ISMB 2014 Special Interest Groups (SIGs) & Satellite Meetings (SMs)

 

Satellite Meetings

 

SIGS

 

ISMB 2014 will hold a number of one and two-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.

Program information and registration details are noted below. To inquire about the possibility of forming a new SIG for ISMB/ECCB 2015 or beyond, please address your inquiry to This email address is being protected from spambots. You need JavaScript enabled to view it.

 

One-Day SIGs – Friday, July 11, 2014

Integrative RNA Biology SIG (IRB-SIG)

NetBio SIG

 

One-Day SIGs – Saturday, July 12, 2014

Mass Spectrometry SIG (MS-SIG)

New Challenges in Computational Single Cell Biology

Regulatory Genomics Special Interest Group (RegGenSIG)

Vari SIG (formerly SNP-SIG)

 

 

Two-Day SIGs – Friday, July 11 and Saturday, July 12, 2014

Automated Function Prediction (AFP-SIG)

Bio-Ontologies

BioVis SIG

BOSC:15th Annual Bioinformatics Open Source Conference

HitSEQ: High Throughput Sequencing Algorithms & Applications

 

 

Satellite Meetings

 

3Dsig: Structural Bioinformatics & Computational Biophysics

URL: http://bcb.med.usherbrooke.ca/3dsig14

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 210

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. This year we are celebrating our 10th meeting and highlighting the 2013 Nobel prize in Chemistry awarded to Martin Karplus, Michael Levitt & Arieh Warshel, the pioneers of the field.

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: Russ Altman, Patricia Babbitt, Ivet Bahar, Nir Ben-Tal, Tom Blundell, Phil Bourne, James U. Bowie, Steven Brenner, Janusz Bujnicki, Stephen Burley, Wah Chiu, Cyrus Chothia, Charlotte Deane, Keith Dunker, Arne Elofsson, Dmitrij Frishman, Adam Godzik, David Goodsell, Nick Grishin, Kevin Karplus, Amy E. Keating, Tanja Kortemme, Gunnar von Heijne, Barry Honig, David Jones, Thomas Lengauer, Michael Levitt, Olivier Lichtarge, Andrei Lupas, François Major, George I. Makhatadze, John Moult, Klaus Mueller, Ruth Nussinov, Arthur Olson, Christine Orengo, Robert Preissner, Burkhard Rost, Rob Russell, Andrej Sali, Chris Sander, Jeffrey Saven, Tamar Schlick, Torsten Schwede, Luis Serrano, Brian Schoichet, Michael Schroeder, 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, Ada Yonath.

Abstract submission deadline: April 30, 2014

Relevant topics include:

We look forward to meeting you at 3Dsig

Philip E. Bourne
Associate Director for Data Science, National Institutes of Health, Bethesda, United States
This email address is being protected from spambots. You need JavaScript enabled to view it.

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 of Science; and
Braude College of Engineering, Israel
This email address is being protected from spambots. You need JavaScript enabled to view it.

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CAMDA 2014 Critical Assessment of Massive Data Analysis

URL: http://www.camda.info/

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 209

Currently, the Big Data explosion is the grand challenge in life sciences. Analyzing large data sets is emerging to one of the scientific key techniques in the post genomic era. Still the data analysis bottleneck prevents new biotechnologies from providing new medical and biological insights in  a larger scale. This trend towards the need for analyzing massive data sets is further accelerated by novel high throughput sequencing technologies and the increasing size of biomedical studies. CAMDA focuses on the analysis and integration of the massive data sets in life sciences. It provides new approaches and solutions to the big data problem, presents new techniques in the field of  bioinformatics, data analysis, and statistics for handling and processing large data sets.

CAMDA focuses on the specific challenges and opportunities in the analysis of the massive data sets that are increasingly produced in several fields of the life sciences. The conference offers researchers from the computer sciences, statistics, molecular biology, and other fields a unique opportunity to benefit from a critical comparative evaluation of the latest approaches in the analysis of life science's "Big Data".

This year, CAMDA's scientific committee set up three challenges to integrate multi-track -omics data:
1. dual dose response profiles for 14 unknown and 2 known compounds from the InnoMed PredTox project of the EU FP7 program;
2. selected cancers from International Cancer Genome Consortium (ICGC), and;
3. the prediction of drug compatibility from an extremely large toxicogenomic data set.

