ISMB2016

ISMB 2016 - Equal Opportunity Session

Leader:Bonnie Berger
Date: Sunday, July 10, 12:45 pm - 1:45 pm
Room: America's Seminar

Description

ISCB understands the importance of diversity in science and promoting diversity in every way possible. This panel is the first of a possible series to come together to discuss how we as a community, discipline, and Society can promote the advancement of women in our research community. The panel will explore career challenges and give specific advice on how to overcome obstacles, highlight the initiatives taken by ISCB to promote women, and open the discussion to the audience for questions on the topic.

We recognize that diversity is more than just gender but feel it is important to tackle the issue one step at a time. Future panels will highlight other areas of diversity, including race, age, ethnicity, etc.

Industry Poster Package

For-profit organization $1,250
Not-for-profit organization $1000

Industry posters are intended to convey information about commercially available software and services.

One poster display in industry poster section
Name listed in conference program book
One full conference registration

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

Award Winners

Art & Science Award
Wikipedia Award
Wikidata Award
Fight Against Ebola Award
Ian Lawson Van Toch Memorial Award for Outstanding Student Paper
Late Breaking Research Award sponsored by PLOS
University of California Berkeley Center for Computational Biology Outstanding Oral Poster Prize
F1000Research Poster Award
RCSB PDB Poster Prize

Art & Science Award

The Dark Proteome
Sean O'Donoghue CSIRO & Garvan Institute, Australia
Christopher Hammang, Garvan Institute, Australia
Julian Heinrich, CSIRO, Australia

Wikipedia Competition

1^st Place - Alexander Hausser & Leonie Jahn - Docking (molecular)
2^nd Place - Leandro Poli - BioJava
3^rd Place - Vivek Rai - Vienna RNA Package

Wikidata Competition

1^st Place - Vivek Rai - Vienna RNA Package

Fight Against Ebola Award

Winner

Mark N. Wass, University of Kent, United Kingdom
Title: Using Computational Biology to Investigate Ebola Virus Pathogenicity
Authors: Morena Pappalardo¹, Miguel Julia¹, Diego Cantoni¹, Francesca Collu², James Macpherson², Mark J Howard¹, Franca Fraternali², Jeremy S. Rossman¹, Martin Michaelis¹ 1. School of Biosciences, University of Kent, UK.
2. Randall Division, King's College London, UK.

Honourable Mentions

Ahmed Arslan, KU Leuven, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
Title: From conserved protein residues to therapeutic targets for Ebola Virus Disease
Co-author: Vera van Noort, KU Leuven, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium

Tamir Tuller, Tel-Aviv University, Israel
Title: Computational large scale exploration of functional regions in Ebola for therapy and vaccination
Authors: Eli Goz¹, Kiril Lomakin^2,3, Leslie Lobel¹
¹Department of Biomedical Engineering, Tel-Aviv University, Israel.
²Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.
³Department of Emerging and Re-emerging Diseases and Special Pathogens Uganda Virus Research Institute (UVRI) Entebbe, Uganda

Ian Lawson Van Toch Memorial Award for Outstanding Student Paper

TP041: RCK: accurate and efficient inference of sequence and structure-based protein-RNA binding models from RNAcompete data
Presenting Author: Yaron Orenstein MIT, United States

Motivation: Protein-RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein-RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240,000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but was outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers.
Results: We develop RCK, an efficient, scalable algorithm to infer sequence and structure preferences based on a new k-mer model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein-RNA structure-based models on an unprecedented scale.
Availability: Software and models are freely available at http://groups.csail.mit.edu/cb/rck/.
Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.
Supplementary information: Supplementary data are available at Bioinformatics online.

PLOS - Late Breaking Research Award

TP87: Data-Driven Analysis of Lymphocyte Infiltration in Breast Cancer Development and Progression
Presenting Author: Ruth Dannenfelser, Princeton University, United States
Additional Authors: Josie Ursini-Siegel, Lady Davis Institute for Medical Research, Canada
Vessela Kristensen, Radiumhospitalet, Norway
Olga Troyanskaya, Princeton University, United States

The tumor microenvironment is now widely recognized for its role in tumor progression, treatment response, and clinical outcome. The intratumoral immunological landscape, in particular, has been shown to exert both pro-tumorigenic and anti-tumorigenic effects. Thus far, direct detailed studies of the cell composition of tumor infiltration have been limited; with some studies giving approximate quantifications using immunohistochemistry and other small studies obtaining detailed measurements by laboriously isolating cells from newly excised tumors and sorting them using flow cytometry. Herein we utilize a machine learning based approach to identify lymphocyte markers with which we can quantify the presence of B cells, cytotoxic T-lymphocytes, T-helper 1, and T-helper 2 cells in any gene expression data set and apply it on the studies of breast tissue. By leveraging many samples from existing large scale studies, we are able to find an inherent cell heterogeneity in clinically characterized immune infiltrates, a strong link between estrogen receptor status and infiltration in normal and tumor tissues, changes with genomic complexity, and identify characteristic differences in lymphocyte expression among molecular groupings. Furthermore, we explore the effects detailed infiltration patterns have on patient survival and changes with anti-estrogen therapy.

University of California Berkeley Center for Computational Biology Outstanding Oral Poster Prize

OP34: Hidden RNA Codes Revealed from in vivo RNA Structurome
Presenting Author: Yin Tang, Pennsylvania State University
Additional Authors:
Anton Nekrutenko, Pennsylvania State University, University Park, United States of America
Philip Bevilacqua, Pennsylvania State University, University Park, United States of America
Sarah Assmann, Pennsylvania State University, University Park, United States of America

RNA can fold into secondary and tertiary structures, which are important for regulation of gene expression. We recently developed a method to perform genome-wide RNA structure profiling in vivo employing high-throughput sequencing techniques, and applied this methodology to Arabidopsis. This method makes it possible to probe thousands of RNA structures at one time in living cells. Hidden RNA codes have been revealed by bioinformatic analyses of our RNA structuromes including RNA structures related to alternative polyadenylation and splicing [1].
Recently, further analysis of this dataset revealed a correlation between mRNA structure and the encoded protein structure, wherein the regions of individual mRNAs that code for protein domains generally have significantly higher structural reactivity than regions that encode protein domain junctions. This relationship is prominent for proteins annotated for catalytic activity but is reversed in proteins annotated for binding and transcription regulatory activity. We also found that mRNA segments that code for ordered regions have significantly higher structural reactivity than those that encode disordered regions [2].
We also developed a new computational platform, StructureFold, to facilitate the analysis of high throughput RNA structure profiling data. As a component of the Galaxy platform (https://usegalaxy.org), StructureFold integrates four computational modules in a user-friendly web-based interface or via local installation [3].

[1] Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. Nature. 2014;505:696-700.
[2] Tang Y, Assmann SM, Bevilacqua PC. J Mol Biol. 2016;428:758-766.
[3] Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM. Bioinformatics. 2015;31:2668-75.

University of California Berkeley Center for Computational Biology Outstanding Oral Poster Prize

OP14: Widespread misannotation of samples in genomics studies
Presenting Author: Lilah Toker, University of British Columbia, Canada
Additional Authors:
Min Feng, University of British Columbia, Canada
Paul Pavlidis, University of British Columbia, Canada

Concern about the reproducibility and reliability of biomedical research has been rising. A bedrock principle of research conduct is that the samples analyzed are correctly identified and not mixed up during processing, but this has rarely been assessed formally.
Here we studied the prevalence of sample misannotation in a large corpus of genomics studies by comparing meta-data annotations of sex to predictions from expression of sex-specific genes. We identified apparent misannotated samples in 46% of the datasets sampled. Extrapolating beyond our corpus, we estimate that at least 33% of all studies have at least one such mix-up (99% confidence interval). Because this method can only identify a subclass of potential misannotations, this provides a conservative estimate for the breadth of the problem. In an additional set of studies that used samples from the same subjects, 2/4 had misannotatated samples. These misannotations are likely to result from laboratory mix-ups rather than subject meta-data collection errors.
Our findings emphasize the need for genomics researchers to implement more stringent sample tracking and data quality control steps, and suggests that re-use of published data should be done in conjunction with careful re-examination of meta-data.

