Pacific Symposium on Biocomputing workshop on cellular heterogeneity

July 31, 2012 § Leave a comment

The Pacific Symposium on Biocomputing will be held on the Big Island of Hawaii from January 3 to 7, 2013, and our very own Eric Batchelor (well, he used to be ours) is co-organizing the workshop described below.  You can submit abstracts here (requires sign-up).

PSB 2013 Workshop: Modeling cell heterogeneity: from single-cell variations to mixed cell populations

Co-chairs: Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Ben Raphael, and Damian Wojtowicz

CALL FOR PARTICIPATION:

Short description:

Emerging technologies such as single cell gene expression analysis and single cell genome sequencing provide an unprecedented opportunity to quantitatively probe biological interactions at the single cell level. This new level of insight has begun to reveal a more accurate picture of cellular behavior, and to highlight the importance of understanding cellular variation in a wide range of biological contexts. The aim of this workshop is to bring together researchers working on identifying and modeling cell heterogeneity that arises by a variety of mechanisms, including but not limited to cell-to-cell noise, cell-state switches and cell differentiation, heterogeneity in immune responses, cancer evolution, and heterogeneity in disease progression. We will welcome algorithms to process single-cell experimental data and to provide a system-level view of the interplay of diverse, fluctuating biological components.

Call for participation:

Quantifying the molecular mechanisms underlying cellular behaviors and functions is one of the ultimate goals of biology and medicine. Until recently, most characterization of cellular behavior has been performed on the average of all cells in a sample instead of on individual cells. However, measurements derived from pooled populations of cells can mask the true behavior of individual cells and lack the specificity to capture outlier cell behavior that might explain cell differentiation and transitions from normal to disease cellular states.

Emerging technologies such as single cell gene expression analysis and single cell genome sequencing provide an unprecedented opportunity to quantify single cell level differences. These technologies will provide a wealth of new information at single-cell resolution,  including protein abundance, methylation patterns, promoter structure, gene expression, copy number variations, gene function and essentiality, DNA structure, evolutionary plasticity, and selective advantage.  These data can all be leveraged in the quest to understand the emergence and consequences of cell heterogeneity.

The focus of this section is on identifying and modeling cell heterogeneity that arises by any of the above-mentioned mechanisms – sporadically, programmed, and through evolution. Some examples of topics covered in this session will be questions related to:

–       cell-to-cell noise

–       cell-state switches and cell differentiation

–       heterogeneity in immune responses

–       cancer evolution

–       heterogeneity in disease progression

–       algorithms to process single-cell experimental data

Abstracts

We are soliciting abstracts of published and unpublished work (up to 500 words) related to the topics mentioned above.  The workshop will combine invited talks, talks selected from abstract submissions to this call, and a panel discussion.
Please submit abstracts online at https://www.easychair.org/conferences/?conf=psbmch2013

Important dates

Abstract deadline: August 31st, 2012

Speaker notification: September 15th, 2012

All speakers should be registered to PSB 2013 by October 1st, 2012.

Workshop organizers:

Eric Batchelor, Ph.D. is an Investigator in the Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH). He recently joined the NIH as one of the first Earl Stadtman Investigators, following graduate work in the Physics Department at the University of Pennsylvania and postdoctoral studies in the Systems Biology Department at Harvard Medical School. His research uses a combination of experimental and computational approaches to quantitatively understand the regulation and function of mammalian stress responses. His work emphasizes single cell-level analysis of the regulatory motifs that control stress signaling dynamics. His recent work has focused on the dynamical response of the tumor suppressor p53 upon activation by various forms of DNA damage. His areas of expertise include long-term time-lapse fluorescence microscopy, single-cell level variability, and dynamical systems.

Maricel Kann, Ph.D. is an assistant professor at the University of Maryland, Baltimore County. Her research interests include integration of sequence-based with predictors of protein–protein interactions and other technologies for the classification of human variants and diseases. She is one of the leading experts in the area of translational Bioinformatics, an associate editor of Journal of Biomedical Informatics, and has chaired several international conferences, including several PSB sessions.

Teresa M. Przytycka, Ph.D. is a Senior Investigator at the National Center for Biotechnology Information, NIH. She is heading a research group focusing on developing algorithmic and graph theoretical approaches to study problems arising in Computational and Systems Biology. Dr. Przytycka’s research interests include:  biological networks, gene regulation, phenotypic variability and systems level modeling of genotype-phenotype associations. She serves as an associate editor of PLoS Computational Biology, IEEE Transactions of Bioinformatics, BMC-Bioinformatics.  She has chaired a number of conferences including PSB session on network dynamics, ISMB Comparative Genomics section, WABI 2012 conference, and 2010 Keystone meeting on Systems Biology and Diseases.

