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    The ISCB Affiliates program is designed to forge links between ISCB and regional non-profit membership groups, centers, institutes and networks that involve researchers from various institutions and/or organizations within a defined geographic region involved in the advancement of bioinformatics. Such groups have regular meetings either in person or online, and an organizing body in the form of a board of directors or steering committee. If you are interested in affiliating your regional membership group, center, institute or network with ISCB, please review these guidelines (.pdf) and submit your application using the online ISCB Affiliated Group Application form. Your exploratory questions to ISCB about the appropriateness of a potential future affiliation are also welcome by Diane E. Kovats, ISCB Executive Director (This email address is being protected from spambots. You need JavaScript enabled to view it.).

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Professional Development, Training and Education

ISCBintel and Achievements

THE STORY BEHIND THE SYMPOSIUM



Please check back soon for updates.


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ISCB Hosts the Second Youth Bioinformatics Symposium


The International Society for Computational Biology (ISCB) in partnership with George Mason University, will host the Youth Bioinformatics Symposium (YBS), Exploring Computational Biology at George Mason University in winter 2019.

At our first YBS, in 2016, nearly 100 students from the greater Washington DC area gathered for this event. This engaging one-day event introduces students to the amazing world of computational biology, allowing them to engage with and learn about three popular tools used in research in our hands-on workshop, inform them of the many career areas that bioinformatics is now appearing in, and spark the spirit of competition in our team-based mini science challenges.

We hope you join us to make YBS 2019 just as successful!

REGISTRATION IS NOW CLOSED



Click here to see the 2016 symposium photos.


What IS computational Biology?! Watch this video to find out and click here for additional resources.

 


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TECHNOLOGY TALKS



Bioinformatics as the main protagonist of the microbiome field

Speaker: Dr. Daniel Almonacid

The human microbiome, the microorganisms that live in and on the human body, is one of the most diverse ecosystems on Earth. Our mission at uBiome is to advance the science of the microbiome and make useful products that improve human life. The company’s technological platform is based on the largest microbial dataset in the world (over 300,000 samples), allowing us unprecedented coverage of the microbial diversity across multiple sites of the human body. Using nucleotide sequencing, including our own approach called Precision Sequencing TM, bioinformatics, and machine learning methods, we are developing precision medicine solutions based on microbiome information, empowering doctors, patients, and citizen scientists to improve their quality of life.

Our current portfolio goes from tools for citizens scientists to study their own microbial communities (Explorer TM), to screening tests that can inform doctors of conditions associated with intestinal health (SmartGut TM) and vaginal health (SmartJane TM). The information generated with these analyses allow us continuous improvement of these products.  Additionally, we continually monitor the scientific literature to add new targets as well as novel correlations in our tests. Moreover, the sequencing information combined with the metadata collected from patients has allowed us to discover novel correlations between the microbiome and host conditions, some of which we have been able to understand mechanistically. This knowledge has presented uBiome with the opportunity to in silico design and test drugs that target the microbiome (drugs for bugs), drugs that are naturally produced by the microbiota to modulate the host (drugs from bugs), in addition to identifying and testing potential live biotherapeutics for different health conditions (bugs as drugs).

In this talk I will provide an overview of the work that we are currently doing at uBiome, emphasizing the use of reproducible approaches (both in the laboratory and bioinformatics).  This talk will also highlight the road that uBiome is taking from the research and implementation of clinical tests, toward the development of therapeutics products, having bioinformatics as the main protagonist.


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SPECIAL SESSIONS



links in this page: Bioinformatics EducationDevelopment and application of tools for microbiome studies | Integrative approaches for RNA biology | Precision Medicine | Workshop on Docker | UCSC Genome Browser Workshop | Higher Understanding with Lower Dimensions


Special Sessions at GLBIO 2019

Many of the sessions listed below will consider submissions for contributed talks, including full papers in addition to our regular track. All such papers should be submitted through EasyChair, by the relevant GLBIO 2019 submission deadline. Please contact the organizer of the individual sessions for more information. 


