Award Winners

Ian Lawson Van Toch Memorial Award for Outstanding Student Paper | RCSB PDB Poster Prize | Bio-ontologies COSI | BioVis COSI | CompMS COSI | CAMDA Trophy Award for Best Presentation | EvolCompGen COSI |  HiTSeQ Award | iRNA Award | MLCSB COSI | RegSys COSI | SysMod COSI | TransMed COSI

Award Winner:

Quentin Garrido, Université Gustave Eiffel, ESIEE Paris, LIGM, France
Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder

Honorable Mentions:

Mohammadamin Edrisi, Rice University, United States
Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Bing-Xue Du, School of Life Sciences, Northwestern Polytechnical University, China
MLGL-MP: A Multi-Label Graph Learning Framework Enhanced by Pathway Interdependence for Metabolic Pathway Prediction

With Support From:

Nicola Bordin, University College London, London
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bio-ontologies COSI

Best Poster

Michael Bradshaw, University of Colorado Boulder, United States
Identification of clusters containing future gene-to-phenotype relations across heterogeneous data sources

Best Talk

Frederic B. Bastian, University of Lausanne, SIB Swiss Institute of Bioinformatics, Switzerland
Creation and unification of development and life stage ontologies for animals

BioVis COSI

Best Long Abstract

Mark Keller, Harvard Medical School
Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis

Best Poster

Camilo Valdes, Lawrence Livermore National Laboratory, United States
Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles

CompMS COSI

Best Talk

Daniela Klaproth-Andrade, Technical University of Munich, Germany
A genetic algorithm with deep learning-based guided mutations improves de novo peptide sequencing

Best Poster

Chathurani Ranathunge, Eastern Virginia Medical School, United States
promor: An Integrative Approach for Proteomics Data Analysis and Modeling

CAMDA Trophy Award for Best Presentation

Eunyoung Kim, Gwangju Institute of Science and Technology, South Korea  
DeSIDE-DDI: Interpretable prediction of drug-drug interactions using drug-induced gene expressions

EvolCompGen Award

Talks
Winners

Taeyoung Kim, Giltae Song | Multi-modal Transformer based deep neural network for determining false positive structural variation calls
Joel Nitta, Eric Schuettpelz, Santiago Ramírez-Barahona, Wataru Iwasaki | An Open and Continuously Updated Fern Tree of Life (FTOL)

Honorable mentions

Mathieu Gascon, Yoann Anselmetti, Nadia El-Mabrouk | Non-binary Tree Reconciliation with Endosymbiotic Gene Transfer
Yuting Xiao, Maureen Stolzer, Dannie Durand | Domain Promiscuity Correlates with Rates of Domain Gain and Loss

Posters
Winner

Sungsik Kong, David Swofford, Laura Kubatko | Inference of phylogenetic networks from sequence data using composite likelihood

Honorable mentions

Ethan Wolfe, Joseph Burke, Stephanie Shames, Janani Ravi | Characterizing effector-metaeffector pairs in Legionella pneumophila
Chao Chun Liu, William Hsiao | Supervised machine learning reveals high efficacy of mobile elements to predict Salmonella outbreak linkage
Yiyan Yang, Xiaofang Jiang | Evolink: a Phylogenetic Approach for Rapid Identification of Phenotype-Genotype Associations in Large-scale Microbial Data

HiTSeQ Award

Best Talk

Rachael Aubin, University of Pennsylvania, United States
ConDecon: a clustering-independent method for estimating single-cell abundance in bulk tissues using reference single-cell RNA-seq data

iRNA Award

Best Posters

Christina Akirtava, Carnegie Mellon University, United States
Unraveling the roles of 5’ transcript leaders in gene regulation

Subhashis Natua, University of Illinois at Urbana-Champaign, United States
Post-transcriptional silencing of the nuclear poly(A) binding protein expression is essential for postnatal cardiac maturation and function

MLCSB COSI

Best Poster

Yusuf Roohani, Stanford University, United States
GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations

NetBio COSI

Best Talk

Mikaela Koutrouli, Novo Nordisk Foundation Center of Protein Research, Denmark FAVA: High-quality functional association networks inferred from massive scRNA-seq and proteomics data 

RegSys COSI

Best Talk

Jointly awarded to:

Pia Rautenstrauch, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany “Liam tackles complex multimodal single-cell data integration challenges”

and

Anusri Pampari, Stanford University, United States “Base-resolution deep learning models of chromatin accessibility reveal combinatorial sequence motif syntax and regulatory variation”

SysMod COSI

1st Best Poster: Caroline I. Larkin, University of Pittsburgh, United States
A Mechanistic Model of Alphavirus Replication within a Mammalian Host Cell

2nd Best Poster: Kang Jin, Cincinnati Children's Hopsital Medical Center, United States
CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data

3rd Best Poster Award: Shaimaa Bakr, Stanford University, United States
Identifying key multifunctional components shared by critical cancer and normal liver pathways via sparseGMM

TransMed COSI

Best Talk (Best Oral Presentation)

Madison Darmofal, Memorial Sloan Kettering, Weill Cornell Graduate School, United States
Genome-Derived Diagnosis: Deep Learning Model for Tumor Type Prediction using MSK-IMPACT data

Yue Wang, University of Pittsburgh, United States
Perturbed Transcriptomic Analyses Identify Chemo-immunotherapy Synergisms to Shift Anti-PD1 Resistance in Cancer

Best Poster

Junjie Peng, University College London, United Kingdom    
Patient-specific and disease-related determinants for cardiovascular disease (CVD) risk stratification in the APPLE (Atherosclerosis Prevention in Paediatric Lupus Erythematosus) clinical trial cohort

Jeppe Severens, Leiden University Medical Center, Netherlands
Joint genetics and transcriptomics based classification of acute myeloid leukaemia patients

Exhibitor Floor Plan ISMB 2022

Download Full Floor Plan

ISMB 2022 Exhibitors and Recruiters

Exhibitors

Virtual Exhibitors

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www.iscb.org

The International Society for Computational Biology (ISCB) (www.iscb.org) was the first and continues to be the only society representing computational biology and bioinformatics worldwide. ISCB serves a global community of nearly 3,400 scientists dedicated to advancing the scientific understanding of living systems through computation by:

• convening the world’s experts and future leaders in top conferences
• partnering with publications that promote discovery and expand access to computational biology and bioinformatics
• delivering valuable information about training, education, employment, and relevant news
• providing an influential voice on government and scientific policies that are important to our members

ISCB has three official journals – OUP Bioinformatics, PLOS Computational Biology and F1000Research ISCB Community Journal, and has affiliations in place with several other publications for the benefit of our members.

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http://www.overleaf.com/

Overleaf is a free, collaborative, cloud-based LaTeX editor which makes the process of writing, editing and publishing scientific documents quicker and easier. This intuitive online platform has seen rapid adoption across science and research, and Overleaf's award-winning collaboration technology is now in use by over 9 million researchers, students and technical writers in institutions, labs and industry worldwide. It’s simple and intuitive to use – all you need is a web browser – try it out and use it for free at www.overleaf.com.

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https://www.stjude.org/education-training/advanced-training/postdoctoral-fellowship-opportunities.html

At St. Jude, we have one common goal: find cures for children with cancer and other life-threatening diseases through research and treatment. As both a world class research institute and a specialized children’s hospital, St. Jude provides an unparalleled opportunity to advance your scientific training and launch your career.

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https://f1000research.com/?utm_source=shared_link&utm_medium=post&utm_campaign=JRG25016

F1000Research is an Open Research publishing platform for scientists, scholars and clinicians across all disciplines offering rapid publication of articles and other research outputs without editorial bias. We publish research across all academic disciplines and in multiple formats, including original articles, data notes, software tool articles and method articles.

