20th Annual International Conference on
Intelligent Systems for Molecular Biology

Special Interest Group Meetings (SIGs) & Satellite Meetings

ISMB 2012 will hold a number of one, two and three-day specialized meetings in computational biology. These meetings consist of Special Interest Group Meetings (SIGs) and Satellite Meetings (SMs) and will be held prior to the main conference. A SIG meeting is a one- or two-day focused workshop. It provides a broad and/or deep perspective on developments in a field of research, and is intended as a way to address a topic more extensively than can be done in the main conference. A Satellite Meeting is similar to a SIG meeting but is more of a mini-conference. Satellite meetings are held in conjunction with ISMB.

 
Program information and registration details are noted below. To inquire about the possibility of forming a new SIG for ISMB/ECCB 2013 or beyond, please address your inquiry to This email address is being protected from spambots. You need JavaScript enabled to view it.


 

Satellite Meetings

3Dsig:Structural Bioinformatics & Computational Biophysics
 
Date: Friday, July 13 - Saturday, July 14,  2012
Day 1 Start time: 8:30 a.m.     End time: 6:00 p.m.
Location: Hyatt Regency Long Beach Hotel (adjacent to Long Beach Convention Center)
Room: Regency Ballroom A
 
Day 1 Dinner/Keynote*: Start time: 6:45 pm. - 9:00 p.m.
Location: Hyatt Regency Long Beach Hotel (adjacent to Long Beach Convention Center)
Room: Regency Ballroom B
 
Day 2 Start time: 8:30 a.m.     End time: 6:00 p.m.
Location: Hyatt Regency Hotel Long Beach (adjacent to Long Beach Convention Center)
Room: Regency Ballroom A
 
*Friday, July 13 - 3Dsig Dinner and Evening Presentation included in 3Dsig Satellite Meeting registration
  • 6:45 p.m. Reception (Cash bar)
  • 7:30 p.m. Dinner

3Dsig, a Satellite Meeting of the ISMB/ECCB conference, focused on structural bioinformatics and computational biophysics and has become the largest meeting in this growing field.

 

Confirmed Keynotes:

Ada Yonath, Nobel Laureate, Weizmann Institute of Science, Israel

Adam Godzik, Sanford-Burnham Medical Research Institute, CA, USA 

David Goodsell, The Scripps Research Institute, CA, USA

Art Olson, The Scripps Research Institute, CA, USA

Olivier Lichtarge, Baylor College of Medicine, TX, USA

Francois Major, U. Montreal, Canada


More Keynotes to come!

In addition to keynotes our diverse program will include talks selected from submitted abstracts, our traditional after dinner speaker, daily discussion on important topics to this community, laptop software demos and poster sessions. Simply put, 3DSIG is the most comprehensive conference in the field and should not be missed by anyone using macromolecular structure to computationally unravel the mysteries of living systems.

 

Over the years, 3DSig has brought the leaders of the field of Structural Bioinformatics and Computational Biophysics in an ideal environment for personal contacts and discussions. The list of past keynotes includes: Ivet Bahar, Nir Ben-Tal, Phil Bourne, James U. Bowie, Steven Brenner, Wah Chiu, Cyrus Chothia, Charlotte Deane, Arne Elofsson, Dmitri Frishman, Nick Grishin, Kevin Karplus, Amy E. Keating, Tanja Kortemme, Gunnar von Heijne, Barry Honig, David Jones, Thomas Lengauer, Michael Levitt, George I. Makhatadze, John Moult, Klaus Mueller, Ruth Nussinov, Christine Orengo, Burkhard Rost, Rob Russell, Andrej Sali, Jeffrey Saven, Tamar Schlick, Torsten Schwede, Luis Serrano, Brian Schoichet, Kim A. Sharp, Manfred Sippl, Michael Sternberg, Joel Sussman, Devarajan Thirumalai, Janet Thornton, Anna Tramontano, Ron Unger, Alfonso Valencia, Sandor Vajda, Rebecca Wade, Haim Wolfson.