F1000 Poster Awards

OP23/B11: The evolutionary origin of orphan genes
Presenting Author: Zebulun Arendsee, Iowa State University, United States of America
Additional Author:
Eve Syrkin Wurtele, Iowa State University, United States of America

Many of the most powerful tools in biology rely on inference of homologs via sequence-based algorithms. However, many loci are invisible to such methods. Those that are short or rapidly evolving, such as orphan genes and small non-coding RNAs, may yield no significant hits. Whereas low-complexity or high-copy number loci may hide in a crowd of false positives. Searching by context bypasses this problem. We present an algorithm for tracing loci between genomes using a synteny map, and test its efficacy by mapping all Arabidopsis thaliana-specific genes to the genomes of eight related species. By reducing the search space and winnowing false positives, we were able to assess the origin of the individual orphan genes with unprecedented resolution. We traced many to their non-genic cousins, identifying the non-genic footprint from which they arose. We linked others to putative genes in related species from which they diverged beyond recognition. Knowing the approximate location of each gene across species also provides a starting point for future studies. Our pipeline can easily be adapted to contextualize elusive elements such as small RNAs and lineage-specific genes in any species for which reliable synteny maps can be built.

OP27/O42: TRACE: Reconstructing trajectories of cell cycle evolution using single-cell mass cytometry data
Presenting Author: Maria Anna Rapsomaniki, IBM Research Zurich
Additional Authors:
Xiaokang Lun, University of Zurich, Switzerland
Bernd Bodenmiller, University of Zurich, Switzerland
Maria Rodriguez Martinez, IBM Research Zurich, Switzerland

As single-cell experimental approaches become increasingly popular, cell-to-cell heterogeneity has emerged as a key determinant factor contributing to variability in gene expression and signaling responses. Mass cytometry (CyTOF) is a new proteomic technology that enables the simultaneous quantification of dozens of proteins in thousands of individual cells. In the context of cancer research, recent applications of CyTOF include the characterization of inter- and intra-tumor heterogeneity and the identification of novel cell subpopulations. However, as already demonstrated for single-cell RNA-seq, the resulting measurements are largely influenced by confounding factors, such as the cell cycle and cell volume. We present here TRACE, a novel computational approach to quantify this source of variability. TRACE first exploits a hybrid machine learning approach to classify single cells into discrete cell cycle phases according to measurements of established markers. Next, a metric embedding optimization technique creates a one-dimensional continuous marker that tracks biological pseudotime and individual cells are subsequently ordered according to this pseudotime marker. The resulting cell cycle trajectories across perturbation time points allow us to separate cell cycle effects from experimentally induced responses, enabling the direct comparison of signaling responses through cell cycle progression. Additionally we show that volume biases can be corrected using housekeeping gene measurements. Our approach, implemented in a simple and intuitive Graphical User Interface, was used to analyze data from various cell lines subject to different stimulations. In each case, TRACE was able to separate confounding effects from signaling responses, enabling the unbiased analysis of biological processes.

OP06/N16: The Landscape of Circular RNA in Cancer
Presenting Author: Nguyen Vo, University of Michigan-Ann Arbor, United States of America
Additional Authors:
Marcin Cieslik, University of Michigan-Ann Arbor, United States of America
Yajia Zhang, University of Michigan-Ann Arbor, United States of America
Xuhong Cao, University of Michigan-Ann Arbor, United States of America
Alexey Nesvizhskii, University of Michigan-Ann Arbor, United States of America
Arul Chinnaiyan, University of Michigan-Ann Arbor, United States of America

Circular RNAs (circRNA) are a new class of abundant, non-adenylated, and stable RNAs that form a covalently closed loop. Recent studies have suggested that circRNAs play important regulatory roles through interactions with miRNAs and ribonucleoproteins. High-throughput RNA-sequencing to detect circRNAs requires non-poly(A) selected protocols. In this study, we established the use of Exome Capture RNA-Seq protocol to profile circRNAs across more than 1000 human cancers samples. We validated our protocol against two other gold-standard methods, depletion of rRNA (Ribo-Zero) and digestion of linear transcripts (RNase-R). Capture RNA-seq was shown to greatly facilitate the high-throughput profiling of circRNAs, providing the most comprehensive catalogue of circRNA species to-date. Specifically, our method achieved significantly better enrichment for circRNAs than rRNA depletion, and, unlike RNase-R treatment, preserved accurate circular-to-linear ratios. Although the correlation between circular and linear isoform abundance was modest in general , we found strong evidence that the lineage specificity of circular RNAs is due to the lineage specificity of their parent genes. To shed light on the mechanism of circRNAs biogenesis, we are investigating the associations between mutations in canonical splicing sites and splicing factors with aberrant formation of circRNAs. Finally, ratio of circular to linear transcript abundance was explored to give insight in the dynamics between transcriptome stability/turnover and cell proliferation. Overall, our compendium provides a comprehensive resource that could aid the exploration of circRNAs as a new type of biomarkers, or as intriguing splicing and regulatory phenomena.

OP17/O20: Deconvolution of Cell and Environment Specific Signals and Their Interactions from Complex Mixtures in Biological Samples
Presenting Author: Urszula Czerwinska, Institut Curie, France
Additional Authors:
Emmanuel Barillot, Institut CURIE, France
Vassili Soumelis, Institut Curie, France
Andrei Zinovyev, Institut Curie, France

Background :
In many fields of science observations on a studied system represent complex mixtures of signals of various origin. Tumors are engulfed in a complex microenvironment (TME) that critically impacts progression and response to therapy. It includes tumor cells, fibroblasts, and a diversity of immune cells. It is known that under some assumptions, it is possible to separate complex signal mixtures, using classical and advanced methods of source separation and dimension reduction.

Description :
In this work, we apply independent components analysis (ICA) to decipher sources of signals shaping transcriptomes (global quantitative profiling of mRNA molecules) of tumor samples, with a particular focus on immune system-related signals. We use ICA iteratively decomposing signals into sub-signals that can be interpreted using pre-existing immune signatures through correlation or enrichment analysis.

Results :
Our analysis revealed a possibility to identify signals related to groups of immune cell types with unsupervised learning approach in a Breast Cancer dataset. Through Fisher exact test we identified significative groups corresponding to three out of five sub-signals: (1) T-cells, (2) DC/Macrophages, (3) Monocytes/ Macrophages/ Eosynophiles/Neutrophiles. T-cells metagene correlates well with the tumor grade (Kruskall-Wallis test p-value=0.003).

Discussion :
Ongoing analysis aims to evaluate the robustness of the represented groups and eventual differences between several types of cancer. We are to characterize the immune infiltration degree in the cancer transcriptome dataset and further correlate with patients’ survival and tumor characteristics. In the case of success, the results will be used in the diagnosis and cancer therapy, especially immunotherapies.

OP20/B02: AODP: An improved method for signature oligonucleotide design
Presenting Author: Christine Lowe Agriculture and Agri-Food Canada
Additional Authors:
Manuel Zahariev, Skwez Technology Corp
Min-Ru Lin, Agriculture and Agri-Food Canada
Jonathan Litovitz, Agriculture and Agri-Food Canada
Hai D.T. Nguyen, Agriculture and Agri-Food Canada
C. André Lévesque, Agriculture and Agri-Food Canada
Wen Chen, Agriculture and Agri-Food Canada

High-throughput Next Generation Sequencing (NGS) technologies and reference databases have enhanced our ability to explore diversity at genetic and taxonomic levels. Most off-the-shelf tools for examining genetic diversity implement algorithms that rely on sequence similarity and composition, which can lead to resolution loss in genetic comparisons, particularly at the species/sub-species taxonomic ranks. We present a new version of the Automated Oligonucleotide Design Pipeline (AODP). AODP designs signature oligonucleotides (SO) with specificity and fidelity based on genome or DNA barcode sequence identity, reducing the resolution loss observed with existing approaches. SO designed with AODP highlight regions with taxon or clade-specific polymorphisms that are useful for comparative genomics and provide suitable candidates for the design of primers/probes in diagnostic assays. AODP has several unique features: 1) The AODP algorithm uses a novel packed-Trie data structure, with support for multi-threaded insertion, optimized for DNA nucleotide strings, which scales well to multi-processor architectures; 2) SO can be designed for a large dataset with relatively small memory footprint; 3) Regions of DNA with a single nucleotide polymorphism (SNP) can be optionally ignored to minimize noise caused by sequencing errors during NGS; 4) The specificity of SO can be further validated against large reference databases; 5) SO thermodynamic properties can be calculated for wet-lab experimental conditions; and 6) SO can be directly used for in silico identification of taxa from environmental NGS data.