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https://dbmi.hms.harvard.edu/

The Harvard Medical School Department of Biomedical Informatics offers a variety of opportunities to increase your knowledge base and skill set in the application of quantitative principles to biomedical discovery. Come learn about our educational programs which include a Master’s, PhD, and Summer Institute and hear about our postdoctoral fellowships, faculty positions and other career opportunities.

Visit our booth to learn more about educational and career opportunities. For more information please visit: http://dbmi.hms.harvard.edu

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https://academic.oup.com/BIOINFORMATICS

Oxford University Press publishes a range of computational biology journals, including Bioinformatics, Bioinformatics Advances, GigaScience, Nucleic Acids Research, NAR Genomics and Bioinformatics, Database, Briefings in Bioinformatics, Briefings in Functional Genomics, and more. Bioinformatics publishes the highest quality scientific papers and review articles with its main focus is on new developments in genome bioinformatics and computational biology.

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https://www.ibm.com/

With 3,000+ researchers in 12 labs on six continents focused on Accelerated Discovery and Exploratory Sciences, IBM Research pioneers the most promising and disruptive technologies in hybrid cloud, AI and quantum computing. The combination of increasingly powerful computers and AI offers the possibility to be able to detect, diagnose, understand and cure diseases like never before. At IBM Research, we’re working on creating software and AI systems that can convert reams of health data into useable information for researchers and clinicians the world over. Scientific discovery is driven by two forces: the development of new capabilities and the relentless tenacity of the world’s sharpest minds. We see it as our duty to accelerate scientific progress by developing cutting-edge technologies, demonstrating scalable processes, and deploying new models of collaborative innovation.

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https://www.med.wisc.edu/

Biomedical Data Science (BDS) encompasses the study and pursuit of the effective uses of biomedical data, information, and knowledge for scientific inquiry, problem-solving, and decision-making, driven by efforts to improve human health. The graduate programs in BDS blend the best of statistics, computer sciences, biostatistics and biomedical informatics and train students to develop computational and mathematical approaches to analyze large-scale biomedical data and to lead collaborative, interdisciplinary team science efforts.

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https://www.mdpi.com/journal/life/sections/biochemistry_biophysics_computational

Life is an international, peer-reviewed, open access journal of scientific studies related to fundamental themes in life sciences, published monthly online by MDPI. It publishes topics include, but are not limited to biomolecular design, activation and function; molecular evolution; biomolecular trafficking, and networks; membranes, and molecular organization in cells. We encourage the submission of manuscripts that fall in the broad areas of:
Structural biology
Computational biology
Biochemistry and biophysics of subcellular and molecular processes

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https://www.syngenta.com/

Syngenta plays a vital role in enabling the food chain to feed the world safely and take care of our planet. Our ambition is to be the most collaborative and trusted team in agriculture, providing leading seeds and crop protection innovations to enhance the prosperity of farmers, wherever they are.

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http://www.jax.org/

The Jackson Laboratory is an independent, nonprofit biomedical research institution with more than 2,400 employees. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.

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https://www.corteva.com/

Corteva Agriscience is a global pure-play agriculture company that provides farmers around the world with the most complete portfolio in the industry - including a balanced and diverse mix of seed, crop protection and digital solutions focused on maximizing productivity to enhance yield and profitability. With some of the most recognized brands in agriculture and an industry-leading product and technology pipeline well positioned to drive growth, the company is committed to working with stakeholders throughout the food system as it fulfills its promise to enrich the lives of those who produce and those who consume, ensuring progress for generations to come. More information can be found at www.corteva.com

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https://memverge.com/

As the world's enterprises accelerate their digital transformations, they discover that next-generation applications must deal with data that are bigger and faster at the same time, outstripping the capabilities of today's infrastructure. MemVerge's mission is to deliver a new architecture, called Big Memory Computing, that converges memory and storage, thereby removing the storage I/O bottleneck once and for all. MemVerge's Memory Machine™ Software virtualizes heterogeneous memory hardware into a software-defined memory service that has both high capacity and high performance. MemVerge ZeroIO™ In-Memory Snapshot technology captures the state of running applications, and can be used for application roll-back, cloning and high availability. The results are new levels of productivity, performance, availability, and mobility for today's data-centric applications, both on-premises and in the cloud.