 

 
Relevant topics include:
  • Application of structure to systems biology
  • Structure-based drug discovery including polypharmacology and network pharmacology.
  • Structure representation, classification and prediction.
  • Macromolecular assemblies.
  • Structural genomics.
  • 3D databases and data mining.
  • Molecular visualization.
  • Relevant methods of structure determination, particularly hybrid methods.
  • Structure-based function prediction.
  • Evolution Studied through Structures.
  • Docking, analysis, prediction and simulation of biomolecular interactions such as protein-protein, protein-ligand and protein-nucleic acid.
  • Prediction and analysis of protein domains.
  • Membrane protein structure analysis and prediction.
  • Protein dynamics and disorder
  • The structural basis of immunology.
 We look forward to meeting you at 3Dsig
 
Organizers:
 
Program Chair
Philip E. Bourne
University of California San Diego

Rafael Najmanovich
Université de Sherbrooke, Canada
This email address is being protected from spambots. You need JavaScript enabled to view it. 

Ilan Samish
The Weizmann Institute
This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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CAMDA 2012 – Critical Assessment of Massive Data Analysis
URL: http://www.camda.info/
Date: Friday, July 13 – Saturday, July 14
Start time: 8:30 a.m. - 6:00 p.m.
Location: Hyatt Regency Long Beach Hotel (adjacent to Long Beach Convention Center)
Room: Regency Ballroom D
 
We cordially invite you to attend this year's CAMDA. See our Call for Papers, including the annual CAMDA challenge!
 
CAMDA was founded in 2000 to provide a forum for the critical assessment of different techniques used in large-scale data analysis in the life-sciences, such as for high-dimensional gene expression profiling.  It aims to establish the state-of-the-art in analysis methods, as well as identify progress and highlight promising directions for future efforts. To this end, CAMDA adopted the approach of a community-wide contest, with the scientific community analyzing the same data sets.  Researchers worldwide are invited to take the CAMDA challenge, which has become a prominent fixture (cf. Nature Methods 5, 569).  Accepted contributions are presented though talks and posters, and the results and methods of the different analyses are discussed and compared at the conference. Typically, well over 100 scientists join us each year.
 
The 2012 conference will focus on two challenge data sets:
1) The decoding of drug compatibility from an extremely large toxicology data set, and
2) The decoding of personal genomes.
 
CAMDA was founded by Simon Lin and Kimberly Johnson at Duke University (Nature 411, 885. Nature 424, 610). In 2006 CAMDA became a roving conference, with recent venues including Valencia, Chicago, and Vienna. For the past two years, the conference is run as an official satellite meeting of ISMB.
 
Important Dates:
Public release of Contest Data Set definition
20 Jan 2012
Extended Abstract Proposals Due
20 May 2012
Abstract deadline for Poster Submission
25 May 2012
Notification of accepted contributions
30 May 2012
Early registration closes
1 Jun 2012
CAMDA 2012 Conference
13–14 Jul 2012
ISMB 2012 Conference
15–17 Jul 2012
Full paper submission
17 Aug 2012
 
Organizers:
Joaquin Dopazo, CIPF, Spain, bioinfo.cipf.es
David Kreil, Boku University, Austria, www.bioinf.boku.ac.at
Simon Lin, Marshfield Clinic, U.S.A., www.marshfieldclinic.org/birc


Special Interest Group Meetings (SIGs)

Alternative Splicing - Integrative RNA Analysis and Disease (AS-SIG)
 
Date: Friday, July 13 - Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 201A – Long Beach Convention Center (LBCC)
 
The meeting for Integrative RNA Analysis and Disease is designed to bring together world experts in RNA processing, non-coding RNAs, and computation to discuss recent advances in the integrated view of RNA biology and its relation to human disease. We aim to bridge the gap between the different research fields in order to generate new research ideas for deciphering the regulation of RNA processing and its role in human disease. Moreover, as many of the studies involved rely heavily on clever computational approaches to analyze high-throughput data sets, we expect that the context of the ISMB conference and the participation of computational experts will give rise to fruitful interactions and will provide the basis for building a port for shared resources and tools in this fast developing field.
 
RNA processing involves complex and highly regulated mechanisms that affect many biological processes, such as cell type differentiation, sex-determination, or apoptosis. One important component of RNA processing  is alternative splicing (AS), by which pre-RNA can be spliced differently to produce different mRNA isoforms. Defects in either cis-acting regulatory elements or trans-acting factors that mediate alternative pre-mRNA processing can lead to aberrant mRNA isoform generation and even human disease. Additional components involved in RNA processing include alternative polyadenylation (APA) and the expression of many non-coding RNAs, such as micro-RNAs (miRNAs), small-interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), or long nuclear RNAs. 
 
