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

INFORMATION FOR POSTER PRESENTERS

updated Oct 23, 2013

The following is a schedule of poster sessions for the 6th Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges.

If you are scheduled to present a poster, please check the number of your poster (click here) and determine whether you are scheduled to participate in a DREAM Challenges, Regulatory Genomics, or Systems Biology poster session, and whether you have an odd or even numbered poster. Once you have determined your track and number, see the Poster Display Schedule below. 

Important: Poster authors should be available to present their poster during your assigned poster session.

Only authors who have confirmed their participation in a poster session are scheduled below.

Poster Size
The ideal poster size should be a maximum of 44 x 44 inches. The organizers will provide pins for fastening your poster to the board. >>CLICK HERE<< to view an image of the poster board.

Location
Posters will be on display in the Appel Salon – Novella Room.

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SCHEDULE

DREAM Challenges: Friday, November 8

• DREAM posters set-up time: November 8, 10:00 – 11:00 am
• DREAM poster session: November 8, 12:10 – 1:30 pm
• DREAM poster removal deadline: November 8, 5:00 pm
• >>Click here to find your poster number<<

Systems Biology (SB): Saturday, November 9 and Sunday, November 10

• Please note that all SB posters will be on display both days.
• SB posters set-up time: November 9, 8:30 – 10:00 am
• SB ODD NUMBERS poster session: November 9, 12:15 – 1:30 pm
• SB EVEN NUMBERS poster session: November 10, 12:15 – 1:30 pm
• SB poster removal deadline: November 10, 5:00 pm
• >>Click here to find your poster number<<

Regulatory Genomics (RG): Monday, November 11 and Tuesday, November 12

• Please note that all RG posters will be on display both days.
• RG posters set-up time: November 11, 8:30 – 10:00 am
• RG ODD NUMBERS poster session: November 11, 12:15– 1:30 pm
• RG EVEN NUMBERS poster session: November 12, 12:15 – 1:30 pm
• RG poster removal deadline: November 12, 2:00 pm
• >>Click here to find your poster number<<

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

AGENDA

Please note that this schedule is tentative and is subject to change without notice. Any updates will be posted on this page as soon as possible. (Last update: November 10, 2013)

All talks will be held in the Appel Salon at the Toronto Reference Library
(789 Yonge Street, Toronto). >>Click here<< for the map.

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

KEYNOTE SPEAKER ABSTRACTS & BIOGRAPHIES

updated Oct 27, 2013

DREAM Challenges

Trey Ideker
University of California, San Diego
United States

Turning Networks Into Ontologies: Towards A Data-driven Gene Ontology

Abstract: Ontologies have been very useful for capturing knowledge as a hierarchy of concepts and their interrelationships. In biology, a prime challenge has been to develop ontologies of gene function given only partial biological knowledge and inconsistency in how this knowledge is curated by experts. I will discuss how large networks of gene and protein interaction, as are being mapped systematically for many species, can be transformed to assemble an ontology with equivalent coverage and power to the manually-curated Gene Ontology (GO). Our network-extracted ontology contains 4,123 biological concepts and 5,766 relations, capturing the majority of known cellular components as well as many additional concepts, triggering subsequent updates to GO. Using genetic interaction profiling we provide further support for novel concepts related to protein trafficking, including a link between Nnf2 and YEL043W. This work enables a shift from using ontologies to evaluate data to using data to construct and evaluate ontologies.

Biography: Trey Ideker, Ph. D. is Professor of Medicine at the University of California at San Diego. He serves as Division Chief of Medical Genetics and Director of the National Resource for Network Biology, as well as being Adjunct Professor of Bioengineering and Computer Science and Member of the Moores UCSD Cancer Center. Ideker received Bachelor’s and Master’s degrees from MIT in Electrical Engineering and Computer Science and his Ph.D. from the University of Washington in Molecular Biology under the supervision of Dr. Leroy Hood. He is a pioneer in assembling genome-scale measurements to construct network models of cellular processes and disease. His recent research activities include assembly of networks governing the response to DNA damage; development of the Cytoscape and NetworkBLAST software packages for biological network visualization and cross-species network comparison; and methods for identifying network-based biomarkers in development and disease. Ideker serves on the Editorial Boards for Bioinformatics and PLoS Computational Biology, is on the Scientific Advisory Boards of the Sanford-Burnham Medical Research Institute and the Institute for Systems Biology, and is a regular consultant for companies such as Monsanto and Mendel Biotechnology. He was named one of the Top 10 Innovators of 2006 by Technology Review magazine and was the recipient of the 2009 Overton Prize from the International Society for Computational Biology. His work has been featured in news outlets such as The Scientist, the San Diego Union Tribune, Forbes magazine and the New York Times.
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Timothy R. Hughes
University of Toronto
Canada