Bioinformatics Education

Accepting abstracts only for oral presentations through EasyChair.
The GLBIO 2019 Special Session on Bioinformatics Education seeks to create a platform for presentation and discussion on the topic of bioinformatics education broadly defined.  The session will mix invited talks from leaders in bioinformatics education with contributed talks and posters from the community.  The intention is to provide a broad representation of perspectives, goals, and topics engaging the bioinformatics education community.  The session is soliciting short abstracts for proposed talks or posters.  Topics of interest include but are not limited to

  • bioinformatics curriculum development for bioinformatics professionals, life scientists, healthcare professionals, K-12 students, or other communities
  • education policy and practices
  • pedagogical strategies or experiences
  • community education resources
  • outreach and diversity efforts
  • case studies in bioinformatics education


The session will conclude with a Panel Discussion and Community Forum organized around the theme of identifying the aims for Bioinformatics Education community over the next five years.

Organizer(s): This email address is being protected from spambots. You need JavaScript enabled to view it.
Web page: https://qubeshub.org/community/groups/glbioedu

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Development and Application of Tools for Microbiome Studies

Accepting abstracts only for oral presentations through EasyChair.
Microbiome research is a rapidly growing area of science. Over the last decade, the number of microbiome sequencing studies has expanded enormously, exploring the intricate communities of microbes within soil, water, the built environment, and the human body, amongst others. There is a need to ensure that adequate expertise and infrastructure is in place to meet the challenge of analyzing the data generated as well as a robust and reliable framework for interpreting the data. This session will cover (1) different computational and statistical methods for analyzing microbiome data sets, and (2) investigations of microbiomes uncovering new insight into functions and dynamics.

Organizers:This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: https://microbiome.wisc.edu/events/glbio2019/


Integrative approaches for RNA biology

Accepting full papers and abstracts for oral presentations through EasyChair.
Post-transcriptional processes play a key role in eukaryotic gene regulation, yet it is not well understood how such processes contribute to the level of functional RNAs within the cell. Such regulation is orchestrated through a variety of mechanisms acting on all aspects of RNA metabolism, including pre-mRNA splicing, stability, polyadenylation, localization, editing, modification, and translation. The diversity of these mechanisms as well as the the increase in RNA-related high-throughput sequencing approaches highlight the need for research into new computational tools addressing post-transcriptional gene regulation.

This session focuses on research findings and methods related to the sequence and structure of RNA as well as its post-transcriptional gene regulation. These include but are not limited to the analysis of transcriptomics and protein-RNA interaction datasets, novel methods for interpretation of single-cell transcriptomes and approaches for RNA structure prediction. The session comprises of invited and selected talks, as well as a workshop on analyses of RNA splicing from high-throughput transcriptome-wide sequencing, and identification of protein/RNA binding sites from CLIP-seq data. The audience is expected to have a basic understanding and experience with computational biology, but not to be experts on RNA biology or the current computational and experimental approaches used in RNA research.

Organizer(s): This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: http://www.iupui.edu/~jangalab/rss_glbio19/

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Precision Medicine

Accepting abstracts only for oral presentations through EasyChair.
Advances in computing have led to a data-driven revolution in biology and promise to guide progress in precision medicine. This session will explore the spectrum of challenges and opportunities in precision medicine, including genomics, electronic health record analytics, and drug discovery. Confirmed speakers apply systems approaches to disease, biomarker, and other complex trait prediction by building computational models that leverage and integrate similarity in genetic, transcriptomic and other omics-level data. The intended audience for this session includes those interested in integrative genomics, statistical modeling, machine learning, and human population genetics applications in medicine.

Organizers: This email address is being protected from spambots. You need JavaScript enabled to view it., This email address is being protected from spambots. You need JavaScript enabled to view it., and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: http://glbio19-precisionmedicine.strikingly.com/

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Workshop on Docker

Half-day Tutorial.  Will not accept submissions.
This workshop aims to be the next step in reproducibility for computational biologists and will focus on using and developing software containers. We will review best practices for practicing reproducible research and teach participants how to use Docker, a popular software for containerization (which can also be used by Singularity, another commonly used containerization platform). Using containers can help overcome the many interoperability and dependency issues often encountered when distributing or installing software. Docker images used conjunction with continuous integration is considered to be a possible solution for the reproducibility crisis plaguing research at large. Similar to a Carpentries workshop, a majority of the proposed workshop will be hands-on live-coding. Workshop attendees are expected to have familiarity with the Unix shell and git/github, bring their own laptops, and follow along with the training.