RCSB and PDB Poster Prize

OP24/L28: Tertiary Structural Propensities Reveal Basic Sequence-Structure Relationships in Proteins
Presenting Author:
Fan Zheng, Dartmouth College, United States of America
Additional Authors:
Jian Zhang, Dartmouth College, United States of America
Gevorg Grigoryan, Dartmouth College, United States of America

The Protein Data Bank (PDB) is a key resource of general principles that has shaped our understanding of protein structure. Most of the existing statistical generalizations of protein structures are made for secondary structures, which are often too generic to satisfy many specific design goals, or for protein domains, for which the PDB distribution is highly biased by evolution or human sampling, and thus not being physically meaningful. To fill this gap, we proposed the local tertiary motifs (TERMs) as a new fundamental level of structural unit. TERMs are combinations of non-continuous small secondary fragments connected by inter-residue contacts. We hypothesized that the PDB contains valuable quantitative information on the level of TERMs. We studied the propensities of TERMs within their corresponding ensembles, i.e. geometrically similar structural fragments from completely unrelated proteins. The TERM propensities are physically meaningful in many contexts. By breaking a protein structure into its constituent TERMs, we can evaluate the accuracy of structure-prediction models with poorly predicted regions identifiable, via a metric we named “structure score” capturing the sequence-structure relationships in TERMs. Also, querying TERMs affected by point mutations enables straightforward prediction of mutational free energies. Our performance exceeds or is comparable to state-of-art methods. Our results suggest that the data in the PDB are now sufficient to enable the quantification of complex structural features, such as those associated with entire TERMs. This should present opportunities for advances in computational structural biology techniques, including structure prediction and design.

Serafim Batzoglou

ISCB 2016 Innovator Award Keynote

Department of Computer Science, Stanford University
United States

Presentation Title: Computational Challenges in Personalized Genomics
Time: Tuesday, July 12th, 9:00 am - 10:00 am
Introduction by: Bonnie Berger
Room: Northern Hemisphere BCD, Dolphin Hotel

Abstract:
I will discuss personalized genomics from a computational perspective. Computational contributions have been instrumental in the brief history of personalized genomics, starting from the sequencing of the first human genomes. Looking at the present and future, personalized genomics is likely to soon have massive positive impact in our understanding of human biology and practice of medicine; algorithms, artificial intelligence and large scale computing will be at the heart of these advances.
Biography:
Serafim's research focuses on computational genomics: developing algorithms, machine learning methods, and systems for the analysis of large scale genomic data. He received a BS in Computer Science, BS in Mathematics, and MEng in EE&CS from MIT in June 1996, and a PhD in Computer Science from MIT in June 2000. He joined Stanford in 2001. He is a recipient of the Sloan Fellowship, the NSF Career Award, and was named Technology Review's "Top 100 Young Technology Innovators" in 2003. He is also co-founder of DNAnexus.

Common NetBio/SysMod COSI Session

Attention Conference Presenters - please review the Speaker Information Page available here.

Room: Northern Hemisphere BCD

Sunday, July 10 10:10 am - 12:40

Organizers

Nicolas Le Novere, Babraham Institute, Cambridge, United Kingdom
Alex Pico, Gladstone Institutes, San Francisco, United States

Overview

Over the last two decades, systems biology has become a large and diverse field of research in life sciences, building up on the successes of molecular biology and genomics. Computational biology is at the core of systems biology investigations and several ISCB Communities of Special Interests (COSIs) have been created that focus on relevant scientific aspects or approaches. Because systems biology's main interest lies in understanding the emergent properties of complex systems, the study of network structures and the quantitative descriptions of systems' behaviour are its two main pillars.

The NetBio (Network Biology) COSI provides an interface between tool developers and users in the field of network biology. It particularly focuses 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 and medicine. Mathematical modeling of biological systems has recently become more reliant on bioinformatic data to build, train and validate models. The SysMod (Computational Modeling of Biological Systems) COSI aims at bridging the gap between bioinformatic analysis and systems biology modeling.

This ISMB COSI session will focus on the conjoint use of network analysis and mathematical modeling. Two short presentations will introduce the COSIs, their aims and their activities. The session will feature four scientific talks by leading experts. Lars-Juhl Jensen (University of Copenhagen) developed some of the leading network databases and prediction tools. Nathan Price (Institute of Systems Biology and University of Washington) is an expert of multi-scale modelling of metabolism and regulatory genomics. Dr. Natasa Przulj developed innovative approaches to extract biological knowledge from network topology. Jonathan Karr (Mount Sinai School of Medicine) developed the first mathematical model of a complete cell. The session will be completed with discussions around the challenges and opportunities of mathematical modeling of biological networks, and the possible synergies between the two COSIs.

We expect the audience to be made partly of researchers involved in network analysis and mathematical modeling, and partly of ISMB attendees interested to learn more about those domaines of research. Therefore we will particularly welcome participants who did not attend the NetBio and SysMod Special Interest Groups (SIGs).

Agenda

10-10 a.m. - 11:10 a.m. Chair: Alexander Pico
Presentation of NetBio and SysMod COSIs

Lars Juhl Jensen, University of Copenhagen, Denmark
Nathan Price, Institute of Systems Biology, United States

11:10a.m. - 11:40a.m. Coffee break

11:40a.m. - 12:40 p.m. Chair: Nicolas Le Novère

Joint Community Discussion
Natasa Przulj, University College London, United Kingdom
Jonathan Karr, Mount Sinai School of Medicine, United States
Closing Comments - Co-chairs

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

When preparing accepted posters please note that your poster should not exceed the following dimensions: 46 inches wide by 45 inches high. There will be 2 posters per side on the each poster board. One poster will be an odd number and the other will be an even number. View a diagram of the the poster board in pdf format here.

Satellite Meetings (SMs)

3Dsig: Structural Bioinformatics & Computational Biophysics

CAMDA 2016 Critical Assessment of Massive Data Analysis

Special Interest Group Meetings (SIGs)

Bio-Ontologies

BioVis SIG

BOSC: The 17th Annual Bioinformatics Open Source Conference

Function SIG (formerly AFP-SIG)

HitSEQ 2016: High Throughput Sequencing Algorithms & Applications

Integrative RNA Biology SIG

NetBio SIG

Regulatory Genomics Special Interest Group (RegGenSIG)

SysMod: Computational modeling of biological systems

TransMed 2016: Translational Medicine Informatics & Applications

VarI SIG

One-Day SIGs – Friday, July 8, 2016

BioVis SIG

Integrative RNA Biology SIG

NetBio SIG

TransMed 2016: Translational Medicine Informatics & Applications

One-Day SIGs – Saturday, July 9, 2016

Function SIG (AFP-SIG)

Regulatory Genomics Special Interest Group (RegGenSIG)

SysMod: Computational modeling of biological systems

VarI SIG

Two-Day SIGs – Friday, July 8 and Saturday, July 9, 2016

Bio-Ontologies

BOSC:17th Annual Bioinformatics Open Source Conference

HitSEQ 2016: High Throughput Sequencing Algorithms & Applications

Satellite Meetings (SMs)

3Dsig: Structural Bioinformatics & Computational Biophysics

URL: http://bcb.med.usherbrooke.ca/3dsig16/

Date: Friday, July 8 & Saturday, July 9

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

Room: Osprey 1/2 (Swan Hotel)