DNA and RNA Binding Motifs for Mapping Gene Regulation

Abstract: A challenge to our understanding of genome function is lack of accurate and complete knowledge of the sequence preferences of DNA and RNA binding proteins. Current work in my laboratory is aimed at using in vitro assays to catalogue motifs on a genomic scale, thus separating the intrinsic activities of the proteins from confounding effects present in vivo. These data are invaluable in understanding how cells recognize genomic features, how gene regulatory networks are organized, and nucleic acid-binding proteins regulate healthy and disease states. I will highlight the contributions that the DREAM framework has made to this enterprise.

Biography: Timothy R. Hughes is a Professor at the Donnelly CCBR at the University of Toronto. He studied engineering and music at the University of Iowa, and received his Ph.D. in Cell and Molecular Biology from Baylor College of Medicine, working on telomere replication proteins with Vicki Lundblad. He did his postdoctoral work at Rosetta Inpharmatics (now Merck) working on microarray technology and its applications, including the development of ink-jet arrays now available from Agilent. Since moving to Toronto in 2001, Dr. Hughes has been the recipient of a Canada Research Chair in Genome Biology, the Ontario Premier’s Research Excellence Award, the Terry Fox Young Investigator award, and an HHMI foreign scholarship. He has authored or co-authored over 100 manuscripts, and is a scholar of the Canadian Institutes For Advanced Research. His laboratory has worked in gene regulation, systems biology, functional genomics, RNA processing, and genome sequencing.

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Systems Biology

Brenda Andrews
University of Toronto
Canada

From Phenotypes to Pathways: Global Exploration of Cellular Networks Using Yeast Functional Genomics

Abstract: The entire landscape of eukaryotic genetic research has been transformed by our ability to rapidly sequence genomes – while we can now map genomes efficiently, we do not yet know how to interpret genome variation to predict inherited phenotypes. Emerging evidence suggests that we must account for genetic interactions in order to relate genotype to important phenotypes in any eukaryotic system. To systematically explore genetic interactions, our group developed a unique functional genomics platform called ‘synthetic genetic array’ (SGA) analysis that automates yeast genetics and enables the systematic construction of double mutants. We developed two powerful pipelines which combine SGA and automated microscopy for systematic and quantitative cell biological screens or phenomics. Our first pipeline uses SGA to introduce fluorescent markers of key cellular compartments, along with sensitizing mutations, into yeast mutant collections. We then perform live cell imaging on the mutant arrays using HTP confocal microscopy to quantitatively assess the abundance and localization of our fluorescent reporters, providing cell biological readouts of specific pathways and cellular structures in response to thousands of genetic perturbations. Our second pipeline exploits the yeast GFP collection, a unique resource consisting of thousands of strains with different genes uniquely tagged with GFP. This remarkable collection has been arguably underutilized for systematic analysis of the proteome, largely due to the challenges associated with analysis of large sets of cell biological data. We addressed this challenge by adopting a high-content screening approach to measure protein abundance and localization changes in an automated fashion on a genome scale. Our general approach, in particular our network analysis and visualization methods, are readily extensible to other systems.

Biography: Brenda Andrews is Professor and Chair of the Banting & Best Department of Medical Research within the Faculty of Medicine at the University of Toronto, where she holds the Charles H Best Chair in Medical Research. She is also Director of the Terrence Donnelly Center for Cellular and Biomolecular Research (the Donnelly Centre), an interdisciplinary biomedical research institute with a focus on technology development for post-genome biology, functional genomics, systems & computational biology and bioengineering.

After receiving her PhD in Medical Biophysics from the University of Toronto, Dr. Andrews obtained her early training in genetics with the late Dr. Ira Herskowitz at the University of California San Francisco. In 1991, Dr. Andrews was recruited to the Department of Medical Genetics (now Molecular Genetics) at the University of Toronto. She became Chair of the Department in 1999, a position she held for 5 years before assuming her current positions. Dr. Andrews’ current research interests analysis of genetic interaction networks in budding yeast, using automated genetics platforms that include high content microscopy for systematic analysis of cell biological phenotypes. Specific interests in the Andrews lab include mechanisms of cell cycle control, control of cell function by kinases and other enzymes and the regulation of cell polarity and morphogenesis. Her research is currently funded by the CIHR, the National Institutes of Health, the Ontario Research Fund, the Canadian Foundation for Innovation and the Canadian Institute for Advanced Research (CIFAR).