Organizers: This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: https://uw-madison-datascience.github.io/2019-05-19-glbio-docker/

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UCSC Genome Browser Workshop

Half-day Tutorial.  Will not accept submissions.
As the flood of data from high-throughput sequencing threatens to overwhelm scientists with data generated within individual labs and distributed on the web, visualization becomes even more important.  The UCSC Genome Browser has developed tools that assist in understanding the import of data and provides a platform to view data from multiple sources together.  The endpoint of a data pipeline need not be statistical or tabular.  A potent visualization tool such as the Browser can add an important dimension to data analysis.

This UCSC Genome Browser workshop will offer a tour through recent data releases and new features.  New data include a pre-computed CRISPR guides track on human, mouse and other genome assemblies, a mapping of transcript-specific GTEx expression data, a Gene Interactions track which collects data from multiple curated databases and from data-mining of the literature, and gnomAD.  Recently added features include multi-region mode, which allows for display of exons only or of any regions specified by the user, whether contiguous in the genome or not and Track Collections, which allows co-configuration of multiple tracks and new data formats for loading your data (interation and barChart).

Organizers:  This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Website: https://users.soe.ucsc.edu/~kuhn/workshops/glbio2019/ 

 

Higher Understanding with Lower Dimensions
Tutorial on Dimensionality Reduction Methods for Biomedical Data
Student Run Event

Evening Tutorial.  Will not accept submissions.
Many real-world datasets are high-dimensional in their raw form but have low-dimensional structure, groupings, or representations. Dimensionality reduction methods have been applied to various biomedical datasets with the aim of cancer subtype extraction from mutational signatures, genotype-to-phenotype mapping, gene regulatory program identification, unsupervised multi-omics data integration, and cell differentiation trajectory visualization. This workshop will provide an opportunity to explore a handful of powerful dimensionality reduction methods: matrix factorization, PCA/LDA/GDA, t-SNE and UMAP, diffusion map, and autoencoders. All demos and exercises will use real biomedical datasets from single cell RNA-seq, Hi-C, and de-identified medical records.
 

Organizers: Brittany Baur, Erika Da-Inn Lee, Xiaotong Liu and Henry Neil Ward
Website: https://dimension-reduction.github.io/


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SPONSORS & EXHIBITORS



Gold Sponsors


Bronze Sponsors


Copper Sponsors


General Sponsors


Lunch N' Learn Exhibitors


Exhibitors


Click thumbnail to view pdf of Exhibitors map


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ISCB Town Hall



Topic: ISCB Town Hall
Date: Sunday, July 8 (12:45 PM - 1:45 PM)
Room: Columbus IJ

Description
Join us at the ISCB Town Hall meeting on Sunday, July 8, from 12:45 PM - 1:45 PM to learn more about the latest programs, initiatives, and conferences. This is also your chance to help shape the future of ISCB by providing feedback and suggestions. The Town Hall will close with a celebration of achievement with the announcement of the Student Council Symposium award winners.

TOP 10 PAPERS READING LIST, 2016-2017

Top Reading Papers 2016 - 2017 - RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges



As selected at RECOMB/ISCB Regulatory systems Genomics 2017
(Papers are listed alphabetically by title.  Due to a draw, this year's list contains 11 papers.)

A prior-based integrative framework for functional transcriptional regulatory network inference, Siahpirani A, Roy S. Nucleic Acids Res 45(4):e21

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data, Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. Nat Methods 14(10):975-978

Denoising genome-wide histone ChIP-seq with convolutional neural networks, Koh PW, Pierson E, Kundaje A. Bioinformatics 33(14):i225-i233

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions, Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M. Nat Biotechnol 34(11):1180-1190

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility, Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z. PLoS Comput Biol 13(1):e1005311

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network, Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Genome Biol 18:141

Is a super-enhancer greater than the sum of its parts?, Dukler N, Gulko B, Huang YF, Siepel A. Nat Genet 49:2-3

Quantifying the impact of non-coding variants on transcription factor-DNA binding, Zhao J, Li D, Seo J, Allen AS, Gordan R. Res Comput Mol Biol 10229:336-352

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Nat Genet 49(10):1428-1436

SMiLE-seq identifies binding motifs of single and dimeric transcription factors, Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B. Nat Methods 14(3):316-322

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models, Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R. Mol Syst Biol 13(2):910

CONGRATULATIONS TO ALL AUTHORS!


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    ISCB Members enjoy discounts on conference registration (up to $150), journal subscriptions, book (25% off), and job center postings (free).

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