While many of these phenomena have been studied separately, accumulating evidence now points towards the interplay between transcription, RNA processing, RNA turnover and the effects non-coding RNAs exert on these machineries. This interplay leads to a new, interconnected system view of gene expression regulation. In parallel, the advent of high-throughput methodologies enabled researchers to obtain genome-wide measurements of the make-up and the regulation of the transcriptome within a well-defined biological context. However, the complexity of these data also poses interpretation challenges, particularly when considering that the snapshot of the transcriptome that high-throughput methodologies permit us to obtain are the result of many integrated regulation processes.
 
In this meeting we aim to bring together world experts in the fields of RNA processing, non-coding RNAs, and computation to discuss recent advances in RNA biology and its relation to human disease. We hope the meeting will foster new interactions and help bridge the gap between researchers in the different fields.
 
Organizers:
Klemens Hertel , University of California, Irvine, United States,  s This email address is being protected from spambots. You need JavaScript enabled to view it.
Yoseph Barash , University of Pennsylvania, United States This email address is being protected from spambots. You need JavaScript enabled to view it.
Gene Yeo, University of California, San Diego, United States , This email address is being protected from spambots. You need JavaScript enabled to view it.
Eduardo Eyras, Pompeu Fabra University & ICREA, Spain, This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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Automated Function Prediction Special Interest Group (AFP-SIG)
 
URL: http://biofunctionprediction.org
Date: Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 202A – Long Beach Convention Center (LBCC)
 
Sequence and structure genomics have generated a wealth of data. However, extracting meaningful information from genomic data is becoming increasingly difficult. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just did not recognize that target for what it is: it is currently annotated as a "domain of unknown function".
 
The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
 
About the CAFA experiment
 
The problem: There are far too many proteins in the database for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence or structure. At the same time, how can we judge how well these function prediction algorithms are performing?
 
The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is a challenge designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. The first CAFA challenge was held in ISMB 2011 at Vienna and was highly successful. We will be holding discussions about the previous and the anticipated next CAFA challenge. This is a great opportunity to get involved with a rapidly-growing community. We always need more predictors, assessors, web-programmers and bioinformaticians.
 
Important Dates:
 
March 1, 2012: Call for Abstracts opens
April 13, 2012: Deadline for submitting abstracts
May 7, 2012: Notification of accepted talk abstracts emailed to authors
July 14, 2012: AFP 2012
July 15-17, 2012 ISMB 2012
 
Organizers:
Iddo Friedberg, Miami University, United States
Sean Mooney, Buck Institute for Aging Research, United States
Predrag Radivojac, Indiana University, United States
 
Contact: Iddo Friedberg This email address is being protected from spambots. You need JavaScript enabled to view it.
 
 
 
Bio-Ontologies SIG
Date: Friday, July 13 - Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 201B – Long Beach Convention Center (LBCC)
 
Description: The Bio-Ontologies SIG provides a forum for discussion of the latest and most innovative research in the appplication of ontologies and more generally the organization, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 14 years, making it one of the longest running. In addition to our usual focus on reports on newly developed Bio-Ontologies, and the use of ontologies in data sharing standards; this year we will focus on using ontologies for pre-competitive, translational research as well as data-driven approaches to evaluate ontologies.
 
Key dates (subject to change; Be sure to check back in January!)
 
Submissions Due: April 13th, 2012 (Fri)
Notifications: May 11th, 2012 (Fri)
Final Version Due: May 18th, 2012 (Fri)
Bio-Ontologies SIG: July 13th-14th, 2012 (Fri, Sat)
 
 
Organizers:
 
Nigam Shah, Stanford University, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Susanna-Assunta Sansone, University of Oxford, Oxford e-Research Center, United Kingdom, This email address is being protected from spambots. You need JavaScript enabled to view it.
Michel Dumontier, Carleton University, Canada, This email address is being protected from spambots. You need JavaScript enabled to view it.
Larisa Soldatova, University of Aberswyth, United Kingdom, This email address is being protected from spambots. You need JavaScript enabled to view it.

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.
 