Dr. Andrews is a Fellow of the Royal Society of Canada, Fellow of the American Association for the Advancement of Science, a Fellow of the American Academy of Microbiology and Director of the Genetic Networks Program of the CIFAR.
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Levi A. Garraway
Dana-Farber Cancer Institute and the Broad Institute
Boston, United States




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Peter Jackson
Stanford University School of Medicine
United States

Building Protein Networks to Understand Human Disease: Ciliopathies Explain Retinal Degeneration, Obesity, and Cancer

Abstract: Our ability to navigate the landscape of human disease is limited because the map of functional pathways connecting proteins to specific diseases is poorly drawn. The Jackson Laboratory uses high throughput mass spectrometry methods to identify disease-linked proteins and to construct dense protein interaction maps. These improved maps provide important biological insights, and identify new diagnostics and drug targets. The presentation will explain the technology and analysis methods and show new disease maps. To exemplify the methods, our discoveries of ciliopathies, newly identified neurological and kidney diseases with links to obesity, retinal degeneration, and cancer will be presented.

Biography: Dr. Peter Jackson is Professor in the Baxter Laboratory for Stem Cell Research at Stanford, and formerly Director and Staff Scientist at Genentech. His laboratory develops cancer drug targets and pioneered proteomic network building to identify diagnostics and targets in human disease. Their discovery of new disease genes and signaling pathways in the primary cilium, a rediscovered signaling organelle, helps explain neurological and kidney disease, obesity, retinal degeneration, and cancer.
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Galit Lahav
Harvard Medical School
Cambridge,
United States

Encoding Cellular Information through p53 Dynamics in Individual Cells

Abstract: Many signaling molecules exhibit complex dynamical behaviors, yet little is known how these dynamics affect cellular responses. In this talk I will focus on the dynamics of p53, a critical tumor-suppressive protein that controls genomic integrity and cell survival. I will present our recent work on p53 dynamics in individual cells and ask how these dynamics are shaped and affect cell fate decisions

Biography: Galit Lahav received her PhD in 2001 from the Department of Biology in the Technion, Israel Institute of Technology. In 2003, she completed her postdoctoral fellowship at the Weizmann Institute of Science in Israel. She then spent a year at Harvard’s Bauer Center for Genomics Research, and in the fall of 2004, joined the Department of Systems Biology at Harvard Medical School. Her research group combines experimental and computational approaches to understand how drugs act on different cell types and organs, and to gain insight into the reasons why different cells and people respond differently to specific drugs. Lahav is also a dedicated mentor to new faculty and highly committed to furthering the advancement of women in science.
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Tony Pawson and Modular Biology: From Domains to Cell Signalling Systems
by Dr. Jeff Wrana
Mt. Sinai Hospital
Toronto, Canada

The organizers of the RECOMB ISCB DREAM Conference were saddened to learn of the passing of Dr. Tony Pawson in August. Dr. Jeff Wrana will present a special tribute lecture at the 2013 conference where Dr. Pawson was to be a featured keynote speaker.

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Bernhard Palsson
University of California, San Diego
United States

Predictive Uses of Metabolic Reconstructions

Abstract: The prediction of cellular function from a genotype is a fundamental goal in biology. Constraint-based modelling methods systematize biochemical, genetic, and genomic knowledge into a mathematical framework enabling a mechanistic description of the genotype-phenotype relationship. The deployment of constraint-based approaches has evolved over roughly 30 years and recently, there has been a critical mass of studies combining them with high-throughput datasets and prospective experimentation. These studies have led to the validation of increasingly significant and relevant biological predictions. As reviewed herein, these recent successes have tangible implications in the fields of microbial evolution, interaction networks, genetic engineering, and drug discovery.

Biography: Bernhard Palsson is the Galletti Professor of Bioengineering and the Principal Investigator of the Systems Biology Research Group in the Department of Bioengineering at the University of California, San Diego. Dr. Palsson has co-authored more than 360 peer-reviewed research articles and has authored three textbooks, with one more in preparation. His research includes the development of methods to analyze metabolic dynamics (flux-balance analysis, and modal analysis), and the formulation of complete models of selected cells (the red blood cell, E. coli, hybridoma, and several human pathogens). He sits on the editorial broad of several leading peer-reviewed microbiology, bioengineering, and biotechnology journals. He previously held a faculty position at the University of Michigan for 11 years and was named the G.G. Brown Associate Professor at Michigan in 1989, a Fulbright fellow in 1995, and an Ib Henriksen Fellow in 1996. He is the author of 40 U.S. patents, the co-founder of several biotechnology companies, and holds several major biotechnology awards. He received his PhD in Chemical Engineering from the University of Wisconsin, Madison. Dr. Palsson is a member of the National Academy of Engineering and is a Fellow of both the AAAS and the AAM.
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Olivier Pourquié
Institut de Génétique et de Biologie Cellulaire et Moléculaire (IGBMC)
Université de Strasbourg, France

Title & Abstract: Check back for updates.