We cordially invite you to attend this year's CAMDA.

Keynotes:
Chris Sander, Memorial Sloan-Kettering Cancer Center, NY, USA
Temple F. Smith, Boston University, MA, USA
Jun Wang, Beijing Genomics Institute (BGI), Shenzhen, China

Key dates:
Extended Abstract Proposals Due May 20, 2014
Abstract Deadline for Poster Submission May 25, 2014
Notification of Accepted Contributions May 30, 2014
Early Registration Closes June 6, 2014
CAMDA 2014 July 11 & 12, 2014
Full Paper Submission: Aug 25,  2014

Organizers:
Djork-Arné Clevert, JKU Linz, Austria, This email address is being protected from spambots. You need JavaScript enabled to view it.
Joaquin Dopazo, CIPF, Spain, This email address is being protected from spambots. You need JavaScript enabled to view it.
Lan Hu, Dan-Farber Cancer Institute, U.S.A., This email address is being protected from spambots. You need JavaScript enabled to view it.
David Kreil, Boku University, Austria, This email address is being protected from spambots. You need JavaScript enabled to view it.
Simon Lin, Marchfield Clinic, USA, 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.

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SIG Meetings

 

Automated Function Prediction (AFP-SIG)

URL: http://biofunctionprediction.org

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 201

The Automated Function Prediction Special Interest Group (AFP-SIG)

The accurate annotation of protein function is key to understanding life at the molecular level. However, with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available. The computational annotation of protein function has therefore emerged as a problem at the forefront of bioinformatics. Recently, the availability of genomic-level sequence information for thousands of species, coupled with massive high-throughput experimental data, has created new opportunities as well as challenges for function prediction. Many methodologies have been developed by research groups worldwide, many based in comparing unsolved sequences with databases of proteins whose functions are known. Other methods aim at mining the scientific literature associated with some of these proteins, yet others combine sophisticated machine-learning algorithms with an understanding of biological processes to decipher what these proteins do. Indeed, we may have already identified a protein that is an ideal drug target for cancer, but it is lost in the myriad of data labeled as "function unknown".

The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists, experimental biologists, and biocurators who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations. The AFP-SIG holds annual meetings alongside the ISMB. This year, we are also conducting a multi-year Critical Assessment of Functional Annotation, or CAFA, experiment.

 

About the CAFA experiment

The problem: There are far too many proteins in the databases for which the sequence and various other information are known, but the function is not. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence, structure, or other data. At the same time, how can we judge how well these function prediction algorithms are performing and whether they are useful for experimental scientists?

Our approach: The Critical Assessment of protein Function Annotation (CAFA) is a challenge designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. The first CAFA challenge took place between September 2010 and January 2011 with an initial evaluation meeting held at AFP-SIG during ISMB 2011 in Vienna. The experiment and the associated meeting were highly successful – resulting in 15 peer-reviewed publications and an overview article published in Nature Methods. The CAFA 2 experiment has been running since September 2013, and the methods will be initially evaluated during the second day of AFP-SIG 2014 in Boston. Among the new challenges for CAFA 2 are the prediction of subcellular localization and the prediction of human phenotypes. We will also provide a re-assessment of the prediction accuracy from the 2010-2011 CAFA experiment, now on a significantly larger number of protein targets.

 

Important Dates:

March 1, 2014: Call for Abstracts (talks & posters) Open

April 4, 2014: Deadline for Submitting Abstracts

July 11-12, 2014: AFP/CAFA 2014, Boston, MA USA.

July 12-16, 2014: ISMB 2014, Boston, MA USA.

 

Keynote speakers:

Philip E. Bourne, Associate Director for Data Science, National Institutes of Health, Bethesda, United States

Fiona Brinkman, Simon Fraser University, Canada

Mark Gerstein, Yale University, United States

 

Organizers:

Iddo Friedberg, Miami University Oxford, USA

Michal Linial, the Hebrew University of Jerusalem, Israel

Sean Mooney, Buck Institute for Research on Aging, USA

Predrag Radivojac, Indiana University, Bloomington, USA

 

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Bio-Ontologies

URLwww.bio-ontologies.org.uk

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 204

 

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 organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 17 years, making it one of the longest running.