View Program
3Dsig Structural Bioinformatics & Computational Biophysics has become the largest meeting in this growing field. This year we are celebrating our 12th meeting. The keynote list will be announced shortly

In addition to keynotes our diverse program will include 20 talks selected from submitted abstracts, 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, Steve Bryant, Janusz Bujnicki, Stephen Burley, Amadeo Caflisch, Guido Capitani, Wah Chiu, Cyrus Chothia, Charlotte Deane, William Degrado, Roland Dunbrack, Keith Dunker, Aled Edwards, Arne Elofsson, Lucy Forrest, Stephen Friend, Dmitrij Frishman, Adam Godzik, David Goodsell, Nick Grishin, Kevin Karplus, Amy E. Keating, Tanja Kortemme, Gunnar von Heijne, Des Higgins, Barry Honig, David Jones, Lynn Kamerlin, Thomas Lengauer, Michael Levitt, Olivier Lichtarge, Andrei Lupas, François Major, George I. Makhatadze, Debora Marks, John Moult, Klaus Mueller, Masha Niv, 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 Shoichet, Michael Schroeder, Kim A. Sharp, Jeffrey Skolnick Manfred Sippl, Michael Sternberg, Raymond Stevens, Joel Sussman, Sarah Teichmann, Devarajan Thirumalai, Janet Thornton, Anna Tramontano, Ron Unger, Alfonso Valencia, Sandor Vajda, Rebecca Wade, Harel Weinstein, Haim Wolfson and Ada Yonath.

Abstract submission deadline: TBD
April 15th – abstract submission deadline (to be considered for oral presentation)

Relevant topics are listed in http://bioinformatics.oxfordjournals.org/content/31/1/146.long These include:

Macromolecular (tertiary and quarternay) structure prediction.

Application of structure to systems biology and vice versa.

Structure-based drug discovery including polypharmacology and network pharmacology.

Structure representation, classification and prediction.

Macromolecular assemblies and multi-domain protein structures.

Structural genomics.

3D databases and data mining including integration and accessibility of methods and databases.

Molecular visualization.

Relevant methods of structure determination, particularly hybrid methods.

Structure-based function prediction.

Evolution Studied through structures and evolution (e.g. correlated mutations) utilized to predict and study structures

Docking, analysis, prediction and simulation of biomolecular interactions such as protein-protein, protein-ligand and protein-nucleic acid.

Chemical systems biology and small molecule docking simulations.

Prediction and analysis of protein domains.

Membrane protein structure analysis and prediction.

Protein dynamics and disorder

The structural basis of immunology.

3D RNA structures

Protein engineering and synthetic biology.

We look forward to meeting you at 3Dsig

Philip E. Bourne (chair)
Associate Director for Data Science, National Institutes of Health, Bethesda, United States
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Rafael Najmanovich
Université de Sherbrooke, Canada
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Ilan Samish The Weizmann Institute of Science; and
Braude College of Engineering, Israel
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CAMDA 2016 Critical Assessment of Massive Data Analysis

URL: http://www.camda.info

Date: Friday, July 8 (begins at 4: 00 pm) & Saturday, July 9 (9:00 a.m - 5:45 p.m.)

Room:Macaw 1/2 (Swan Hotel)

Delegate Note:
We are delighted to welcome you to this year's meeting, featuring a range of diverse and exciting contributions of original research, and complemented by topical keynotes.

Please find this year's program at http://agenda.camda.info/

Please note that on Friday Camda opens at 4pm with a short session led by the keynote of Curtis Huttenhower (Harvard), followed by drinks and dinner, and the majority of the talks then take place in compact format on Saturday.

In anticipation of a lively and stimulating meeting and discussions we much look forward to welcoming you in Florida soon!

CAMDA focuses on the analysis and integration of the massive data sets now prevalent in the life sciences. It introduces new approaches and solutions to the Big Data problem, and presents new techniques in the field of bioinformatics, data analysis, and statistics for handling and processing challenging large data sets. By discussing cutting-edge problems and opportunities, the conference offers researchers from a wide range of fields a unique opportunity to benefit from a critical comparative evaluation of approaches to exploiting Big Data in the life-sciences.

This year, the scientific committee of CAMDA has set three data analysis contest challenges:

The Oxford Nanopore ‘wiggle space’ challenge where several samples had their DNA sequenced by Nanopore long read next-next-generation sequencing as well as more established sequencing technology. This is then to be evaluated on a 'mystery' sample of patient microbiota.

Sequencing Quality Control neuroblastoma study - a comparison of RNA-seq and Agilent microarray gene expression profiles for clinical endpoint prediction.

A toxicogenomics study with matched NGS and microarray profiles for the response of over 100 rat livers to 27 chemicals with 9 different modes of action.

During on-line registration you will be able to buy tickets ($50.00) for the CAMDA dinner on Friday, July 8.

We cordially invite you to attend this year's CAMDA in Orlando!

Key Dates

May 20, 2016 - Extended Abstract Proposals Due
May 30, 2016 - Notification of Accepted Contributions
June 2, 2016 - Early Registration Closes
July 8 & 9, 2016 - CAMDA 2016
Sept. 25, 2016 - Full Paper Submission

Organizers:

Djork-Arné Clevert, JKU Linz, Austria
Joaquin Dopazo, CIPF, Spain
Lan Hu, Exosome Diagnostics, Cambridge, MA, USA
David Kreil, Boku University Vienna, Austria
Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

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Special Interest Group Meetings (SIGs)

Bio-Ontologies

URL:http://www.bio-ontologies.org.uk

Date: July 8 & Saturday, July 9

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

Room: Mockingbird 1 (Swan Hotel)

Bio-Ontologies has been a Special Interest Group (SIG) at ISMB for the last 18 years, providing a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in the life sciences. The informal nature of the SIG offers a constructive environment to nurture discussion of innovative and scientifically sound work from both young and experienced investigators alike.

Key Dates:

- April 8th, 2016 Submissions Due
- May 6th, 2016 Notifications
- May 13th, 2016 Final Version Due

Topics:

Papers are welcome in traditional areas, such as the biological applications of ontologies, newly developed Bio-Ontologies, and the use of ontologies in data sharing standards. In addition, papers will also be welcomed in the following areas:
- Semantic Web Enabled Applications
- Bio-Curation Platforms
- Use of Ontologies in Data Standards
- Role of Bio-Ontologies in the Learning Health System
- Collaborative Ontology Authoring
- Deep learning with Ontologies
- Automated Annotation Pipelines
- Use of ontologies in text mining applications
- Ontology growth, mapping and repair
- Research in Ontology Evaluation
- "Flash updates" on Newly Developed or Existing Bio-Ontologies

As we have done over the past 2 years, the second day is focused on phenotypes. Phenotype day will once again bring researchers together from across many disciplines to share information about phenotype resources and issues as well as experiences with defining, representing, processing and using phenotype data.

Organizers:

Michel Dumontier, Stanford University, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Nigam Shah, Stanford University, United States, 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.
Karin Verspoor, University of Melbourn, Australia, This email address is being protected from spambots. You need JavaScript enabled to view it.

Phenotype Day co-ordinators: Nigel Collier, Anika Oellrich, Tudor Groza, and Karin Verspoor

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

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BioVis SIG

URL: http://biovis.net

Date: Friday, July 8

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

Room: Pelican 2 (Swan Hotel)

Keynote Speaker

To be announced

The rapidly expanding field of biology creates enormous challenges for the computational visualization techniques that are necessary in order to enable 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 symposium serves as a platform for researchers from these fields to increase the impact of data visualization approaches in biology. The breadth and diversity of biological research topic areas will enable researchers from all parts of the visualization and bioinformatics communities to contribute to this effort and the symposium will provide an excellent opportunity to initiate interdisciplinary collaborations.

Forms of participation: Find the latest information on the BioVis website (http://biovis.net). We offer three possibilities to participate:

1) Highlights
Participants may submit an abstract describing work published in the previous year as well as additional work undertaken since publication. The program committee will review these abstracts. Additionally, the BioVis SIG program committee will also invite authors of outstanding publications from other venues. The authors of selected abstracts will be asked to present a short oral presentation during the SIG meeting.