Biography: Olivier Pourquié, Ph.D. is currently Professor at Strasbourg University Medical School (France). He was the director of the Institute for Genetics and Molecular and Cellular Biology in Strasbourg from 2009 to 2012 and before he was a Howard Hughes Medical Institute Investigator at the Stowers Institute for Medical Research in Kansas City, USA. His lab provided the first evidence of the existence of a molecular oscillator -the segmentation clock- associated to the rhythmic production of vertebral precursors (the somites) in the embryo. This discovery was listed as one of 25 milestones in Developmental Biology in the 20th century by Nature magazine. The work from the Pourquié laboratory has imposed vertebrate segmentation as a novel paradigm to study spatiotemporal regulation of signaling in development. Together, his discoveries have had important consequences for our understanding of the patterning of the vertebrate embryonic axis and provided a conceptual framework to explain human spine malformations such as congenital scoliosis. Pr Pourquié is an elected EMBO and Academia Europea member and is the recipient of several prestigious awards including the Lounsbery Grand Prize of the French and American Academy of Sciences, the Allianz Grand Prize of the French Academy of Sciences and a European Research Council Advanced grant.
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Peter Sorger
Harvard Medical School
Cambridge, United States

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Regulatory Genomics

Ziv Bar-Joseph
Carnegie Mellon University
Pittsburgh
United States

Algorithms in Nature

Abstract: Computer science and biology have enjoyed a long and fruitful relationship for decades. Computational methods are widely used to analyze and integrate large biological data sets while several algorithms were inspired by the high-level design principles of biological systems. However, so far these two directions did not intersect and bio-inspired computational methods rarely led to new biological insights. With our increasing understanding of biological systems it is now possible to design bi-directional studies that will mutually benefit both fields. In this talk I will discuss the similarities and differences between the mechanisms and objectives of biological and computational systems. Relying on these similarities, I will present a few example where studying in detail how information processing is carried out in biological systems leads to both, efficient algorithms and better understanding of biology. These examples include fault tolerance in distributed regulatory networks, the selection of a Maximal Independent Set (MIS) during fly development and network design in the brain. In a number of these cases, the biological algorithms employs novel ideas that improve upon state of the art computational methods.

Biography: Ziv Bar-Joseph is an Associate Professor in the Lane Center for Computational Biology and the Machine Learning Department at the School of Computer Science at Carnegie Mellon University. His work focuses on the analysis and integration of static and temporal high throughput biological data for systems biology and on bi-directional studies linking information processing in biological and computational systems. Dr. Bar-Joseph has been the co-chair of the RECOMB meeting on Regulatory Networks and Systems Biology and is currently an associate editor for Bioinformatics. He received his Ph.D. from the MIT in 2003. He was the recipient of the DIMACS-Celera Genomics Graduate Student Award in Computational Molecular Biology, the NSF CAREER award and the 2012 Overton prize in computational biology.
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Emmanouil (Manolis) Dermitzakis
University of Geneva Medical School
Switzerland

From Genome Function to Personalised Omics

Abstract: Molecular phenotypes are important phenotypes that informs about genetic and environmental effects on cellular state. The elucidation of the genetics of gene expression and other cellular phenotypes are highly informative of the impact of genetic variants in the cell and the subsequent consequences in the organism. In this talk I will discuss recent advances in three key areas of the analysis of the genomics of gene expression and cellular phenotypes in human populations and multiple tissues and how this assists in the interpretation of regulatory networks and human disease variants. I will also discuss how the recent advances in next generation sequencing and functional genomics are bringing closer our hopes for personalized medicine.

