Program BioVis@ISMB

BioVis@ISMB 2019 Program

July 22, 2019

LOCATION: Boston 1/2 (Ground Floor)

Invited Speakers

Physical, Contextual, and Full of Value? What do novel directions in Visualization teach us about judging the value of visualization?
Petra Isenberg, AVIZ/INRIA
Petra Isenberg
Bio: Petra Isenberg is a research scientist (CR) at Inria, Saclay, France in the Aviz research group. Prior to joining Inria, she received her PhD from the University of Calgary in 2010 working with Sheelagh Carpendale on collaborative information visualization. Petra also holds a Diplom-engineer degree in Computational Visualistics from the University of Magdeburg. Her main research areas are information visualization and visual analytics with a focus on off-desktop data analysis, interaction, and evaluation. She is particularly interested in exploring how people can most effectively work together when analyzing large and complex data sets on novel display technology such as small touch-screens, wall displays, or tabletops. Petra is associate editor-in-chief at IEEE CG&A, associate editor of the IEEE Transactions on Visualization and Computer Graphics, has served on many organizing committee roles at IEEE VIS including as papers co-chair for Information Visualization (InfoVis), and has been the co-chair of the biennial Beliv workshop since 2012.

Visualisation as a Partner to AI and Machine Learning in Drug Discovery
Lindsay Edwards, GSK
Bio: Lindsay Edwards is UK Head of Artificial Intelligence and Machine Learning (AI/ML) for Glaxo Smith Kline (GSK)’s Pharma R&D, having previously led the Digital, Data & Analytics Unit globally for GSK’s Respiratory division. Alongside his role at GSK, he is also a Fellow of the Royal Society of Biology and a member of the scientific strategy board of the Xtreme Everest Project. Originally a specialist in systems biology, he joined GSK in 2014 from a Lectureship in Physiology at King’s College London, and has held positions in both Australia and the UK. With a background that spans human physiology and biochemistry, metabolomics, computational biology and data science, he has extensive experience of applying novel analytical methods (including machine learning) to biological datasets. His interests currently centre on the use of contemporary analytical tools (including AI) to bring transformational change to drug discovery.


10:15 - 10:20
BioVis Welcome
Jim Procter

10:20 - 12:40
Tools and Techniques
Session Chair: TBD
10:20 - 11:20
[Keynote] Visualisation as a Partner to AI and Machine Learning in Drug Discovery
Authors: Lindsay Edwards
11:20 - 11:40
[Long Talk 1] Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations
Authors: Alex Reynolds, Eric Rynes, Manolis Kellis and Wouter Meuleman
11:40 - 11:50
[Short Talk] GeneDMRs: an R package for Gene-based Differentially Methylated Regions analysis
Authors: Xiao Wang and Haja Kadarmideen
11:50 - 12:00
[Short Talk] The gene Expression and Analysis Resource (gEAR) Portal
Authors: Joshua Orvis, Brian Gottfried, Dustin Olley, Jayaram Kancherla, Beatrice Milon, Kevin Rose, Yang Song, Hector Bravo, Anup Mahurkar and Ronna Hertzano
12:00 - 12:10
[Short Talk] Proactive Visual and Statistical Analysis of Genomic Data in Epiviz
Authors: Zhe Cui, Jayaram Kancherla, Niklas Elmqvist and Hector Corrada Bravo
12:10 - 12:20
[Short Talk] ImmuneRegulation: A web based tool for identifying human immune regulatory elements
Authors: Selim Kalayci, Myvizhi Esai Selvan, Irene Ramos, Chris Cotsapas, Eva Harris, Ruth R. Montgomery, Gregory Poland, Bali Pulendran, John S. Tsang, Robert J. Klein and Zeynep H. Gümüş
Poster Talks - Tools & Techniques I
12:20 - 12:30
[Poster Talk] Addressing Scientific Reproducibility with Data Sharing Platforms: INTERVALS, a case study
Authors: Sylvain Gubian, Adrian Stan, Stephanie Boue, Julia Hoeng and Manuel Peitsch
12:20 - 12:30
[Poster Talk] Advanced Visualization of Data Comparisons with BiocompR
Authors: Yoann Pageaud and Pavlo Lutsik
12:20 - 12:30
[Poster Talk] Nightingale: A library of re-usable data visualisation components
Authors: Xavier Watkins, Daniel Rice, Gustavo Salazar, Leyla Garcia and Aurelien Luciani
Poster Talks - Applications I
12:20 - 12:30
[Poster Talk] Interoperable web-based data visualisation components for the future: Working towards BioJS 3.0
Authors: Dennis Schwartz and Yochannah Yehudi
12:30 - 12:40
[Poster Talk] A network-based approach for visualization and simplification of single-cell RNA sequencing data
Authors: Mariia O. Bilous, Santiago J. Carmona and David Gfeller
12:30 - 12:40
[Poster Talk] GenesetPCA for multi-variate model interpretation
Authors: Rachel Cavill, Nordine Aouni, Luc Linders, David Robinson, Len Vandelaer and Jessica Wiezorek
12:30 - 12:40
[Poster Talk] Cliques of single-cell RNA-seq profiles reveal insights into cell ecology during development and differentiation
Authors: Baihan Lin
12:30 - 12:40
[Poster Talk] Enhancing gene set enrichment using networks
Authors: Michael Prummer
12:30 - 12:40
[Poster Talk] GO Cluster Finder: Visualization tool to identify gene clusters that are composed of functionally related genes
Authors: Mingeun Ji, Jaehee Jung, Jeongkyu Kim and Gangman Yi