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https://www.fulgentgenetics.com/

Fulgent Genetics is a global leader in next-generation sequencing with a focus on developing flexible and affordable genetic testing panels. By merging the fields of genetics, molecular biology, and computer science, we pursue excellence in genetic sequencing, scalability, and data analysis. We offer an unrivaled catalog of genetic testing covering over 18,000+ single genes, 800+ rare disease tests, whole-genome sequencing, whole-genome copy number variation analysis, mitochondrial sequencing, and CLIA/CAP quality sequencing services.

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https://www.tempus.com/

We are a technology company that has built the world’s largest library of clinical and molecular data and an operating system to make that data accessible and useful, starting with cancer. Our goal is for each patient to benefit from the treatment of others who came before.

We’re looking for people who can help us change the world. Who question the status quo and don’t shy away from tough problems. For the builders who are never done building and the learners who are never done learning. We’re looking for passionate people with undying curiosity. Those who want to attack one of the most challenging problems ever faced… head on.

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https://www.mygoblet.org/

GOBLET is an international organisation with the mission to cultivate a global community of bioinformatics trainers who support learning, education and training. GOBLET’s mission was defined under the vision that there is a clear need to harmonise bioinformatics training activities and to unite, inspire, and equip bioinformatics trainers worldwide. Towards this, GOBLET collaborates with national and international bioinformatics organisations. Relevant activities include the initiation of a series of standards and guidelines, work on the definition of competencies, promotion of best practices, and providing high-quality resources for learning, education and training in bioinformatics and computational biology, on a global scale.

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https://www.frontiersin.org/journals/bioinformatics#

Frontiers in Bioinformatics is a young open-access journal, led by Prof. Adam Godzik (University of California Riverside). The journal provides a forum where new discoveries in all aspects of bioinformatics and the analysis of biological data are presented. Frontiers in Bioinformatics focuses on new bioinformatics tools and novel applications that can bring new insights to specific biological problems, efforts that cross standard field boundaries.

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CAREER CENTER @ ISMB 2022

Recruit – Engage – Inform

Connect with over 1,400 researchers, students, & postdocs from around the world!

Promote, Discuss, & Interview – Enjoy three-days of connecting all in one place!

**Jobs will be posted on the ISCB career page giving you 60 days of promotion**

For further information, Contact: Nadine K Costello This email address is being protected from spambots. You need JavaScript enabled to view it.

Career Fair

Career Fair will take place Thursday, July 14th from 12:30pm - 2pm in the Exhibition Area - Grand Terrace.

Click HERE for the digital ISMB Jobs Board and visit the physical boards in the Grand Terrace.

Attending the Career Fair

• Conference attendees participating in the Career Fair must upload their resume into the ISCB Career Center (https://careers.iscb.org/) resume repository and will have a 'Talent' ribbon on their conference badge.
  • Sign-up is allowed on-site to attend the Career Fair but attendees MUST stop by the ISCB Booth and sign up.

Recruiting at the Career Fair

• Institutions/Exhibitors participating in the Career Fair will have a blue identifier on their exhibit booth/recruiter tables. Additional institutions that are recruiting will have a table in the Exhibit Hall near the Jobs Board.
  • Recruiters participating in the Career Fair will have available positions posted on the jobs board and/or additional opportunities at their tables and will have a 'Talents Seeker' ribbon on their conference badge.
• Please stop by the ISCB booth to see Bel Hanson or email This email address is being protected from spambots. You need JavaScript enabled to view it. with any questions.

Career Fair Recruiters

Exhibitor Info

Please read the following information carefully and ensure that you have reviewed your Sponsor/Exhibitor Listing at  https://www.iscb.org/ismb2022-exhibitors/floor-plan  If you have questions contact:

Steven Leard
ISMB Conference Director
This email address is being protected from spambots. You need JavaScript enabled to view it.