Biography: Emmanouil Dermitzakis is currently a Louis-Jeantet Professor of Genetics in the Department of Genetic Medicine and Development of the University of Geneva Medical School. He is a member of the executive board of the Institute of Genetics and Genomics in Geneva (iGE3) and is also an affiliated Faculty member at the Biomedical Research Foundation of the Academy of Athens in Greece. His current research focuses on the genetic basis of cellular phenotypes and complex traits. He has authored and coauthored more than 100 papers in peer-reviewed journals and many of them in journals such as Nature, Science and Nature Genetics. His papers have been cited more than 20000 times and his H-index is 49. His research is supported by the Louis-Jeantet Foundation, the Wellcome Trust, the Swiss National Science Foundation, the European Commission, the Juvenile Diabetes Foundation and the US National Institutes of Health (NIH). He is also the recipient of a European Research Council (ERC) grant. He has been invited to give talks and keynote lectures in most of the prestigious genetics meeting and is the organizer of training courses including the Wellcome Trust HapMap course and founder and organizer of the Leena Peltonen School of Human Genomics. He is currently an analysis co-chair in the GTex project and has served as an analysis co-chair in the pilot phase of the ENCODE (ENCyclopedia Of Dna Elements) consortium and member of the analysis group of the Mouse Genome Sequencing Consortium and the International HapMap project. He had a leading analysis role in the HapMap3 project and is a member of the analysis group of the 1000 genomes project. He has served in the Board of Reviewing Editors of Science (2006-2011), and as a Senior Editor in PLoS Genetics (2006-2012) and is currently a member of the Board of Reviewing editors for the new scientific journal eLIFE. He is also in the advisory board of DNAnexus.
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Brenton R. Graveley
University of Connecticut Health Center
Farmington
United States

The Transcriptome of Drosophila Melanogaster

Abstract: We have generated RNA-seq, CAGE, and cDNA sequences from 30 developmental time points, 29 tissues, 21 environmental perturbations and 25 cell lines from Drosophila melanogaster. These data have substantially enhanced and improved the annotation of the D. melanogaster genome and lead to the discovery of >2,000 new genes including numerous non-coding transcripts. We also examined the extent and dynamics of alternative splicing and polyadenylation. For example, we identified hundreds of genes that utilize alternative polyadenylation to express long 3' UTR extensions in neural tissues and that the majority of sex-specific splicing is gonad-specific. In summary, the Drosophila transcriptome is substantially more complex than previously recognized and arises from tissue-specific, combinatorial usage of well-defined promoter elements, splice sites, and polyadenylation sites.

Biography: Brenton R. Graveley obtained hi B.A. manga cum laude in 1991 from the Department of Molecular, Cellular, and Developmental Biology at the University of Colorado, Boulder where he performed research with David M. Prescott. He conducted his Ph.D. Research under the guidance of Gregory M. Gilmartin in the Department of Microbiology and Molecular Genetics at the University of Vermont and graduated in 1996. He was a Jane Coffin Childs postdoctoral fellow from 1996-1999 with Tom Maniatis in the Department of Molecular and Cellular Biology at Harvard University. Since 1999, he has been a faculty member in the Department of Genetics and Developmental Biology at the University of Connecticut Health Center in Farmington, CT where he is currently a Professor. He is also Associate Director of the Institute for Systems Genomics at the University of Connecticut, a Member of the Board of Directors for the RNA Society, and an Editor of the journal RNA.
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Jason D. Lieb
Princeton University
United States

Reduce, Reuse, Recycle: The Dynamics of Regulatory Information Usage in Development

Abstract: Genomic technologies have opened a window into how regulatory information is encoded in DNA, and how access to that information is controlled. I’ll discuss these issues on at least one of three scales (1) How continual competition between nucleosomes and transcription factors may act as a clutch for transcriptional regulation; (2) How the nuclear envelope acts as an organizer for regulatory information; and (3) surprising re-use of the same subset of DNA regulatory elements to control the development of wings, legs, and halteres in Drosophila.

Biography: Jason Lieb is a Professor of Molecular Biology at the Lewis-Sigler Institute for Integrative Genomics at Princeton University. Prior to coming to Princeton, Lieb was the Beverley W. Long Chapin Distinguished Professor of Biology in the UNC College of Arts and Sciences, and the Director of the Carolina Center for Genome Sciences. Research projects in the Lieb lab are united by the scientific goal of understanding relationships between chromatin, transcription factor targeting, and gene expression. In particular, Lieb studies how information is encoded and dynamically utilized in living eukaryotic genomes, focusing on those areas of the genome that serve to regulate chromosomal functions, including transcription, DNA replication and repair, recombination, and chromosome segregation. Lieb came to UNC in 2002 after completing a postdoctoral fellowship at Stanford University. He earned his undergraduate degree in biology at the University of North Carolina at Chapel Hill and his PhD in genetics at the University of California at Berkeley.
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Aviv Regev
Broad Institute
Cambridge
United States

Reconstructing Regulatory Circuits: Lessons from Immune Cells

Abstract: Check back for updates.