12:40 - 14:00
Lunch break

14:00 - 16:00
Session Chair: TBD
14:00 - 15:00
[Keynote] Physical, Contextual, and Full of Value? What do novel directions in Visualization teach us about judging the value of visualization?
Authors: Petra Isenberg
15:00 - 15:20
[Long Talk] Combining programmatic visualization and interactive exploration of large phylogenetic trees using ETE toolkit
Authors: Jaime Huerta-Cepas
15:20 - 15:30
[Short Talk] Flud: a hybrid crowd-algorithm approach for visualizing biological networks
Authors: Aditya Bharadwaj, David Gwizdala, Yoonjin Kim, Kurt Luther and T. M. Murali
15:30 - 15:40
[Short Talk] Evidente – A visual analytics tool for data enrichment in SNP-based phylogenetic tre
Authors: Mathias Witte Paz, Alexander Seitz and Kay Nieselt
15:40 - 15:50
[Short Talk] BioCicle: A Tool for Summarizing and Comparing Taxonomic Profiles out of Biological Sequence Alignments
Authors: Meili Vanegas-Hernandez, Fabio Andres Lopez-Corredor, Tiberio Hernandez, Alejandro Reyes and John Alexis Guerra-Gomez
15:50 - 15:00
[Short Talk] PubScore: quantifying and visualizing the literature relevance of a gene set about any topic
Authors: Tiago Lubiana and Helder Nakaya

16:00 - 16:40
Coffee Break

16:40 - 17:50
Afternoon II
Session Chair: TBD
16:40 - 17:00
[Long Talk] Fast and curious: Efficient exploratory visualization of cross-domain interaction networks
Authors: Mehmet Gönen
17:00 - 17:10
[Short Talk] Density-Preserving Visualization of Single Cells
Authors: Ashwin Narayan, Hyunghoon Cho and Bonnie Berger
17:10 - 17:20
[Short Talk] iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space
Authors: Ahmet Sureyya Rifaioglu, Ataberk Donmez, Aybar Can Acar, Tunca Dogan, Maria Jesus Martin, Rengul Cetin-Atalay and Volkan Atalay
17:20 - 17:30
[Short Talk] Biovis Challenges
Authors: Ana Crisan
Poster Talks - Tools & Techniques II
17:30 - 17:40
[Poster Talk] Visualising Variant Data on 3D Structure Using Jalview
Authors: Mungo Carstairs, James Procter and Geoff Barton
17:30 - 17:40
[Poster Talk] A Customized Force-Directed Layout Algorithm With Genetic Algorithm Techniques For Biological Graphs
Authors: Fırat Aksoydan, Rengül Atalay and Volkan Atalay
17:30 - 17:40
[Poster Talk] The nd_scatter widget in Jupyter and other web contexts
Authors: Aaron Watters
17:30 - 17:40
[Poster Talk] Trend Analysis of Biological Big-data in NABIC
Authors: Dong-Jun Lee, Tae-Ho Lee, Hye-Jin Lee, Do-Kyung An, Yil-Cho Cho and Mi-Sun Lee
Poster Talks - Applications II
17:40 - 17:50
[Poster Talk] ExploSig: Hypothesis-driven Exploration of Mutation Signature Etiology
Authors: Mark Keller, Welles Robinson and Mark Leiserson
17:40 - 17:50
[Poster Talk] Cellxgene: enabling performant, interactive exploration of single-cell transcriptomics data
Authors: Sidney Bell, Jeremy Freeman, Fiona Griffin, Genevieve Haliburton, Justin Kiggins, Bruce Martin, Colin Megill and Charlotte Weaver
17:40 - 17:50
[Poster Talk] Advances in Neuronal Morphology Analysis, Meshing and Visualization with NeuroMorphoVis
Authors: Marwan Abdellah, Samuel Lapere, Felix Schürmann and Henry Markram
17:40 - 17:50
[Poster Talk] Developing web tools for mass cytometry data analysis
Authors: Gabor Beke, Lubos Klucar, Dana Cholujova and Jana Jakubikova

17:50 - 18:00
Closing Remarks
Ana Crisan & Michel Westenberg

18:00 - 20:00
Poster Session