Ben Raphael, Ph.D. is an Associate Professor of Computer Science at Brown University.  His research interests include the design and application of algorithms to study human genomic variation and somatic evolution in cancer.  His recent work has focused on finding driver mutations in cancer genomes, including approaches that address both inter- and intra-tumor heterogeneity.  He is co-founder and a member of the Steering Committee for RECOMB Computational Cancer Biology (RECOMB-CCB) meeting and have served on Program Committees for numerous computational biology / bioinformatics conferences.

Damian Wojtowicz, Ph.D. is a Postdoctoral Visiting Fellow in the Computational Biology Branch of National Center for Biotechnology Information, NIH. Before joining NIH, he graduated from University of Warsaw (Poland), where he subsequently held an assistant professor position. His research is focused on function and evolution of DNA structure, gene regulation, protein and genome evolution, as well as on developing and applying bioinformatics approaches to problems in computational biology.

EMBO conference: from functional genomics to systems biology

July 16, 2012 § Leave a comment

…will be held November 17-20, 2012 in Heidelberg and is  now open for registration here with a deadline of 20 September for both registration and abstract submission.

Speaker list here.

Why You Should Attend

Summary
The EMBO ‘From Functional Genomics to Systems Biology’ conference has served as an important venue in helping to shape the field and generate a community of scientists that come from very diverse disciplines. The common goal is to understand the systems level properties of complex systems at all scales from molecular processes to cells, tissues and organisms. The meeting was initiated in 2002 and has been held every two-years at EMBL Heidelberg, with the 2012 meeting being the sixth biennial conference. Due to the excellent line up of speakers, the interactive atmosphere and lively discussions after the talks, the feedback from both the participants and speakers at past meetings has always been excellent, with many 2010 speakers calling the meeting ‘the highlight of the year’. For 2012, there is a full program of confirmed speakers available online. Given their caliber, at the cutting edge of genomics, the 2012 meeting will be a major event and a must attend for people interested in Genomics and Systems biology.

Aims of event
The main objective of this conference is to bring people together from these diverse disciplines to exchange ideas, promote cross-disciplinary collaborations and to form a synthesis of appropriate systems-level approaches.

Topics
The meeting is purposely very broad and covers all aspects of functional genomic approaches to systems biology, going from the genome to phenotype. These include general principles of transcription, transcriptional networks, protein interactions, functional interaction networks (synthetic lethal screens, genetics, RNAi), synthetic biology, multi-dimensional data integration and qualitative and quantitative modeling.

Calling future leaders in Synthetic Biology

July 16, 2012 § Leave a comment

SynBio LeAP: Synthetic Biology Leadership Accelerator Program
October 1-5th, 2012
Airlie Center, near Washington, DC

• Do you have great ideas for advancing synthetic biology in the public interest?

• Do you want time, tools and partners to develop your ideas into action?

• Do you want to build a community working to best advance biotechnology?

Then join us as one of twenty emerging leaders who will spend a week developing plans for how they – and others – can best advance synthetic biology for the public good.

• Work with your peers, a professional creative facilitation team, and guest experts across sectors in biotechnology.

• Explore frameworks for assessing how biotechnologies can create public value.

• Develop leadership skills for engaging across diverse organizational contexts shaping biotechnology.

• Create actionable plans for mobilizing your ideas for best advancing synthetic biology.
Share your plans with individuals and organizations that can support your goals beyond LeAP.

• Relax in Airlie’s beautiful grounds, enjoy great food and drink, network, and benefit from focused time to develop your ideas.

LeAP is shaped by your ideas and goals. If you want to lead a great future for – and through – synthetic biology, LeAP with us. We welcome participants across career stages, disciplines and sectors.

LeAP participation is fully sponsored by an open consortium of community funders and organizers, including the NSF, Alfred P. Sloan Foundation, SynBERC, BioBricks Foundation, and the Woodrow Wilson Center’s Synthetic Biology Project. If you or your organization is interested in supporting LeAP, please contact us.

Applications are now being accepted on a rolling basis. Limited spots are available and will fill up soon. Tell your friends and don’t wait to apply!

More information: synbioleap.org
Contact us: info AT synbioleap.org
Spread the word: #synbioLEAP

Systems Biology of Diversity in Cancer

July 11, 2012 § Leave a comment

The Center for Cancer Systems Biology at MSKCC’s Second Annual Symposium, Systems Biology of Diversity in Cancer, will be held Thursday, October 18 – Friday, October 19, 2012, at Memorial Sloan-Kettering Cancer Center, RRL-120 (430 East 67th Street, New York, NY 10065)

Registration: Event is free, but registration is required by September 28, 2012. Register here.