Biography: Aviv Regev, a computational biologist, joined the Broad Institute as a core member and MIT as a faculty member in 2006. Regev’s research centers on understanding how complex molecular networks function and evolve in the face of genetic and environ¬mental changes, over time — scales ranging from minutes to millions of years. Prior to joining the Broad Institute, Regev was a fellow at the Bauer Center for Genomics Research at Harvard University, where she developed new approaches to the reconstruction of regulatory networks and modules from genomic data. Regev also worked for several years in the biotech industry in Israel, where she established and directed a bioinfor¬matics research and development team at QBI, a functional genomics company. Regev is also an associate professor in the Department of Biology at MIT and director of the Klarman Cell Observatory at the Broad. She was named an Early Career Scientist of the Howard Hughes Medical Institute in 2009. She is a recipient of the NIH Director’s Pioneer Award, a Sloan fellowship from the Sloan Foundation, and the Overton Prize from the International Society for Computational Biology. Regev received her M.Sc. from Tel Aviv University, studying biology, computer science, and mathematics in the Interdisciplinary Program for the Fostering of Excellence, where she did research in both theoretical biology (on the evolution of development) and experimental biology (on genomic instability). She received her Ph.D. in computational biology from Tel Aviv University.
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Jussi Taipale
Karolinska Institutet
Stockholm, Sweden

Genome-wide Analysis of Protein-DNA Interactions

Abstract: Understanding the information encoded in the human genome requires two genetic codes, the first code specifies how mRNA sequence is converted to protein sequence, and the second code determines where and when the mRNAs are expressed. Although the proteins that read the second, regulatory code – transcription factors (TFs) – have been largely identified, the code is poorly understood as it is not known which sequences TFs can bind in the genome. To understand the regulatory code, we have analyzed the occupancy of the majority of all expressed TFs in human colorectal cancer cells, and analyzed the sequence-specific binding of human, mouse and Drosophila TFs using high-throughput SELEX. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. Comparison of the human binding profiles with those of house mouse and Drosophila, revealed that the monomer binding specificity of TFs evolves very slowly, and has been almost completely fixed between vertebrates and invertebrates despite complete lack of regulatory element conservation. However, TF flanking sequences, and dimer spacing and orientation preferences appear to evolve much faster than monomer binding preferences, indicating that such changes are a potential source of evolutionary novelty. A binding model that is required to understand binding of TFs to the genome, which incorporates information about protein-protein interactions induced by DNA, and inheritance of epigenetic states across cell division will be discussed.

Biography: Professor Jussi Taipale earned his Ph.D. from the University of Helsinki in 1996. He initially continued his postdoctoral work at the University of Helsinki and later at Johns Hopkins University (Baltimore, MD, USA). Since 2003, he has headed an independent research laboratory focusing on systems biology of growth control and cancer. He has published 63 articles of which thirteen are in the most prestigious scientific journals (Nature, Science, Cell), won numerous awards and grants (e.g., Anders Jahre Prize for Young Researchers, EMBO Young Investigator, ERC Advanced Grant), and is internationally recognized as a leader in the field of genomics and systems biology. The Taipale group’s main expertise is on high-throughput screening using cDNA (Varjosalo et al. Cell 2008) and RNA interference (Björklund et al. Nature 2006), and computational and experimental methods to identify causative regulatory mutations in non-protein coding DNA and to analyze genetic networks (see Jolma et al., Cell 2013; Yan et al., Cell 2013). In addition, Taipale group has extensive expertise on mouse models of gene and regulatory region function (see Dumont et al., Science 1998; Ma et al., Cell 2002; Hallikas et al. Cell 2006; Sur et al., Science 2012).

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

PROMOTION

Updated November 07, 2013

Description	File type/link
	.pdf
Promotional Flyer	.pdf

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

DREAM8 CHALLENGES: The 8th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS 

Updated June 10, 2013

>> Click here <<  to download a PDF of this announcement.

Dear Colleague,    

We are pleased to announce that the DREAM8 Challenges are now open for participation.  During the “Challenge season” spanning from June 10 to September 15, 2013, Sage Bionetworks and DREAM will run the three Challenges described below.  Best performers in the DREAM8 Challenges will be invited to present at the RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges (November 8-12, Toronto, Canada) with travel expenses covered by the Sage/DREAM organizers. Sage Bionetworks and DREAM are also working with high impact journals to ensure that the methodology developed by the Challenges' best performers will be considered for publication under the Challenge-assisted Peer Review format.