ISMB 2022 is a table top-display exhibition in the Grand Terrace at the Monona Terrace Convention Center.

Virtual Exhibit Booth details:

• Audio Visual Equipment
• Badges
• Catering
• Conference Venue & Location
• Damage to Premises
• Delivery Information / In-house Transport (Shipping Instructions)
• Demonstrations
• Exhibitor After Hours Access
• Exhibitor Package
• Exhibition Schedule
• Helium Balloons
• Hotel Accommodation
• Indemnification
• Internet
• ISMB Exhibitor Rules
• Lead Generation
• Leaflet Distribution
• Security
  
  

If you require AV rental equipment please contact This email address is being protected from spambots. You need JavaScript enabled to view it. 

Exhibitors who are participating in Madison should collect their name badges from the ISMB 2022 Conference Registration located on Level 4 of the conference center.

If you require catering please contact This email address is being protected from spambots. You need JavaScript enabled to view it. 

Please note NO outside food or beverages can be brought into the exhibit hall.

No nails, screws or other fixtures may be driven into any part of the premises including the floors. Should any damage occur, the Exhibitor would be invoiced for repair charges incurred.

Please review the ISCB Exhibitor and Technology Track guidelines for presentations available here. 

Leaflets may not be distributed from anywhere other than the exhibition stand without receiving prior permission from the Organizers. Leaflets displayed or distributed at any other point throughout the venue, without prior permission, will be removed and destroyed by the Organizers.

No lead generation technologies are offered at ISMB 2022. The conference platform allows delegates to network and exhibitors can use access the platform and this method of networking.

ISMB does not provide security in the exhibit area during off-hours. Exhibitors are encouraged to remove any valuable items from the exhibit area each evening. Please note that ISMB, ISCB and the Monona Terrace Community and Convention Center are not responsible for missing or lost articles at the conference.

Tools for Shareable Protein Analysis: ProteinCodeathon@ISMB2022

Location: Doty Room, 2^nd Floor, Hilton Madison Monona Terrace Hotel and Zoom

Introduction to codeathon themes, projects, teams, and logistics (Allissa Dillman, Alexa Salsbury, Philippe Youkharibache) - July 10, 1pm - 2pm CT
Introduction to iCn3D (Alexa Salsbury) - July 10, 2pm - 2:45pm CT
iCn3D in Biology LibreTexts (Henry Jakubowski) - July 10, 2:45pm – 3:30pm CT
Codeathon - 10 - 14, July 2022
Final Project Presentations and Discussion - Wednesday, July 13, 6:15pm - 8:15pm CT
Project/Team Wrapups - Thursday, July 14, 12:15pm - 1:15pm CT

Organizers: Ravi Abrol, Philippe Youkharibache, Jiyao Wang, Allissa Dillman, Alexa Salsbury, Tom Madej

Codeathon Website
Registration Link

Towards integrating protein sequence-structure-function analysis, visualization and open collaborative research

The two main goals of this hybrid codeathon are:

• To develop open source software modules and collaboration tools for universal biomolecular analyses enabling integration of diverse knowledge and datasets.
• To create a sustainable diverse community of developers and designers for continued development of such tools

Preamble

During the last two hackathons, Hackathon at ISMB2020 and Hackathon at ISMB2021, we started a series of developments towards the in-depth and systematic analysis of molecular interactions, effects of mutations, protein flexibility, analysis of large datasets, annotations of topological domains of membrane protein receptors, and we opened up iCn3D to evolve towards an open platform to interoperate with external data and software. A feature unique to iCn3D is the ability to share data analysis and structural views through a simple web link (example).

We will continue these developments at this year’s codeathon with a focus on biochemical analysis of proteins including mutations, large sequence/structure datasets (AlphaFold, Uniprot, PDB, etc), and iCn3D User interface.

Registration and fees

Registration Link
Applications are due 9 July 2022.
There is no registration fee for the Codeathon@ISMB2022 beyond your normal ISMB 2022 registration fees. You have to be registered at ISMB 2022 to participate in this codeathon.