2) New Research:
Participants are invited to submit an abstract describing high-quality original research. Abstracts will be reviewed by the program committee and all accepted abstracts will be included in the poster session. The authors of selected abstracts will be asked to give a brief oral presentation during the SIG meeting.

3) Posters:
We seek work in progress and preliminary results; previously published work from other venues; visualization challenges. Submissions consist of a 250 word abstract and an image.

Key Dates:

May 1, 2016 - Submission deadline for the Highlights
May 1, 2016 - Submission deadline for New Research
May 29, 2016 - Poster abstract submission

*(all deadlines are 5:00pm PDT)

Co-Organizers:

Kay Nieselt, University of Tübingen, Germany, This email address is being protected from spambots. You need JavaScript enabled to view it.
Nils Gehlenborg, Harvard Medical School, Department of Biomedical Informatics, This email address is being protected from spambots. You need JavaScript enabled to view it..
G. Elisabeta Marai, University of Illinois at Chicago, USA, This email address is being protected from spambots. You need JavaScript enabled to view it.
Jan Aerts, KU Leuven, Department of Bioinformatics, 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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BOSC: 17th Annual Bioinformatics Open Source Conference

URL:http://www.open-bio.org/wiki/BOSC_2016

Date: Friday, July 8 & Saturday, July 9

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

Room: Swan 3 (Swan Hotel)

The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. It is sponsored by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results and software. Two full days of talks, posters, panel discussions, and informal discussion groups 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.

We welcome one-page abstracts on any topic of relevance to open source bioinformatics and open science. Some of the abstracts will be chosen for lightning talks, longer talks, and/or posters. We are offering a limited number of travel fellowships to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC. Details are available at: http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

Key dates:

Call for one-page abstracts opens: March 1, 2016
Abstract submission deadline for full talks: April 4, 2016
Abstract submission deadline for Late-Breaking Lightning Talks and posters: June 2, 2016
Notification of acceptance for Late-Breaking Lightning Talks and posters: June 10, 2016
BOSC 2016: July 8-9, 2016
ISMB 2016: July 8-12, 2016

Session topics:

Open Science and Reproducible Research
Standards and Interoperability
Data Science
Workflows
Developer Tools and Libraries
Panel: Growing and sustaining open source communities

Keynote speakers: Jennifer Gardy (University of British Columbia / British Columbia Centre for Disease Control)
Steven Salzburg (Johns Hopkins University)

Co-Chairs:

Nomi L. Harris <This email address is being protected from spambots. You need JavaScript enabled to view it.> (Lawrence Berkeley National Laboratory, USA)
Peter Cock <This email address is being protected from spambots. You need JavaScript enabled to view it.> (James Hutton Institute, Scotland, UK)

Organizing Committe members:

Brad Chapman (Harvard School of Public Health, USA)
Christopher Fields (National Center for Supercomputing Applications, USA)
Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)
Hilmar Lapp (Duke University, USA)
Mónica Muñoz-Torres (Lawrence Berkeley National Laboratory, USA)
Heather Wiencko (Equinome Ltd., UK)

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Function SIG (formerly AFP-SIG)

URL:http://BioFunctionPrediction.org

Date: Saturday, July 9

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

Room: Parrot (Swan Hotel)

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.

The mission of the Function Special Interest Group (Formerly Automated Function Prediction 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 Function SIG holds annual meetings alongside the ISMB. Also, we are conducting the multi-year Critical Assessment of protein Function Annotation, or CAFA, experiment.

Talks are sought in, but not limited to, the following topics:

Computational function prediction methods using anything from protein sequence to -omics data.

Discussions of the limitations and horizons of computational function prediction.

Assessing function prediction programs

Talks about the CAFA experiment, including critiques, new initiatives, and overviews

The evolution of protein function

Key Dates:

March 1, 2016: Call for abstracts (talks & posters) opens

April 6, 2016: Deadline for submitting abstracts

May 9, 2016: Authors notified of abstract status

July 9, 2016: Function SIG Orlando, FL, USA

July 8-12, 2016: ISMB 2016, Orlando, FL, USA

Keynote Speakers:

Trey Ideker, University of California, San Diego, USA
Constance Jeffery, University of Illinois, Chicago, USA

Organizers:

Casey Greene: University of Pennsylvania, USA This email address is being protected from spambots. You need JavaScript enabled to view it.
Mark Wass Kent University, UK This email address is being protected from spambots. You need JavaScript enabled to view it.
Predrag Radivojac, Indiana University, USA This email address is being protected from spambots. You need JavaScript enabled to view it.
Sean Mooney, University of Washington, USA This email address is being protected from spambots. You need JavaScript enabled to view it.
Iddo Friedberg Iowa State University, USA This email address is being protected from spambots. You need JavaScript enabled to view it.

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HitSEQ 2016: High Throughput Sequencing Algorithms & Applications

URL: http://hitseq.org

Date: Friday, July 8 & Saturday, July 9

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

Room: Swan 1/2 (Swan Hotel)

The Conference on High Throughput Sequencing Methods and Applications (HiTSeq 2016) is a Satellite of the ISMB 2016 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 2016 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. This year we are hosting two special emphasis sessions on “HTS in cancer genomics & precision oncology” and “Single molecule sequencing applications”. We are soliciting high-quality full papers that will undergo rigorous peer-review. Special consideration will be given to works on the emphasis areas of this year, but other topics as described below are welcome as well. If accepted, these contributions will be presented at the conference and published in Bioinformatics online. Simultaneously, short abstract submissions will be accepted for either a brief oral presentation or presentation during the poster session.

Possible Topics include:

Cancer genomics and precision oncology (special topic)

Single Molecule Sequencing & Read-Cloud Applications (special topic)

Detecting genome variation

Transcriptome analysis

Epigenomics and chromatin regulation (including 5-C, Hi-C etc.)

Clinical genomics

Metagenomics

Human microbiome

Analysis of 3rd and 4th generation sequencing platform data

Integration of HTS data from distinct “omics” assays

Sharing and Federation of HTS “Big Data”

Key Dates/Deadlines

Full paper deadline: April 5
Abstract deadline: May 11
Author notifications: May 25
Early Registration Ends: June 2
Meeting Program: July 8-9

Organizers:

Can Alkan, Ph.D.
Bilkent University, Ankara 06800, Turkey

Valentina Boeva, Ph.D.
Institut Curie, Paris 75005, France

Ana Conesa, Ph.D.
University of Florida, Gainesville, Florida, USA

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

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

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

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

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Integrative RNA Biology - SIG (IRB-SIG)

URL: http://irbgroup.org/irb-sig-16/

Date: Friday, July 8

Start Time: 8:30 a.m - 7:00 p.m.

Room: Mockingbird 2 (Swan Hotel)

The meeting for Integrative RNA Biology brings together computational and experimental experts that drive new advances in RNA biology and overcome the computational challenges involved. The meeting covers different aspects of RNA biology as they relate to phenotype, disease and therapeutics. Aspects of RNA Biology covered in the meeting include alternative splicing, alternative polyadenylation (APA), post-transcriptional regulation, RNA 2D/3D structure, and the expression and function of non-coding RNAs, such as micro-RNAs (miRNAs) and long non-coding RNAs (lncRNA). Studying these aspects of RNA using high-throughput technologies such as RNA-Seq and CLIP-Seq raise many computational challenges that are discussed at the meeting. Join us to learn more about cutting edge RNA related research and the computational challenges involved. The meeting includes invited talks, short talks selected from submitted abstracts, and an interactive poster session with a poster prize. The meeting concludes with a dinner that will give you a chance to mingle and interact with organizers, speakers, and other attendees in an informal and relaxed setting. Limited travel support for students/postdocs (could also be used for child care if traveling with family) may also be available, courtesy of the RNA Society. More details about key dates, abstract submission process and invited speakers can be found at: http://irbgroup.org/irb-sig-16/

We hope to see you with us at the IRB-SIG 2016 in Orlando.
Confirmed Speakers:
Olga Troyanskaya, Princeton, United States
Christine Mayr, MSKCC, United States
Hagen Tilgner, Weill Cornell, United States
Simon (Hualin) Xi, Pfizer, United States

IRB-SIG Traditional Dinner:

Please join us for the traditional IRB-SIG dinner!

