RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges


Updated November 07, 2013

Links within this page: Systems Biology (SB) | Regulatory Genomics (RG)

--> DREAM Challenges: Friday, November 8
Presenter's name is in bold)

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
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
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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