 
Bioinformatics Software Interoperability SIG (BSI-SIG) - CANCELLED (as of June 5)
 
 
BOSC: The 13th Annual Bioinformatics Open Source Conference
Date: Friday, July 13 - Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 104A – Long Beach Convention Center (LBCC)
 
 
The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many open source bioinformatics packages are widely used by the research community across a wide range of application areas. They form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards.
 
Session topics:
  • Cloud and Parallel Computing
  • Genome-scale Data Management
  • Linked Data and Translational Knowledge Discovery
  • Software Interoperability
  • Bioinformatics Open Source Project Updates
  • Bioinformatics Paper Reviews: Open Standards and Standards of Openness (Panel Discussion)
Keynote speakers:
Jonathan Eisen (University of California, Davis)
Carole Goble (University of Manchester)

Organizers:
Nomi L. Harris (Chair); Jan Aerts, Brad Chapman, Peter Cock, Christopher Fields, Hilmar Lapp, Peter Rice
 
 
Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.
 
 
Biological Systems Design 2012: Models, Algorithms and Software for engineering life (BSD-SIG)
Date: Friday, July 13
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 202A – Long Beach Convention Center (LBCC)
 
 
The complexity of the genomic structure and our limited understanding of biological processes require new computational methods to investigate the huge number of possible designs for circuits, pathways, and entire genomes, with the ideal being the ability to model, simulate and redesign a biological system in-silicon prior to fabrication, similar to CAD/CAM for physical devices.
 
Synthetic Biology aims to establish a standard and effective biological design flow, where biological systems are designed and verified computationally, before in vitro synthesis and in vivo experiments. Each phase of this process has multiple challenges ranging from managing high-throughput laboratory operations to developing new software and defining accurate and interoperable computational models.
 
The Special Interest Group in Biological Systems Design (BSD) aims to provide a broad view of the current state-of-the-art for scientists from biology, chemistry, computer science, mathematics and engineering.
 
The SIG is structured in four sessions:
 
Genome Design. The availability of high-fidelity techniques for the synthesis of long DNA strands constitutes the starting point for effective pathway engineering. The aim of this session is to present state-of-the-art methods for genome design, focusing, but not limited to, the following topics: Oligo-nucleotides design, Probe and watermark design, High-throughput techniques, Theoretical aspects of DNA design.
 
Protein Design. An important purpose of synthetic DNA is to express non-native or human-designed proteins. Protein expression and design introduce additional complexities. This session provides a forum to discuss the recent advances in the field, with particular emphasis on the design of therapeutic peptides and proteins.
 
Computer Aided Design Tools. The design of biological systems is often characterized by ad hoc, human-centric procedures, which limit applications to small-scale problems. While Computer-Aided-Design (CAD) tools are standard in many engineering fields, CAD capabilities for synthetic biology are at a very early stage. This session gives a broad view of some emerging approaches in Biological Design Automation (BDA), with the aim of finding and discussing new areas where CAD tools can improve and accelerate the synthesis of living matter.
 
Data management & standards. The enormous amount of data generated by high-throughput techniques and synthesis processes requires the introduction of new and specific representation schemes, along with efficient and open standards for interfacing different data sources. New systems are also required to collect information and performing on-line data analysis. The aim of this session is twofold: first, exploring data structures and representations for synthetic biology; second, promoting and discussing use-case scenarios for the Synthetic Biology Open Language (SBOL).
 
Keynote Speakers:
  • Jef D. Boeke, Johns Hopkins University
  • Christodoulos A. Floudas, Princeton University
  • Dan Gusfield, UC Davis
  • Nathan J. Hillson, Joint BioEnergy Institute
  • Christina Smolke, Stanford University
Invited Speakers:
  • Jake Beal, BBN Technologies
  • Michal Galdzicki, University of Washington School of Medicine
  • Sarah Richardson, Joint Genome Institut
 
Submissions:
We encourage submissions in the form of talk and poster contributions; authors must submit a1-page abstract describing their work and the form of the contribution. Two blind reviewers will review each submission, and suggest the most appropriate form for presentation.
 