Date: July 8th Time: 7:30pm Place: TBD
Price: $60.00 (tickets available for purchase during on-line registration)

*Note: To join the dinner you need to include it during the registration process.

Abstract Submission Instructions:

http://irbgroup.org/irb-sig-16/abstract_submission.html

Organizers:
Yoseph Barash, University of Pennsylvania, United States This email address is being protected from spambots. You need JavaScript enabled to view it.
Eduardo Eyras , UPF & ICREA, Barcelona, Spain, This email address is being protected from spambots. You need JavaScript enabled to view it.
Klemens Hertel, UC Irvine, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.

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NetBio SIG

URL: http://nrnb.org/netbiosig/

Date: Friday, July 8

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

Room: Swan 4 (Swan Hotel)

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 meeting at the NetBio community site. 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 (https://www.linkedin.com/groups/5123610).

Keynote Speakers:

• Lars Juhl Jensen: Gene Association Networks: Large-scale Integration of Data and Text - University of Copenhagen, Denmark

• Olga Troyanskaya - Gene Function and Regulation in Biological Networks - Princeton University, NJ, USA

• Franca Fraternali - Molecular Determinants of Protein-Protein Interactions - King's College London, UK

• Nataša Pržulj - Patient-Specific Network Data Fusion for Stratification, Biomarker Discovery and Personalized Treatment - University College London, UK

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, Graz University of Technology, Austria, This email address is being protected from spambots. You need JavaScript enabled to view it.
Natasa Przulj, University College London, 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.
Rudolf Pillich, University of California, San Diego, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Gerald Quon, University of California, Davis, United States, 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://www.reggen.net/2016

Date: Saturday, July 9

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

Room: Swan 4 (Swan Hotel)
Download Program

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 is an activity of the ISCB Special Interest Group for Regulatory Systems Genomics, a community of shared interest that has multiple activities and interactions throughout the year, rather than solely meeting during the ISMB conference. An important goal of the SIG is to foster a topically-focused collaborative community wherein scientists communicate with one another on research problems and/or opportunities in the area of computational biology as it pertains to regulatory and systems genomics. The SIG holds two meetings per year, (1) RegGenSIG and (2) The RECOMB/ISCB Conference on Regulatory and Systems Genomics and DREAM Challenges.

CALL FOR ABSTRACTS

To make an oral presentation at RegGenSIG, a one-page abstract should be submitted by April 18, 2016 (see format below). Based on the submitted abstracts, selected authors will be invited for oral presentation. Authors will be notified by May 2, 2016. Abstracts submitted for oral presentation may also be considered for poster presentation.

For poster presentations, authors should submit a one-page abstract no later than May 9, 2016. Author notification will occur no later than May 23, 2016.

ABSTRACT SUBMISSION INSTRUCTIONS

For oral presentations, a one-page abstract should be submitted by April 18, 2016, to Jason Ernst (This email address is being protected from spambots. You need JavaScript enabled to view it.), with Subject: "RegGenSIG 2016 - Abstract for oral presentation".

For poster presentations, a one-page abstract should be submitted by May 9, 2016, to Jason Ernst (This email address is being protected from spambots. You need JavaScript enabled to view it.), with Subject: "RegGenSIG 2016 - Abstract for poster presentation".

Please use the template found on the RegGenSIG web page for abstracts (both oral and posters). The abstracts will be made available via this web page before the SIG.

KEY DATES

April 18, 2016 - Due date for abstracts for oral presentations
May 2, 2016 - Author notification for oral presentations
May 9, 2016 - Due date for abstracts for poster presentation only
May 23, 2016 - Author notification for poster presentations
June 2, 2016 - Early registration discount cut-off date
July 9, 2016 - RegGenSIG meeting

RegGenSIG Organizers

Stein Arts, University of Leuven, Belgium, This email address is being protected from spambots. You need JavaScript enabled to view it.
Finn Drablos, Norwegian University of Science and Technology, Norway, This email address is being protected from spambots. You need JavaScript enabled to view it.
Jason Ernst, University of California, Los Angeles, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Saurabh Sinha, University of Illinois Urbana, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Lonnie Welch, Ohio University Athens, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.
Julia Zeitlinger, Stowers Institute for Medical Research, United States, This email address is being protected from spambots. You need JavaScript enabled to view it.

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SysMod: Computational modeling of biological systems

URL: http://www.sysmod.info

Date: Saturday, July 9

Start Time: 9:00 a.m. - 5:30 p.m.

Room: Pelican 1 (Swan Hotel)

SysMod aims at bridging the gap between bioinformatics and systems biology modeling. Recently, aspects of the two fields have converged. Systems modeling has become more reliant on bioinformatics network inference to build models and has begun to use transcriptomics and proteomics data to train models. In addition, more communication between systems modellers and bioinformaticians is needed to build models of whole cells, organs and organisms. Furthermore, the promises of precision medicine lie, in part, on the interplay between bioinformatics-based analysis of patient data and model-based predictions of treatments.

Topics:

The SIG will welcome the presentation of all all types of modeling applied to any biological question. This includes, but is not limited to, chemical kinetics, reaction-diffusion models, constraint-based reconstruction and analysis, multi-agents, qualitative models, hybrid models, multi-scale approaches, PBPK/PD modelling, efficient solvers and algorithms, visualization techniques. This year we seek in particular contributions falling within two major classes:

Modeling metabolism: from kinetics to the whole genome
Over the past 20 years flux balance analysis together with whole-genome sequencing have enabled researchers to construct detailed genome-scale models of metabolism. More recently, researchers have integrated transcriptomics and proteomics data into flux balance analysis models to generate more accurate predictions. This session will feature two keynote talks on the state-of-the-art of genome-scale modeling, how it can be enhanced through combination with genomic data, and its prospects for precision medicine and microbial engineering.

When modeling biochemistry breaks down: Logic and Rule-based modeling
"Classical" dynamical modeling relies on the enumeration of biochemical components and processes, as well as large numbers of quantitative parameters. However, this information is often difficult to obtain. In addition, covalent modifications and assemblies of macromolecules cause a combinatorial explosion of states which is intractable to traditional methods. Several approaches have been designed to overcome these shortcomings and take advantage of the information that is available. This session will feature two keynote talks on logical and rule-based modeling from two researchers who have been instrumental in developing these methods and using these methods to analyze genome-scale data.

How to participate:

The SIG will feature presentations from invited keynote speakers, presentations selected from submitted abstracts and a poster session. Flash presentations will be offered to introduce posters. Details of the abstract submission procedure will be available at http://sysmod.info

Keynote Speakers:

Vincent Danos; CNRS, France; University of Edinburgh, United Kingdom Vassily Hatzimanikatis; EPFL, Switzerland Nathan Price; ISB, USA; University of Washington, United States Ioannis Xenarios; Swiss Institute of Bioinformatics, Switzerland

Key Dates:

April 2, 2016 - Abstract submissions deadline

April 29, 2016 - Poster and Presentation acceptance notifications.

May 13, 2016 - Final programme available

June 2, 2016 - Early registration ends

July 9, 2016 - SysMod SIG

Organizers:

Laurence Calzone, Curie Institute, Paris, France
Andreas Dräger, University of California, San Diego, United States
Jonathan Karr, Icahn School of Medicine at Mount Sinai, New York, United States
Nicolas Le Novère, The Babraham Institute, Cambridge, United Kingdom
Susanna Neves, Icahn School of Medicine at Mount Sinai, New York, United States
Julio Saez-Rodriguez, Aachen University, Aachen, Germany

For more information, contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

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TransMed 2016: Translational Medicine Informatics & Applications

URL: http://transmedit.org

Date: Friday, July 8

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

Room: Pelican 1 (Swan Hotel)

Knowledge-based translational medicine is a rapidly growing discipline in biomedical research and aims to expedite the discovery of new diagnostic tools and treatments by using a multi-disciplinary, highly collaborative, "bench-to-bedside" approach. Large amounts of multi-omics, imaging (medical and molecular) and clinical data can now be captured for given patient populations. In addition to the challenges of data curation and harmonisation, new computational methods are required to identify molecular signatures that suggest disease subtype. These signatures may be predictive of outcome or progression, and impact on disease management by suggesting personalised therapeutic strategies for patients. Such approaches will further the development of a new taxonomy of disease.