 

Key Dates

April 11th, 2014 Submissions Due
May 9th, 2014 Notifications
May 16th, 2014 Final Version Due
 The 2014 meeting will be a two day SIG, with July 12th being the “Phenotype Day” which will be a joint session with the Bio-Link SIG (watch out for the special announcements!).  Papers are invited in areas, such as the applications of bio-ontologies, newly developed bio-ontologies, and the use of ontologies in data sharing standards. Example topics include (but not limited to):
 
Applications of ontologies in bioinformatics
Hypothesis Testing Platforms
Use of Ontologies in Phenotype representation
"Flash updates" on Newly Developed or Existing Bio-Ontologies
Bio-Curation Platforms
Automated Annotation Pipelines
Efforts using ontologies for Bio-NLP or Information Retrieval
Semantic Web Enabled Applications
Role of Bio-Ontologies in Health 2.0
 
Advances in development of biomedical ontologies
Collaborative Ontology Authoring and Peer-Review Mechanisms
Automated Ontology Learning
Mapping between Ontologies 
Research in Ontology Evaluation
Using games for Ontology review and evaluation
 
Organizers:
Nigam Shah, Stanford University, United States,This email address is being protected from spambots. You need JavaScript enabled to view it.
Michel Dumontier, Stanford University, United States,This email address is being protected from spambots. You need JavaScript enabled to view it.
Larisa Soldatova, Brunel University, United Kingdom,This email address is being protected from spambots. You need JavaScript enabled to view it.
Philippe Rocca-Serra, University of Oxford, United Kingdom,This email address is being protected from spambots. You need JavaScript enabled to view it.
 
Phenotype Day co-ordinators: Nigel Collier, Anika Oellrich, and Tudor Groza
 
Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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BioVis SIG: 4th Symposium on Biological Data Visualization

URL: http://biovis.net

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 202

 

The rapidly expanding field of biology creates enormous challenges for computational visualization techniques for enabling researchers to gain insight from their large and highly complex data sets.

The Symposium on Biological Data Visualization (BioVis) is the premier international and interdisciplinary event for all aspects of visualization in biology. The symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. The full call for participation can be found at  http://biovis.net/year/2014/info/cfp.

Options for participation include:

1) Papers:
submit high quality research; published in the symposium proceedings; oral presentation at the symposium;
all accepted manuscripts will be available through the IEEE Digital Library
selected papers will be considered for publication in BMC Bioinformatics

2) Posters:
work in progress and preliminary results; submissions consists of a 250 abstract and an image; previously published work from other venues; visualization challenges

3) Data Contest:
create a visualization (tool) that help identify and understand which rs-fMRI networks, from a large provided dataset, are replicates derived from the same individuals; submit a 2-page extended abstract

 

4) Redesign Contest:
submit a redesigned figure utilizing effective encodings and clear
visual communication to display an improved version of a well-known
biological data visualization


Key Dates: (all deadlines are 5:00pm PDT)

March 15, 2014 – Full manuscript uploaded to submission site
April 17, 2014 – Preliminary notification full manuscript
May 10, 2014 – Revised manuscript submission
June 1, 2014 – Final Notification for full manuscript

Other Deadlines:

May 1, 2014   - Submission deadline for the Data Contest
May 1, 2014   - Submission deadline for the Redesign Contest
May 24, 2014  - Poster abstract uploaded to submission site


General chairs:

 - Kay Nieselt, University of Tübingen, Germany
 - Jos Roerdink, University of Groningen, The Netherlands

For the full committee, see http://www.biovis.net/year/2014/info/committee

Contact:

This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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BOSC: 15th Annual Bioinformatics Open Source Conference

URL: http://www.open-bio.org/wiki/BOSC_2014

Schedule:  http://www.open-bio.org/wiki/BOSC_2014_Schedule

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 203

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation, a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. BOSC covers the wide range of open source bioinformatics software packages that have been successfully developed and adopted by the community, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of open source bioinformatics software and open science, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.