Who can participate and what skills are needed?

As the codeathon will be conducted in a hybrid format, we will have two types of teams: all-in-person teams, and all-virtual teams. A team will be composed of individuals who all have different backgrounds and skills. We know by experience that blending a diverse set of skills is what forms a good team. We are welcoming hard core programmers as well scientists with little programming experience, as long as they have knowledge on the scientific application side. Some participants may have both sides and some may have one side, but the outcome of any project is a team effort.

We encourage researchers working in all areas of computational biology to join us in developing the above mentioned tools. In terms of coding, we will mainly use Python or JavaScript to write code. But any coding experience such as C/C++, JAVA, Perl, Julia, Rust, etc. and/or working knowledge of MySQL, XML, JSON formats should be good enough, especially for algorithmic or database/backend or middleware development. Experience with deployment of web-based tools will also be very useful. Our code will be deposited into GitHub. Some experience in Git/GitHub is helpful. What matters most is to bring new ideas and develop prototype functionality, not a final product. We are also seeking wet lab researchers working on all aspects of protein sequence, structure, and function with to join the codeathon teams to provide scientific input from the point of view of the needs of the community.

Outcome

Participants will contribute to prototype new open source software functionality, learn new skills, and get a chance to become part of a growing community. One of the objectives of this codeathon is to develop tools and publish their development and/or application as a peer-reviewed publication in the Frontiers in Genetics (Computational Genomics), Frontiers in Molecular Biosciences (Structural Biology), or Frontiers in Bioinformatics (Integrative Bioinformatics) journal within 3-6 months after the codeathon. Your contributions will be recognized through co-authorship in the submitted manuscripts. In addition, we would like to sustain this community of developers in between the codeathons through dedicated communication channels, as our hope is that you will continue to help develop these tools.

Getting Started with iCn3D

1. PROGRAM:
   1. iCn3D publications: You can familiarize yourself with iCn3D through our recent publication and preprint.
   2. Try iCn3D now!
   3. iCn3D@GitHub
2. TUTORIALS and DOCUMENTATION
   1. iCn3D Tutorial Part 1 (the basics): Video, Slides
   2. iCn3D Tutorial Part 2 (molecular interactions, structural comparisons, etc): Video, Slides
   3. Full documentation (Help pages)

Technical and Project Support

Each team will have a Slack subchannel for communication with each other and with the team leader. Each participant will also be part of a Technical Support subchannel, which should be used for technical questions related to github, slack, compute nodes, etc. and which will be monitored continuously by the codeathon’s tech-support team.

We look forward to seeing you at the codeathon!
- Ravi, Philippe, Jiyao, Allissa, Alexa, Tom

ISMB 2022 will be held at the Monona Terrace Convention Centre
One John Nolen Drive
Madison, Wisconsin, USA, 53703

The Madison Airport is Dane County Regional Airport, also known as Truax Field, is a civil-military airport located 7 miles northeast of Downtown Madison.

Learn more about the airport at: https://www.msnairport.com 

Options to fly to Chicago O'Hare (ORD); Milwaukee Mitchell International Airport, (MKE); Minneapolis−Saint Paul (MSP) and to drive or shuttle to Madison may be a consideration.

Shuttle options include:

• ORD to UW | Van Galder
• MKE to UW | Badger Bus
• MSP to UW | Metro Transit + Megabus Minneapolis or St. Paul depending on the stop selected

Maps & Transportation | Plan Your Trip to Madison, WI (visitmadison.com)

ISCB Town Hall

Topic: ISCB Town Hall
Date: Monday, July 11 (6:15 PM - 7:30 PM CDT)
Room: Lecture Hall, Level Four

Description:
Join us at the ISCB Town Hall meeting on Monday, July 11, 6:15 PM - 7:15 PM CDT 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 Wikipedia Competition Award winners, Art in Science Award winners, Student Council Symposium award winners, celebration of the 2022 Class of Fellows, and announcement of the incoming Board of Directors.