Confirmed Speakers:
Grégoire Altan-Bonnet, PhD, Computational Biology Center, Memorial Sloan-Kettering Cancer Center
Olivier Elemento, PhD, Cancer Systems Biology, Institute for Computational Biomedicine, Weill Cornell Medical Center
Kevin Janes, PhD, Department of Biomedical Engineering, University of Virginia
Christina Leslie, PhD, Computational Biology Center, Memorial Sloan-Kettering Cancer Center
Christine Mayr, PhD, Cancer Biology & Genetics, Memorial Sloan-Kettering Cancer Center
Sylvia Plevritis, PhD, Diagnostic Radiology, Stanford School of Medicine; Stanford Center for Cancer Systems Biology
Neal Rosen, MD, PhD, Molecular Pharmacology & Chemistry Program; Medical Oncology, Memorial Sloan-Kettering Cancer Center
Chris Sander, PhD, Computational Biology Center, Memorial Sloan-Kettering Cancer Center
Eran Segal, PhD, Department of Computer Science and Applied Mathematics, Weizmann Institute
Henk Stunnenberg, PhD, Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University
Simon Tavaré, PhD, Department of Biological Sciences, University of Southern California; Department of Applied Mathematics and Theoretical Physics, University of Cambridge
Barry Taylor, PhD, Department of Epidemiology and Biostatistics, UCSF School of Medicine
Joao Xavier, PhD, Computational Biology Center, Memorial Sloan-Kettering Cancer Center

CCSB Young Scientist Awards: A limited number of CCSB Young Scientist awards will be granted to selected graduate students and postdoctoral fellows to cover travel and lodging expenses.

Please visit http://ccsbsymposium.mskcc.org for details and abstract submission. Application deadline: August 27, 2012.

Call for Abstracts: Abstract submission deadline for contributed oral and poster presentations is September 5, 2012.

ICSB 2012

June 22, 2012 § Leave a comment

The 13th International Conference in Systems Biology will be held in Toronto this year, from August 19th to 23rd.  The speaker list is here.  You can download a PDF of the schedule (or, oddly, an Excel spreadsheet…?) here.

I really should update my conference links….

PHYSICS OF LIVING MATTER 7 (PLM7)

May 31, 2012 § Leave a comment

Join us on the 13th and 14th of September for a Symposium on the Physics of Living Matter at University College London!

This meeting will be the 7th in the PLM series, which began in 2006, and the 2nd in the Physical Cell series, which began in 2010.

This symposium began as an initiative aimed at developing a community ofinterdisciplinary research groups interested in quantitative systems biology grounded in the physical sciences. By moving the venue to London, we aim to attract an even wider pool of international researchers this year.

Because the field is new, we are seeking new participants and have tried to keep costs low to attract a young audience, which we believe is critical for community building.

The Symposium this year will has the sub-themes: dynamic cell organization, emergent properties of cellular assemblies and information processing at a molecular and cellular level. You will see from the programmethat we have assembled a great set of international speakers who will cover the ground between molecular, cell and developmental biology within the context of quantitative approaches borrowed from or inspired by the physical sciences.
To find out more and to register please see these links:

http://www.ucl.ac.uk/PhysCell/

http://physcell.eventbrite.co.uk/

Twitter account: @PhysCell

Space is limited but we hope to see you there!

Network Science in Biology and Medicine Symposium

April 27, 2012 § Leave a comment

Harvard Catalyst is sponsoring a symposium on Network Science in Biology and Medicine on Thursday, June 7, 2012, in the Amphitheater of the Joseph B. Martin Conference Center at HMS.

Symposium: 4:00pm – 6:30pm
Reception: 6:30pm – 7:00pm

The Network Science in Biology and Medicine Symposium will offer an introduction to a rapidly emerging field that combines systems biology and network science by focusing on the identification and investigation of networks of interacting molecular and cellular components. When integrated into biomedical research, network medicine has the potential to transform investigations of disease etiology, diagnosis, and treatment.

Program:

Co-chairs: Joseph Loscalzo, MD, PhD and Marc Kirschner, PhD.

Complex Networks in BiologyAlbert-Laszio Barabasi, PhD, BWH

Network Medicine: A New Paradigm for Defining Human Disease and TherapyJoseph Loscalzo, MD, PhD, BWH

Microbial Evolution within a Human HostRoy Kishony, PhD, HMS

Systems PharmacologyPeter Sorger, PhD, HMS

Please register by May 21, 2012.

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