Key dates: 

March 1, 2014: Call for abstracts open 
April 4, 2014: Deadline for submitting abstracts 
July 11-12, 2014: BOSC 2014, Boston, MA 

Session topics: 
Open Science and Reproducible Research 
Software Interoperability 
Genome-scale Data and Beyond 
Visualization 
Translational Bioinformatics 
Bioinformatics Open Source Libraries and Projects 
Reproducibility: Rewards and Challenges (Panel discussion) 

Keynote speakers: 
Philip E. Bourne, Associate Director for Data Science, National Institutes of Health, Bethesda, United States
C. Titus Brown, Michigan State University, United States

BOSC 2014 Co-Chairs: 
Peter Cock (Biopython developer; James Hutton Institute) 
Nomi L. Harris (Lawrence Berkeley National Laboratory) 
Organizing Committe members: 
Raoul Jean Pierre Bonnal (Istituto Nazionale Genetica Molecolare (National Institute of Molecular Genetics), Italy) 
Brad Chapman (Biopython developer; Harvard School of Public Health) 
Robert Davey (The Genome Analysis Centre) 
Christopher Fields (National Center for Supercomputing Applications) 
Hans-Rudolf Hotz (Friedrich Miescher Institute for Biomedical Research) 
Hilmar Lapp (National Evolutionary Synthesis Center)

 

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HitSEQ: High Throughput Sequencing Algorithms & Applications

URL: http://hitseq.org

Date: Friday, July 11 & Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 200

 

The Conference on High Throughput Sequencing Methods and Applications (HiTSeq 2014) is a Satellite of the ISMB 2014 conference and brings together biologists and computational scientists interested in exploring the challenges and opportunities in the analysis of high-throughput sequencing (HTS) technologies. HiTSeq 2014 is devoted to the latest advances in computational techniques for the analysis of high-throughput sequencing data including novel algorithms, analysis methods and applications in biology where high-throughput sequencing data has been transformative. It provides a forum for in depth presentations of novel algorithms, analysis methods, and applications in multiple areas of biology that HTS is transforming. HiTSeq seeks full papers submissions to be peer-reviewed. If accepted, these contributions will be presented at the conference and published online. Short abstract submissions will be also accepted for either brief oral presentations or posters.

 

Possible Topics include:

We are soliciting high-quality papers on any of the topics of interest that will go through rigorous peer-review. Simultaneously HiTSeq also allows for the submission of abstracts, which will be evaluated independently for the conference proceedings. Abstracts for consideration should be one page.

 

Key Dates/Deadlines:

 

Organizers:

Ana Conesa, Ph.D.
Centro de Investigación Príncipe Felipe Valencia, Spain

Francisco M. De La Vega, D.Sc.
Stanford University, Stanford CA, USA

Dirk J. Evers, Ph.D.
Molecular Health GmbH, Heidelberg, Germany

Gunnar Rätsch, Ph.D.
Memorial Sloan-Kettering Cancer Center, New York, NY, USA

Kjong-Van Lehmann, Ph.D.
Memorial Sloan-Kettering Cancer Center, New York, NY, USA

 

 

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Integrative RNA Biology - SIG (IRB-SIG)

URL: http://www.irbgroup.org/irb-sig-14/

Date: Friday, July 11

Start Time: 8:30 a.m - 6:00 p.m.

Room: 206

The meeting for Integrative RNA Biology is focused on deriving new RNA Biology using a combination of computational and experimental techniques. The meeting is designed to bring computational experts attending ISMB together with world experts in different aspects of RNA processing.

Many computational challenges are involved in the study of RNA, ranging from quantifying gene isoforms and secondary structure modelling, to detecting miRNA regulatory networks and deciphering splicing regulation. 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. Other components involved in RNA processing that have gained much research attention 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 computational experts attending ISMB together with world experts in the fields of RNA processing and non-coding RNAs to discuss recent advances in RNA biology and related computational and experimental methodology. 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,  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.
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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Mass Spectrometry SIG (MS-SIG)

URL: http://igenomed2.stanford.edu/BeyondProteomics_2014/

Date: Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 205

 

MS-SIG aims to bring together experts from the global research community to discuss current progress and challenges in the field of mass spectrometry based proteomics and computational biology. Our meeting will contain three portions: oral presentation, panel discussion, and poster presentation. We invite abstract submissions on a wide range of topics list below. The poster
session will provide an opportunity to present your work in an informal setting. We will also have a limited number of talks selected from abstracts slots in the program.