1. HPN-DREAM Breast Cancer Network Inference Challenge: Infer the signaling networks in breast cancer cell lines
2. NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge: Predict individual response to environmental and pharmaceutical chemicals
3. The Whole-Cell Parameter Estimation DREAM Challenge: Infer the kinetic parameters underlying biological processes in whole cell models

To sign up for a Challenge and access the data sets and descriptions of the DREAM8 Challenges, please go to www.synapse.org/#!Challenges:DREAM8.

To learn more about the DREAM project and Sage Bionetworks please go to http://sagebase.org/challenges-overview/.

Sincerely,

Gustavo Stolovitzky (DREAM chair)
On behalf of the DREAM8 Challenge Organizers

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

SUBMIT AN ABSTRACT

The RECOMB/ISCB Conference on Regulatory and Systems Genomics invites abstracts for consideration for oral presentations or participation in a poster session. Abstracts may be either original unpublished work or original work that was published or accepted for publication at a high-impact journal between January 1 and November 1, 2013. Unpublished work will be considered for either an oral or a poster presentation. Work already accepted for publication will be considered for an oral presentation only.

Submission deadline: September 13, 2013

Abstracts received before the due date will be considered for oral presentations and/or poster presentations. If your abstract is accepted, it will be included in an abstract booklet that will be distributed to all conference participants. The abstract booklet will also include abstracts of full-length papers accepted in our partner journals Genome Research, G3: Gene / Genome / Genetics and the Journal of Computational Biology.

Any abstracts submitted after the deadline will be included only at the discretion of the conference chairs, and will be eligible for poster presentations only. Abstracts sent after the due date will not be included in the abstract booklet due to printing constraints. Please also note that we can only allow one abstract per presenting author.

Any abstract that is not associated with a submitted paper will be treated as a personal communication. Authors reserve the right to publish their work elsewhere.
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How to submit your abstract

Please use this link to EasyChair to submit your abstract. You will be asked to provide information about yourself and your coauthors, including name, e-mail address, and affiliation. Please check one box for corresponding author to indicate who would be speaking or would be primarily responsible for your poster. You will also be asked to provide an abstract title, the text of your abstract, and keywords.

Important: Please be sure to check the box “abstract only” near the bottom of the page to indicate that your abstract is not being accompanied by a full-length paper.
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Topics

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation. Some possible topics include:

•     Modeling and recognition of regulatory motifs and modules
•     Chromatin state establishment, maintenance, and role in development
•     Post-transcriptional regulation and small regulatory RNAs
•     Regulatory networks, metabolic networks, proteomic networks
•     Cellular signatures of biological responses and disease states
•     Phosphorylation, metabolic fluxes, systematic phenotyping
•     Mathematical modeling and simulation of biological systems
•     Methods for systematic validation of high-throughput biological predictions
•     Approaches for aggregation of results arising from different methodologies
•     Translational systems biology

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

SUBMIT A PAPER

The 2013 RECOMB/ISCB Conference on Regulatory and Systems Genomics has developed partnerships with Genome Research, G3: Gene / Genome / Genetics and the Journal of Computational Biology to publish full-length papers submitted to the conference.

The deadline for submitting all papers is Friday, June 28, 2013, at 11:59 pm (Pacific Time).

We will accept two types of papers for consideration for publication.

• Research article papers will be considered for publication in Genome Research and G3: Genes / Genomes / Genetics. Appropriate experimental validation data is required for manuscript to be considered for this track.

• Theory papers will be considered for publication in the Journal of Computational Biology and to G3: Genes / Genomes / Genetics.
  

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How to submit your paper

Please use this link to EasyChair to submit your paper. Please DO NOT submit your manuscript directly to the journal.

You will be asked to provide information about yourself and your coauthors, the title and abstract for your paper, and keywords. The button to upload your paper is at the bottom of the form, and EasyChair requires that it be submitted as a pdf file. If you do not already have an EasyChair account, you can log in to create one at the link.

IMPORTANT: In the "Keywords" field, please indicate the journal(s) whom you would like to consider your paper for publication. You can indicate Genome Research, G3: Genes / Genome / Genetics or Journal of Computational Biology as keywords. If you would like to submit your paper for consideration at all publications, please indicate the names of all journals as separate keywords on three lines, in addition to other keywords that are relevant to your paper.

Please see the journal websites for information about formatting requirements (see Genome Research format, G3: Genes / Genomes, Genetics format and Journal of Computational Biology format). Abstracts should be a maximum of 250 words.
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Review process

Manuscripts will be reviewed by the program committee, and papers judged to be of high merit will be part of the conference proceedings published by the Journal of Computational Biology. A subset of selected papers will also be submitted to the editorial board of Genome Research for their consideration on an expedited basis. If your paper is selected for publication in Genome Research or another journal, it will not be eligible for publication in the proceedings of Journal of Computational Biology. All accepted papers will be presented orally at the conference.