Key Dates:
  • Abstract Submission Due: April 30, 2012
  • Notification of acceptance: May 7, 2012
  • BSD-SIG: July 13, 2012
     
Organizers:

Joel S. Bader, Johns Hopkins University, Baltimore, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Douglas Densmore, Boston University, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Swapnil Prakash Bhatia, Boston University, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Giovanni Stracquadanio, Johns Hopkins University, Baltimore, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Schedule:
7.30-8.30 AM Registration
8.30-8.45 AM Welcome
   
8.45-9.30 AM Jef Boeke
Synthesizing and scrambling yeast chromosomes
9.30- 10.15 AM Chris Floudas
De Novo Design of Peptides, Proteins and Protein- Peptide Complexes
   
10.15-10.45AM Morning Coffee Break
   
10.45 - 11.30AM Christina Smolke
Designing synthetic regulatory RNAs: new tools for programming biological systems
   
11.30 AM - 11.50 AM D. Egen, J. Kelley, Z. Zhang and D. Lun
MOST: An open, flexible platform for efficient computer-aided design of cellular metabolism
11.50 AM - 12.10 PM Samuel Deutsch
Synthetic Metagenomics: Converting Digital Information Back to Biology
12.10 PM - 12.30 PM J. Carothers, J. Goler, D. Juminaga, F. Zhang and J. Keasling
Progress toward designing and engineering complex genetic control systems with quantitatively-predictable functions
12.30 - 1.130 PM Lunch
   
1.30 - 2.15 PM Dan Gusfield
Three Algorithmic Results that May be of Use in Synthetic Biology
2.15 - 3.00 PM           Nathan Hillson
DNA assembly design software and automation devices
   
3.30 - 4.00 PM Afternoon Coffee Break
   
4.00 - 4.25 PM Sarah Richardson
Algorithms for synthetic construct design
4.25 - 4.50 PM Aaron Adler
A Tool-Chain Approach to Predictive Design of Biological Circuits
4.50 - 5.15 PM Michal Galdzicki
Developing information exchange standards for synthetic biology
   
5.15 - 5.35 PM M. Marchisio and J. Stelling.
Gene circuit design with Parts and Pools 
5.35 - 5.55 PM N. Roehner and C. Myers
A Methodology to Annotate Systems Biology Markup Language (SBML) Models using the Synthetic Biology Open Language (SBOL) 
   
5.55 - 6.00 PM Closing Remarks
   
 

 

 

 

 

 

 
High Throughput Sequencing SIG (HiTSeq SIG)
URL:  www.hitseq.org
Date: Friday, July 13 - Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 104B – Long Beach Convention Center (LBCC)
 
The Conference on High Throughput Sequencing Methods and Applications (HiTSeq 2012) is a Satellite of the ISMB 2012 conference and brings together biologists and computational scientists interested in exploring the challenges and opportunities in the analysis of high-throughput sequencing (HTS) technologies. High Throughput Sequencing is revolutionizing the way biologists generate and analyze biological data. While in the past sequencing was used mainly to characterize individual genomes or transcripts, low-cost high-throughput sequencing can now address a broad range of genetic analysis applications including: comparative genomics, high-throughput polymorphism detection, analysis of coding and non-coding RNAs, identifying mutant genes in disease pathways, and profiling metagenomes. Some of the earlier “high-throughput” technologies, such as Illumina, and ABI SOLiD had compromised read length to increase throughput. Forthcoming, 3rd and 4th generation sequencing technologies are expected to have significantly longer reads, albeit at the cost of high error rates, while maintaining, or increasing the overall throughput.
 
While the promise of high throughput sequencing (HTS) technologies has become a reality, and computational methods for assembly, alignment, and variation detection using HTS reads are becoming available, there is still significant room to improve. Programs and algorithms developed for Sanger-style reads must be scaled, or completely reinvented to match the characteristics of the HTS data. And the diverse application of these platforms must take into account the special characteristics and source of errors of the original raw data to avoid potential pitfalls and false positives & negatives.
 
Suitable topics:
  • Detecting genome variation  
  • Disease association by HT sequencing  
  • Transcriptome Analysis   
  • Epigenomics and chromatin regulation   
  • 3rd or 4th generation sequencing data 
  • Cancer tumor sequencing data analysis  
  • Metagenomicss & microbiome analysis  
  • Proteogenomics 
  • HTS data compression & management 
  • Personal genomes & clinical applications (see special track)
 
New for this year: We will hold a special track on “Personal Genomes for Individualized Medicine”.
 