 

Expected sessions/topics with explanation:

Session I: Current developments in computation of mass spectrometry data

  1. Protein detection, e.g. standards and pipelines, de novo identification
  2. Protein characterization, e.g. site-specific protein modification
  3. Protein quantification, e.g. selected reaction monitoring (SRM), SWATH-MS, label-free vs labelling approach

Session II: Challenges in proteomic applications in biology and medicine

  1. Method developments for population proteomics, e.g. experimental design, analysis of data from large number of samples of a study
  2. Analysis of interaction networks and protein complexes using mass spectrometry
  3. Integration of multiple mass spectrometry studies
  4. Integrative analysis of proteomics and other omics data for biology and medicine


Key Dates:
1st abstract deadline: 05/05/14 (Monday)
1st notification date: 05/12/14 (Monday)
2nd abstract deadline: 05/12/14 (Monday)
2nd notification date: 05/19/14 (Monday)

Organizers:
Alexey I. Nesvizhskii (This email address is being protected from spambots. You need JavaScript enabled to view it.), University of Michigan, United States
Wenzhong Xiao (This email address is being protected from spambots. You need JavaScript enabled to view it.), Massachusetts General Hospital and Harvard Medical
School, United States
Peng Li (This email address is being protected from spambots. You need JavaScript enabled to view it.), East China Normal University, China

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NetBio SIG

URLhttp://nrnb.org/netbiosig/

Date: Friday, July 11

Start Time: 8:30 a.m - 6:00 p.m.

Room: 207

Biological networks provide a context for integrating and analyzing massive amounts of diverse kinds of measurement data, such as expression data from RNA-Seq, protein abundance  and interaction 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.

We will solicit abstracts that cover new developments in network biology, focusing 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 meeting will provide a unique meeting space for tool developers and users in the field of network biology. Through these complementary lenses, the meeting will bring into focus the current state of the field, its future promise and how to get there.

 

How to Participate:

Find the latest information including how to submit an abstract for the upcoming NetBio community meeting.  In addition to the annual meeting, the NetBio group functions year-round as an international virtual community supporting and co-organizing multiple meetings, connecting researchers, results, resources and training opportunities. Find out more via the NetBio Group at LinkedIn.

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.
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.
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.
Frank Kramer, University Medical Center Göttingen, Germany, This email address is being protected from spambots. You need JavaScript enabled to view it.
Martina Kutmon, University of Maastricht, The Netherlands, This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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New Challenges in Computational Single Cell Biology

URL:

Date: Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 206

 

Single cell technologies are transforming biological research and give rise to a new breed of challenges in computational biology.
Recent advances in single cell biology have lead to dramatic improvements in the ability to monitor biological systems in terms of temporal, spatial and molecular resolution at the single cell level. Single cell proteome profiling approaches are capable of jointly monitoring up to 100 different markers. While single cell transcriptomics approaches routinely allow to monitor this amount of transcripts, new sequencing techniques are enable researchers to evaluate whole transcriptomes and genomes for single cells. These improvements enable to acquire informative data about phenotypes of multicellular organisms that result from an intricate dynamic interplay of heterogeneous cell populations. These technologies are driving a systems level characterization of complex diseases such as cancer that feature a disruption of this interplay or itself are the result of a pathologically altered cell population. Single cell technologies are enabling comprehensive molecular and functional characterization of such heterogeneous cell populations and will therefore constitute a cornerstone of a systems-level understanding of complex biological systems, their pathological alterations and opens the perspective to rationally specify novel therapeutic targets.

The complexity of the data acquired by these technologies require computational approaches to perform inference of systems level models of the underlying biological systems. Single cell resolved data of heterogeneous cell populations lends itself to computationally define cell types in a data driven way and thereby opening the perspective to discover novel functionally relevant cell types. The marker breadth represented in this data still poses big challenges to the development of suitable clustering and dimensionality reduction techniques. The analysis of single cell time series experiments has elicited a flurry of modeling approaches for the temporal dynamics of intracellular signaling and transcription networks that range from probabilistic graphical models to deterministic and stochastic dynamical systems. Furthermore, computational approaches have enabled researchers to exploit single cell resolved data to infer intrinsic and extrinsic cell-to-cell variability phenomena in apparently homogeneous cell populations. In summary, single cell technologies enable novel insights on the single cell and cell population level, but at the same time give rise to a diverse spectrum of computational challenges whose solution are combining and will continue to combine concepts from the fields of statistics, machine learning and dynamical systems theory.
 