In the TransMed SIG meeting, we will explore the current status of computational biology approaches within the field of translational medicine.

Topics of interest include, but are not limited to:

Clinical and molecular data storage and integration infrastructure, including: data warehousing for translational medicine, multi-‘omics and clinical data integration, data visualization in translational medicine

Curation and harmonization of clinical, ‘omics and imaging data, including: standards and ontologies in translational medicine, biomedical text mining and semantic representation

Data analytics for patient stratification, biomarker and target discovery, including: disease subtype discovery, Electronic Health Records integration, translational imaging, multi-scale modelling, high performance and cloud computing in translational medicine, mathematical modelling for disease processes, pathways and networks

Computational approaches for target selection and drug discovery, including: druggability assessment and target selection, polypharmacology, drug reuse, chemical library design, virtual screening technologies, drug discovery enabler pipelines and databases, chemical tool analysis.

ADME/PK and Tox models, including: databases and modeling approaches for ADME and PK, machine learning approaches to predicting toxicity, modeling of pharmacokinetics to man and model organism utility models.

Translational Medicine Informatics Applications/Case Studies, including: Next generation sequencing annotation and biomedicine applications, clinical data integration and application.

Abstract Submission

Authors are invited to submit abstracts (1 page) for presentations and posters by April 10, 2016. Acceptance notifications will be sent out by April 29, 2016. Details of submission process will be made available on the TransMed2016 SIG website.

Keynote Speakers Confirmed:

Russ Altman, Professor of Bioengineering, Genetics, Medicine and Computer Science; Director, Biomedical Informatics Training Program, School of Medicine, Stanford University
John Overington, Director of Bioinformatics at Stratified Medical, Visiting Professor at the Institute of Cardiovascular Science, University College London and the Farr Institute
Sean Mooney, Professor of Biomedical Informatics and Medical Education, University of Washington; Chief Research Information Officer (CRIO) of UW Medicine

Key Dates: (*revised May 16)

March 1, 2016 - Call for one-page abstracts opens
May 27, 2016* - Abstract submissions deadline
May 31, 2016* - Poster and Presentation acceptance notifications.
June 10, 2016* - Final program available
July 8, 2016 - TransMed 2016 SIG

Organizers:
Venkata Satagopam, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
Bissan Al-Lazikani, The Institute of Cancer Research, London, United Kingdom
Reinhard Schneider, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
Mansoor Saqi, European Institute for Systems Biology and Medicine, Lyon, France
Wei Gu, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
Irina Balaur, European Institute for Systems Biology and Medicine, Lyon, France

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VarI SIG

URL:http://varisig.biofold.org

Date: Saturday, July 9

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

Room: Mockingbird 2 (Swan Hotel)

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 variation is interesting in the context of its phenotypic manifestations (e.g. diseases). The discrepancy between the significant availability of genomic data and the current lack of its usefulness in the diagnosis of predisposition to disease generates interest in the development of algorithms for the annotation/prediction of the mutation impact. In addition, the study of the relationships between genetic variation and disease and pharmaco-genomics are key factors for the development of personalized medicine. The recent development of single cell genomics techniques has opened yet another frontier in analysis and interpretation of the genome -- how do we qualify the differences between individual cells and predict their impact on the whole organism level? These and many other questions are up for discussion in our field.

The VarI-SIG provides a forum for the organization of a research network, a community of scientific interest (COSI), facilitating the exchange of ideas and the establishment of new collaborations bringing together varying expertise. It thus supports the unprecedented collaborative effort to manage the complexity of the analysis and evaluation of genetic variation.

The meeting will be divided into two sessions will be divided into two sessions (“Evolution, populations, and disease” and “Function, structure, and regulation”) that will encompass the four main research topics of the field (see below). Note that for this year’s meeting we will particularly encourage submission from “wet-lab” scientists and researchers interested in data clinical annotation, qc, and storage/visualization.

We are interested in 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 genetic variants analysis.

Methods for predicting regulatory/structural/functional impacts of SNVs

Personal Genomics, GWAS studies and SNV prioritization

Population genomics and phylogenetic analysis

ABSTRACT SUBMISSION

VarI-SIG accepts submissions for presentation proposals (2-3 pages) and poster abstracts. Both contributions should be submitted by April 10, 2016. Acceptance notification will be sent out by April 24, 2015.

Please indicate in your submission of presentation proposals if you DO NOT plan to attend the main conference and DO NOT wish to present on the second day of the SIG Abstract should be submitted through EasyChair using the following URL https://www.easychair.org/conferences/?conf=varisig2016

KEY DATES

April 19, 2016 - Poster Abstract and Presentation Proposal submissions deadline

April 24, 2016 - Poster and Presentation Proposal acceptance notifications.

May 8, 2016 - Preliminary SIG Program Available

May 27, 2016 - Complete SIG Program Available

July 9, 2016 - Vari-SIG meeting

SIG CHAIRS

Yana Bromberg, Rutgers University, USA
Emidio Capriotti, University of Düsseldorf, Germany
Hannah Carter, University California, San Diego, USA

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Sponsorship, Exhibit & Recruiting Opportunities

ISCB Sponsorship Guidelines Download Prospectus

Gold Sponsorship | $10,000 Sign Up For Gold

In addition to the following, sponsor gets to choose 9 items from “Add-on” List:

2 free conference registrations

Two (2) invitations to Sponsor & Exhibitor Reception

Logo slide during opening session

Logo with link to organization on conference website index page

Logo with link to organization on conference website sponsorship page

Sponsor in conference program with organization name & description

Unlimited job posts to ISMB/ECCB Career Fair (Gold level only)

Sponsor in conference program with organization name & description
Full-page advertisement in conference program (black & white)

Please note all prices are quoted in US dollars

Silver Benefits | $7,500 Sign Up For Silver

In addition to the following, sponsor gets to choose 7 items from “Add-on” List:

Two (2) free conference registrations

Two (2) invitations to Sponsor & Exhibitor Reception

Logo slide during opening session
Logo with link to organization on conference website index page

Logo with link to organization on conference website sponsorship page

Sponsor in conference program with organization name & description

Half-page advertisement in conference program (Silver and Bronze only, black & white)

Bronze Benefits | $5,000 Sign Up For Bronze

In addition to the following, sponsor gets to choose 5 items from “Add-on” List:

1 free conference registration

Two (2) invitations to Sponsor & Exhibitor Reception
Logo slide during opening session

Logo with link to organization on conference website index page

Logo with link to organization on conference website sponsorship page

Sponsor in conference program with organization name & description

Half-page advertisement in conference program (Silver and Bronze only, black & white)

Copper Benefits | $3,500 Sign Up For Copper

In addition to the following, sponsor gets to choose 1 items from “Add-on” List:

1 free conference registration

Two (2) invitations to Sponsor & Exhibitor Reception
Logo slide during opening session

Logo with link to organization on conference website index page

Logo with link to organization on conference website sponsorship page

Sponsor in conference program with organization name & description

"Add-on" List for Sponsorships

One (1) exhibit booth package (preferred location)

One (1) technology track presentations (scheduled by the organizers)

Organization recognized in ISCB Annual Report with logo and link to preferred URL

Logo recognition as sponsor of Delegate Reception with Sponsors

Electronic list of conference delegates pre- and post-event

Brochure in delegate registration bag

Three (3) additional exhibit hall passes (no access to scientific sessions)

Discounted registration at $350 (35% off regular registration fee)

Full-page advertisement in ISCB Newsletter (full color, issue of choice, Gold Level only)

Half-page advertisement in ISCB Newsletter (Silver and Bronze only, full color, issue of choice)

One (1) additional exhibit hall passes (no access to scientific sessions)

Up to 10 job posts to ISMB/ECCB Career Fair

50% discount off of a Quarter-page advertisement in conference program (black & white)

Two (2) Quarter-page advertisements in ISCB Newsletter (Copper level only, full color, issue of choice)

Additional Sponsorship Opportunities Signup for Additional Sponsorship Items

Organizations will benefit by acknowledgement in the conference program, onsite signage, on the conference website, and through delegate appreciation of your support.