There is currently a surge in the sequencing of “personal” genomes (or exomes) with the intent of applying them in clinical decision-making. From the diagnosis of Mendelian and idiopathic diseases, the identification of somatic mutations in cancer tumors to guide therapy selection, to the prediction of susceptibility to complex disease to enable prophylactic actions, the applications of personal genomes herald an imminent change in how clinicians use genetic information in individualized medicine. Nevertheless, an analysis bottleneck is becoming apparent, and thus algorithms, methods, visualizations, and efficient software to handle the onslaught of medical genomic information are badly needed.
 
In this special track of HitSeq 2012 we aim to showcase new methods & tools that academic and industry researchers are developing for this area, and to encourage a vigorous discussion of what is needed to go forward. We are seeking paper and abstract submissions with an emphasis on analysis methods for the case when the sample size is n=1 (i.e. the patient), how to make genome sequence analysis efficient & clinical grade, as well as new techniques to summarize the wealth of genomic information for clinical decision-making. Applications ranging from childhood diseases, cancer therapeutics, and complex disease susceptibility are all welcome. This special track session will be held on the second day of the SIG, July 14.
 
Key Dates:
  • March 1 – Paper submission deadline
  • March 23 – ISMB paper re-submission deadline
  • March 25 – Author Notification
  • June 1 – Abstract submission deadline *updated
  • June 8  – Abstract and Oral/Poster Presentation Decisions *updated
  • June 30 – Late breaking poster deadline
  • July 13-14 - Special Interest Group Meeting
 
Please see the conference web site http://www.hitseq.org for more details.
 
Contact e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Organizers:
 
Gunnar Rätsch,
Sloan-Kettering Institute, United States

Francisco M. De La Vega
Stanford University, United States

Inanc Birol
British Columbia Cancer Agency, Canada

Sohrab Shah
British Columbia Cancer Agency


 
MS-SIG: Computational challenges in high-throughput proteomics
Date: Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 204 – Long Beach Convention Center (LBCC)
 
Proteomics, a rapidly advancing field, attempts to understand biological functions of an organism through the large-scale study of the expressed proteins. Studying the functions and interactions of all proteins in a given organism simultaneously is a challenging task. However, advanced mass spectrometry-based approaches, which generate a large amount of meaningful information, have taken us one step closer to achieve this goal. Currently, the community has the following four specific aspects (Liebler, D. C., 2000): 1) identifying all (or many) of the proteins in a sample, 2) profiling protein expression, 3) determining how proteins interact with each other in the living systems, and 4) identifying how and where proteins are modified. Considering the complexity and enormous size of mass spectrometry data, the role of bioinformatics in this field is critical.
 
Mass spectrometry based proteomics has been broadly applied to biomedical research in various areas. For example, in biology, a better insight into the nature of relationship between proteins and genes can be obtained using mass spectrometry and microarray data. Quantitative profiling of protein abundances and protein posttranslational modifications allows the identification of proteins associated with specific pathways or diseases. Novel candidate biomarkers for disease diagnosis and prognosis can be discovered using this technology. The success in applications heavily depends on good experimental design as well as sound methodology development. 
 
Noting that the importance of bioinformatics in this area, we want to discuss several challenges/issues in analyzing mass spectrometry based high throughput proteomics data. Our meeting contains three portions: oral presentation, panel discussion, and poster presentation. For oral presentation and panel discussion, we will invite experts and focus on the following specific themes:
 
  1. Label vs. label-free protein quantification
                                         i.    Reproducibility/Quality control/Missing data
                                        ii.    Protein abundance inference from peptide abundance
  1. Proteomics applications in biology and medicine
                                         i.    Experimental design
                                        ii.    Data integration (i.e. protein-gene association)
 
For the poster session, we invite abstract submissions on a wide range of topics about mass spectrometry data analysis (including topics listed above, but not limited to). The new challenge you share at the poster session might be the potential topic for the next year MS-SIG meeting. Please register for the MS-SIG meeting in order to attend this meeting.
 