Abstract submission
High quality abstracts will be reviewed and selected to be presented in poster format at the SIG meeting. Additionally, the top 7 abstracts will be invited for oral presentation. Please submit your abstract under:
https://www.easychair.org/conferences/?conf=sigcscb2014
 
Key dates:
March 1, 2014: Call for abstracts open
May 15, 2014: Abstract submission deadline
June 1, 2014: Acceptance notification

Keynote speakers:
Garry Nolan, Stanford University
Tobias Meyer, Stanford University
Mustafa Khammash, ETH Zurich
Daniel Gerlich, IMBA Vienna
Timm Schröder, ETH Zurich
Matthias Meier, University of Freiburg
Matthias Peter, ETH Zurich
Tomer Kalisky, Bar Ilan University
Fabian Theis, Technical University of Munich

Organizers:
Manfred Claassen, ETH Zurich, Switzerland. This email address is being protected from spambots. You need JavaScript enabled to view it.
Bernd Bodenmiller, University of Zurich, Switzerland. This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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Regulatory Genomics Special Interest Group (RegGenSIG)

URL: http://light.ece.ohio.edu/~reggen/2014/

Date: Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 208

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 RegGenSIG meeting focuses on bioinformatics for regulatory genomics.  An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics. 

 

RegGenSIG will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research. The goal is to 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:

  1. inference of gene regulatory networks;
  2. utilization of information pertaining to epigenetics, chromatin structure, and histone modifications;
  3. determination of the roles of regulatory RNAs;
  4. prediction of transcriptional regulation from RNA-seq data and ChIP-seq data;
  5. pattern discovery in sequences; and
  6. 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, 2014. 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 1, 2014. For poster presentations, authors should submit a 250 word abstract no later than May 18, 2014. Author notification will occur no later than May 25, 2014.

 

KEY DATES

 

April 27, 2014 - Due date for extended abstracts (2-3 pages) for oral presentations

May 1, 2014 - Author notification for oral presentations

May 18, 2014 - Due date for short abstracts (250 words) for poster presentations

May 25, 2014 - Author notification for poster presentations

June 6, 2014 - Early registration cut-off date

July 12, 2014 - RegGenSIG meeting

 

SIG CHAIRS

 

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Vari SIG (formerly SNP-SIG)

URL: http://varisig.biofold.org

Date: Saturday, July 12

Start Time: 8:30 a.m - 6:00 p.m.

Room: 207

 

The primary goal of the VarI-SIG is to outline and discuss the recent advances in the methodology for the annotation and analysis of genomic variation data.
Genetic variants are generally very interesting in the context of their phenotypic manifestations. The discrepancy between the significant availability of SNV data and the current lack of its interpretation requires the development of methods for the annotation/prediction of the genetic variant impact. 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 VarI-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.
The SIG will be divided into two sessions - "SNVs as markers: evolution, populations, GWAS" and "Genetic variants  as effectors: function, structure, and regulation". For detailed information please see the SIG website.
We are interested in submissions describing original work in all the fields of genomic variation research including, but not limited to:


ABSTRACT SUBMISSION:
VarI-SIG accepts submissions for presentation proposals (2-3 pages) and poster abstracts.
Both contributions should be submitted by April 6, 2014. Acceptance notification will be sent
out by April 20, 2014.
Abstract should be submitted through EasyChair using the following URL
https://www.easychair.org/conferences/?conf=varisig2014

KEY DATES
April 6, 2014 - Poster Abstract and Presentation Proposal submissions deadline
April 20, 2014 - Poster and Presentation Proposal acceptance notifications.
April 26, 2014 - Preliminary SIG Program Available
May 9, 2014 - Complete SIG Program Available
June 6, 2014 - Early registration cut-off date
July 12, 2014 - Vari-SIG meeting

SIG CHAIRS
    • Yana Bromberg, Rutgers University, USA
    • Emidio Capriotti, University of Alabama, USA

 

 

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