Only papers that are judged by the organizing committee to be of the highest quality will be selected for submission to our partner journals. If you submit a paper and the committee decides against recommending it for publication, we may still invite you to participate in a poster session.
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Topics

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation. Some possible topics include:

•     Modeling and recognition of regulatory motifs and modules
•     Chromatin state establishment, maintenance, and role in development
•     Post-transcriptional regulation and small regulatory RNAs
•     Regulatory networks, metabolic networks, proteomic networks
•     Cellular signatures of biological responses and disease states
•     Phosphorylation, metabolic fluxes, systematic phenotyping
•     Mathematical modeling and simulation of biological systems
•     Methods for systematic validation of high-throughput biological predictions
•     Approaches for aggregation of results arising from different methodologies
•     Translational systems biology

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

NEWS

May 05, 2014

RECOMB/ISCB Systems Biology, Regulatory Genomics,
and DREAM 2013 Special Issue
Guest Editors: Andrea Califano, Manolis Kellis, and Gustavo Stolovitzky is available online at:
http://online.liebertpub.com/toc/cmb/21/5

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November 12, 2013 - Top Ten Paper Awards

>>Click here<< to download PDF

The winners of the Top Ten Paper Awards in the field of Regulatory and Systems Genomics for our Top Ten paper awards announced at RECOMB/ISCB Regulatory and Systems Genomics meeting in Toronto are (in no particular order):

• DNaseI sensitivity QTLs are a major determinant of human expression variation
  Jacob F Degner, AthmaA Pai, Roger Pique-Regi, Jean-Baptiste Veyrieras, Daniel J Gaffney, Joseph K Pickrell, Sherryl De Leon, Katelyn Michelini, Noah Lewellen, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard
  Nature, 482(7385), 390-394, 2012 - February 4, 2012
• Guilt by association is the exception rather than the rule in gene networks
  Gillis J, Pavlidis P.
  PLoS Comput Biol. 2012;8(3):e1002444 - March 29, 2012
• An expansive human regulatory lexicon encoded in transcription factor footprints
  Neph S, Vierstra J, StergachisAB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.
  Nature, 489(7414), 83-90, Sep 2012. – September 6, 2012
• Linking the signaling cascades and dynamic regulatory networks controlling stress responses
  Gitter A, Carmi M, Barkai N, Bar-Joseph Z
  Genome Research, 23(2), 365-376, Feb 2013. - October 11, 2012
• Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
  Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J,
  Mikkelsen TS, Kellis M.
  Genome Research. 2013 May;23(5):800-11. – May 1, 2013
• Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
  Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML.
  Cell Rep. 2013 Apr 25;3(4):1093-104 - April 1, 2013
• Promoter Sequence Determines the Relationship between Expression Level and Noise
  Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E.
  PLoS Biol. 2013;11(4):e1001528. – April 1, 2013
• Probing DNA shape and methylation state on a genomic scale with DNase I
  Lazarovici A, Zhou T, Shafer A, Dantas Machado A, Riley T, Sandstrom R, Sabo P, Lu Y, Rohs R, Stamatoyannopoulos J, Bussemaker H
  Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6376-81 - April 1, 2013
• A statistical framework for joint eQTL analysis in multiple tissues
  Timothée Flutre, Xiaoquan Wen, Jonathan Pritchard, Matthew Stephens
  PLoS Genetics, 9, 5, e1003486, 2013 - May 9, 2013
• Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
  Q. Cheng, M. Kazemian, H. Pham, C. Blatti, S. E. Celniker, S. A. Wolfe,
  M. H. Brodsky, S. Sinha
  PLoS Genetics. 2013 Aug;9(8):e1003571. – August 1, 2013

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October 18, 2013 - Top Ten Paper Awards - Please help nominate papers in the field of Regulatory and Systems Genomics for our Top Ten paper awards at the upcoming RECOMB/ISCB Regulatory and Systems Genomics meeting.

Our goal is to identify seminal papers that will have a lasting impact in the field of Regulatory and Systems Genomics. Read more here.
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August 09, 2013 - The organizers of the RECOMB ISCB DREAM Conference were saddened to learn of the passing of Dr. Tony Pawson. A special tribute to his legacy is planned for the 2013 conference where Dr. Pawson was to be a featured keynote speaker.

Our thoughts are with his friends and colleagues during this difficult time.   

To learn more about Dr. Pawson's life and legacy, please click here for the Toronto Star article.