' Overrepresented TFs Utilizing Motifs) |
| RG47 | Evan Gatev and Irmtraud Meyer | Inference of Transcription Factor Modules Without Clustering of Correlated Expression Time Series |
| RG48 | Ezekiel Maier, Drew Michael, Holly Brown and Michael Brent |
Using a Transcriptional Network Model to Guide Bioengineering |
| RG49 | Stefano de Pretis, Marco Morelli, Theresia Kress, Marcin Gorski, Bruno Amati and Mattia Pelizzola | Transcriptional Scenarios Underlying Regulation of gene expression by c-Myc |
| RG50 | Heejung Shim, Ester Pantaleo and Matthew Stephens | Testing for Differences Between Multiple Groups in High-Throughput Sequencing Data Using Bayesian Multiscale Models |
| RG51 | Eugene Bolotin, Elizabeth Theusch, Marisa W. Medina and Ronald M. Krauss | Simvastatin Treatment Does Not Affect Chromatin Structure in Lymphoblast Cell Lines |
| RG52 | Hamed Najafabadi, Sanie Mnaimneh, Frank Schmitges, Kathy Lam, Ally Yang, Brendan Frey and Timothy Hughes |
Kaleidoscopic Evolution of Metazoan C2H2 Zinc Finger DNA-binding |
| RG53 | Ben Hitz, Eurie Hong and J. Michael Cherry |
Improved Access to Data Sets from ENCODE via Metadata-driven Searches of Experimental Conditions |
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