Key Dates:
- Abstract Submissions are currently being accepted - please forward them to This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Coordinator:
Soyoung Ryu, Stanford University, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
 
 

 
 
Network Biology SIG: On the Analysis and Visualization of Networks in Biology (NetBio SIG)
Date: Friday, July 13
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 104C – Long Beach Convention Center (LBCC)
 
Biological networks provide a context for integrating and analyzing massive amounts of diverse kinds of measurement data, such as gene expression data from microarray experiments, protein abundance data from mass spectrometry, and genetic data from association studies. Network theory provides powerful analysis techniques that can be used to develop insights into large amounts of data. Our use of networks in biology has changed from purely representational and didactic purposes to more analytic and hypothesis formulation purposes. This shift has resulted, in part, from the confluence of advances in computation, informatics, and high throughput techniques in systems biology.
 
For interactions amongst thousands of genes, proteins, and metabolites, these networks can be quite large and complex. Network analysis tools can manage this complexity, for example by identifying clusters of activity – regions of high interconnectivity that are also characterized by high gene expression levels. The most highly connected molecules or hubs of such regions may be control points for the network; modulating their activity may influence the activity of many other molecules. With knowledge of the structure and behavior of biological networks, biologists can identify intervention points for drugs and therapeutics, limit adverse side-effects of treatments, and infer predisposition to disease.
 
We are soliciting abstracts that cover new developments in network biology. The SIG will focus on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology, synthetic biology and medicine. The SIG will provide a unique meeting space for tool developers and users in the field of network biology. Through these complementary lenses, the SIG will bring into focus the current state of the field, its future promise and how to get there.
 
Keynote Speakers:

Chris Evelo - Head of Department of Bioinformatics, BiGCaT at Maastricht University, NL
Hiroaki Kitano - Director of Systems Biology Institute in Tokyo; Professor, Okinawa Institute of Science and Technology Graduate University
Chris Sander - Chair of Computational Biology at Sloan-Kettering Institute
Josh Stuart  - Assoc. Professor of Biomedical Engineering at UC Santa Cruz

Abstract Submission:

Due April 9: Click to submit
 
Organizers:
Alexander Pico, Gladstone Institutes, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Scooter Morris, University of California, San Francisco, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Allan Kuchinsky, Agilent Technologies, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Gary Bader, University of Toronto, Canada, This email address is being protected from spambots. You need JavaScript enabled to view it.
Mario Albrecht, Max Planck Institut, Germany, This email address is being protected from spambots. You need JavaScript enabled to view it.
Ian Donaldson, University of Oslo, Norway, This email address is being protected from spambots. You need JavaScript enabled to view it.
Natasa Przulj, Imperial College London, United Kingdom, This email address is being protected from spambots. You need JavaScript enabled to view it.
Esti Yeger Lotem, National Institute for Biotechnology in the Negev, Israel, This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Regulatory Genomics Special Interest Group – RegGenSIG
Date:  Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 104C – Long Beach Convention Center (LBCC)
 
Regulatory genomics involves the study of the genomic ‘control system,’ which determines how, when and where to activate the ‘blueprint’ encoded in the genome. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the ISMB Regulatory Genomics Special Interest Group - RegGenSIG - focuses on bioinformatics for regulatory genomics. An important goal of the SIG is to foster a collaborative community wherein scientists convene to discuss difficult research problems in all areas of computational regulatory genomics.
 
RegGenSIG 2012 will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research, and a joint panel discussion with the Alternative Splicing SIG. RegGenSIG will bring together experts in experimental methods and computational methods to consider sequence-based reconstruction of regulatory networks and prediction of gene expression. Topics to be addressed in the SIG include the following
·         inference of gene regulatory networks,
·         utilization of information pertaining to epigenetics, chromatin structure, and histone modifications,
·         determination of the roles of regulatory RNAs,
·         prediction of transcriptional regulation from RNA-seq data and ChIP-seq data,
·         pattern discovery in sequences, and
·         sequence based modeling of gene expression.
 