Refreshment Break: ............................................. $3,000

Name Badge Lanyards: ....................................... $5,000

Volunteer T-Shirts: ............................................... $3,000

Inclusion of marketing materials in delegate
bags: .................................................................... $2,000

Student Travel Fellowship: .................................. $1,500

Purchase pre-conference registration list:
exhibitor: ............ $675;non-exhibitor: .......... $900

Purchase post-conference registration list:
exhibitor: .......... $775; non-exhibitor: ........... $1,000

Conference T-Shirts: ........................................... $10,000

Mobile App Exclusive Sponsor: .......................... $6,000

F&B Events:

Networking Reception: ...................................... $10,000

(special branding opportunities are available, please contact ISCB for more information)

Delegate Bags:

Exclusive sponsorship: .................................... $10,000

Multiple sponsors: ............................................ $2,500

Poster Reception: .......................................... $6,000

In addition to sponsoring the poster reception, sponsorship includes:

two tickets to a Disney World theme park that can be part of a drawing when attendees visit the sponsors booth and drops off their business card

Keynote Speaker Sponsorship ..................... $5,000

Sponsorship will receive the following:

Host a private meet and greet with the speaker and up to 20 attendees (sponsors choice of attendees, food and beverage will be the responsibility of the sponsor)

Logoed Key Packets:

Exclusive sponsorship: .................................... $9,000

For multiple sponsors: ..................................... $3,000

Escalator Decals:............................................$1000 ea

maximum of 7

four: 5’6”x27”

three: 6’x27”

Sponsored Water Station area: ..................... $750

IT - $3,000 to sponsor wireless in the meeting space. When an attendees gets on the web in the meeting space, the Sponsor’s logo pop up after the user name and password are entered.

Recharge Lounge in Exhibit Area:

6’ floor model that include video screen: .............................. $8,000

21” table top model that includes video screen: ................... $3,500

Conference Session Video Recording Sponsors: .................... $1,000

If Gold, Silver, Bronze or Copper Sponsor are purchased: ............... $500

ISMB Career Center Recruiters Table Package:
Deadline: June 2nd

ISCB Member:.......... $850 (Not-for-profit, Academic) $1050 (For Profit)
Nonmember:..........$1,350

One 6ft table with two chairs with identification sign

One complimentary registration to ISMB 2016

Unlimited job or program postings on the onsite jobs board, online ISMB jobs board, and 60 days on ISCB Career Center

Complimentary access to an interview room

Space is limited. Sign up today!

To confirm your participation or for additional information contact:
Andrew P. Falter
Exhibit and Sales Specialist
International Society for Computational Biology (ISCB)
email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Office: 203-797-9559
Cell: 571-271-5430

Exhibitor & Technology Track Packages

Exhibitor Sign up Here!

Exhibit at ISMB 2016, July 8-12, in Orlando, Florida, and join over 1500 attendees from the world’s most prestigious research institutions, universities, government agencies and companies.

“My exhibitor experience at ISMB was excellent. I met my goals of gaining leads and strengthening my company's market position,” 2013 exhibitor

Download Exhibitor Pamphlet

EXHIBIT

Promote your brand

Establish your organization as a thought leader

Speak directly to potential customers

Network with scientific and industry leaders

Recruit top talent at the ISMB Career Fair

EXHIBIT BOOTH RATES

Includes one 8ft x 10ft exhibit location**
Advance Rate (Before October 31) $2,750 - SAVE $500
Early Rate (October 31 - January 31) $2,950 - SAVE $300
Standard Rate (After January 31) $3250

**Enhance your company’s visibility and exhibit booth experience with premium placement! Additional fee for premium booth location: +$200

ISMB Exhibitors receive the following package:

Display space, draped booth & furniture package of table, chairs and power

One complimentary conference registration with full access to all conference sessions (excludes SIGs and Satellite Meetings)

Three exhibit hall passes (no session access)

Two complimentary job posts at ISMB Career Fair

Organization listed on conference website with a link back to your organization’s website and in conference program book

Company name on exhibition signage

Wireless internet available in exhibit area

Top 3 Reasons Attendees Visit Exhibit Hall
1) Ability to see new technologies
2)Ability to speak with company experts
3) Ability to interact with new products

TECHNOLOGY TRACK & EXHIBIT PACKAGE

Increase your company’s exposure by including technology track presentation with your exhibit booth! Showcase your software/hardware that is relevant to the bioinformatics and computational biology community. Includes:

All Exhibitor Benefits

One 55-minute session (scheduled by ISMB 2016)

Technology Track presentation listing and overview on conference website

Company name listed in conference program

Presenter must be registered to attend ISMB 2016

(the complimentary registration included in Exhibitor Package may be used for the Tech Track presenter)

*Technology Track presentations are reviewed by the Technology Track selection committee. In the unlikely event your presentation is not accepted, purchaser will have the option to release booth space without penalty or remain in the space and receive a refund in the amount equal to the going rate on purchase date.

Tech Track Presentation + Exhibit Booth (Before January 31) $3,450 – SAVE $500!
Tech Track Presentation + Exhibit Booth (after January 31) $3,650 – SAVE $300
Tech Track Presentation (after January 31) $3,950

TECHNOLOGY TRACK SESSION*

For-profit organization $2,000 – 1 55-minute session
Not-for-profit organization $600 – 1 18-minute session
(Not-for-profit organizations may purchase up to 3 sessions to obtain a consecutive, 55-minute session within a 1-hour presentation block)

Technology Track presentation listing, overview, and 1-page PDF technology description posted on conference website

Company name listed in conference program

Time and date scheduled by ISMB/ECCB 2015

* Does not include conference registration. Presenter must be a registered delegate

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10-10 a.m. - 11:10 a.m.	Chair: Alexander Pico Presentation of NetBio and SysMod COSIs Lars Juhl Jensen, University of Copenhagen, Denmark Nathan Price, Institute of Systems Biology, United States
11:10a.m. - 11:40a.m.	Coffee break
11:40a.m. - 12:40 p.m.	Chair: Nicolas Le Novère Joint Community Discussion Natasa Przulj, University College London, United Kingdom Jonathan Karr, Mount Sinai School of Medicine, United States Closing Comments - Co-chairs

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UPCOMING DEADLINES & NOTICES

Upcoming Conferences

A Global Community

Professional Development, Training, and Education

ISCBintel and Achievements

ISMB 2016 - Equal Opportunity Session

Industry Poster Package

Award Winners

Art & Science Award

Wikipedia Competition

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Fight Against Ebola Award

Winner

Honourable Mentions

Ian Lawson Van Toch Memorial Award for Outstanding Student Paper

PLOS - Late Breaking Research Award

University of California Berkeley Center for Computational Biology Outstanding Oral Poster Prize

University of California Berkeley Center for Computational Biology Outstanding Oral Poster Prize

F1000 Poster Awards

RCSB and PDB Poster Prize

Serafim Batzoglou

ISCB 2016 Innovator Award Keynote

Common NetBio/SysMod COSI Session

Organizers

Overview

Agenda

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

Satellite Meetings (SMs)

Special Interest Group Meetings (SIGs)

Sponsorship, Exhibit & Recruiting Opportunities

ISMB Career Center Recruiters Table Package:

Exhibitor & Technology Track Packages

EXHIBIT

TECHNOLOGY TRACK SESSION*

Exclusively for members

Supporting ISCB

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