ABSTRACT SUBMISSION: 
To make an oral presentation at RegGenSIG, extended abstracts (2-3 pages) should be submitted by April 27, 2012.   Based on the submitted abstracts, each author will be invited to make either an oral presentation or a poster presentation. Authors will be notified by May 11, 2012. 
For poster presentations, authors should submit a 250 word abstract no later than May 18, 2012. Author notification will occur no later than May 25, 2012.
KEY DATES for RegGenSIG
 
April 27, 2012
Due date for extended abstracts (2-3 pages) for oral presentations
May 11, 2012
Author notification for oral presentations
May 18, 2012
Due date for short abstracts (250 words) for poster presentations
May 25, 2012
Author notification for poster presentations
June 1, 2012
Early registration cut-off date
July 14, 2012
RegGenSIG meeting
 
 
Confirmed Speakers:
Harmen Bussemaker, Columbia University, United States
Roderic Guigo, Center for Genomic Regulation, Spain
Alexander Hartemink, Duke University, United States
William Noble, University of Washington, United States (tentative)
Isidore Rigoutsos, Thomas Jefferson University, United States
Saurabh Sinha, University of Illinois, United States
Andrew Smith, University of Southern California, United States
Gary Stormo, Washington University, Saint Louis, United States
Andrei Thomas-Tikhonenko, University of Pennsylvania, USA
Wei Wang, University of California, San Diego, United States
Qing Zhou, University of California, Los Angeles, United States
Igor Zwir, University of Granada, Spain
 
SIG Chairs:
Finn Drabløs, Norwegian Univ. of Science and Technology, Norway, This email address is being protected from spambots. You need JavaScript enabled to view it.
Kathleen Marchal, Univ Ghent/K.U. Leuven, Belgium, This email address is being protected from spambots. You need JavaScript enabled to view it.
Isidore Rigoutsos, Thomas Jefferson University, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Saurabh Sinha, University of Illinois, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Lonnie R. Welch, Ohio University, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Organizers:
Tim Bailey, University of Queensland, Australia
Benoit Ballester, European Bioinformatics Institute, United Kingdom
Laura Elnitski, National Human Genome Research Institute, United States
Ana Teresa Freitas, Technical University of Lisbon, Portugal
Roderic Guigo, Centre for Genomic Regulation, Spain
Tim Hubbard, Wellcome Trust Sanger Institute, United Kingdom
Manolis Kellis, MIT, United States
Sophie Schbath, Institut National de la Recherché Agronomique, France
Gary Stormo, Washington University, United States
Esko Ukkonen, University of Helsinki, Finland
Martin Vingron, Max Planck Institute for Molecular Genetics, Germany
Weixiong Zhang, Washington University, United States
 
 
SNP- SIG
Date: Saturday, July 14
Start time: 8:30 a.m. - End time: 6:00 p.m.
Room Location: 202B/C – Long Beach Convention Center (LBCC)
 
The primary goal of the SNP-SIG is to outline and discuss the recent advances in the methodology for the annotation and analysis of genomic variation data.
 
SNPs are generally very interesting in the context of their phenotypic manifestations. The discrepancy between the significant availability of SNP data and the current lack of its interpretation requires the development of methods for the annotation/prediction of the SNP impact. Direct-to-consumer (DTC) companies, such as 23andMe and Navigenics, offer DNA tests to provide insight on the genetic traits. In the near future the analysis of genetic variation will be a key factor for the understanding of the information encoded in the genome
 
The SNP-SIG provides a forum for the organization of a research network facilitating the exchange of ideas and the establishment of new collaborations bringing together varying expertise. It will thus support the unprecedented collaborative effort to manage the complexity of the analysis and evaluation of genetic variation.
 
This year’s SIG will be divided into two sessions - “SNPs as markers: evolution, populations, GWAS” and “SNPs as effectors: function, structure, and regulation”. For detailed information please see the SIG website.
 
We are interested in attracting submissions describing original work in all the fields of genomic variation research including, but not limited to:
·         Databases, data mining algorithms and visualization tools for SNP analysis.
·         Methods for predicting regulatory/structural/functional impacts of SNPs
·         Personal Genomics, GWAS studies and SNP prioritization
·         Population genomics and phylogenetic analysis
 
Deadlines:
Poster Abstract submissions: March 16th, 2012 URL: https://www.iscb.org/submissions/index.php?id=116
Presentation Proposal submissions: March 26th, 2012 URL: https://www.easychair.org/account/signin.cgi?conf=snpsigismb2012
 
 
Organizers:
Yana Bromberg, Rutgers University, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Emidio Capriotti, University of Balearic Islands, Spain, This email address is being protected from spambots. You need JavaScript enabled to view it.
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