RECOMB 2018

Program timetable

The scientific program also includes 150 selected posters.

Session 1 – Cancer

Chair: Ben Raphael
• Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel and Roded SharanModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules
• Rebecca Sarto Basso, Dorit Hochbaum and Fabio VandinEfficient Algorithms to Discover Alterations with Complementary Functional Association in Cancer

Session 2 – Sequencing

Chair: Veli Makinen
• Ariya Shajii, Ibrahim Numanagić and Bonnie BergerLatent variable model for aligning barcoded short-reads improves downstream analyses
• Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal and Vineet BafnaTargeted Genotyping of Variable Number Tandem Repeats with adVNTR
• Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel PevznerAssembly of Long Error-Prone Reads and Repeat Classification
• Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson and Rob PatroMantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

Session 3 – Proteomics

Chair: Niko Beerenwinkel
• Sujun Li, Alex Decourcy and Haixu TangConstrained De Novo Sequencing of neo-Epitope Peptides using Tandem Mass Spectrometry
• Alexey Gurevich, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Hosein Mohimani and Pavel Pevzner[Highlight] Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra

Session 4 – Deep learning – Sponsored by IBM Research

Chair: Jian Ma
• Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker and Jian PengDeciphering signaling specificity with deep neural networks
• Tristan Bepler, Andrew Morin, Alex Noble, Julia Brasch, Lawrence Shapiro and Bonnie BergerPositive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs
• Tianming Zhou, Sheng Wang and Jinbo XuDeep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
• Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan and Ming Li[Highlight] De novo Peptide Sequencing by Deep Learning

Session 5 – Cross-species Functional Genomics

Chair: Cenk Sahinalp
• Mark Leiserson, Jason Fan, Anthony Cannistra, Inbar Fried, Tim Lim, Thomas Schaffner, Mark Crovella and Benjamin HescottA Multi-Species Functional Embedding Integrating Sequence and Network Structure
• Yang Yang, Quanquan Gu, Takayo Sasaki, Rachel O’neill, David Gilbert and Jian MaContinuous-trait probabilistic model for comparing multi-species functional genomic data

Session 6 – Algorithmic foundations – Sponsored by CNRS

Chair: Paul Medvedev
• Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam and Srinivas AluruAlgorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis
• Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu and Veli MäkinenUsing Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended
• Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Gallagher, S. Cenk Sahinalp and Hamidreza ChitsazGTED: Graph Traversal Edit Distance
• Yaron OrensteinReverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers

Session 7 – Genome Organization

Chair: Mathieu Blanchette
• Linh Huynh and Fereydoun HormozdiariContribution of structural variation to genome structure: TAD fusion discovery and ranking
• Alon Diament and Tamir Tuller[Highlight] Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence

Session 8 – Cancer Phylogenetics

Chair: Layla Oesper
• Jochen Singer, Jack Kuipers, Katharina Jahn and Niko BeerenwinkelSCIPhI: Single-cell mutation identification via phylogenetic inference
• Salem Malikic, Katharina Jahn, Jack Kuipers, S. Cenk Sahinalp and Niko BeerenwinkelIntegrative inference of subclonal tumor evolution from single-cell and bulk sequencing data

Session 9 – Evolution

Chair: Teresa Przytycka
• Sebastien Roch and Kun-Chieh WangCircular Networks from Distorted Metrics
• Gary Larson, Scott Schmidler and Jeffrey ThorneModeling Dependence in Evolutionary Inference for Proteins

Session 10 – Genetics and Association Studies

Chair: Russell Schwartz
• Tyler Joseph and Itsik Pe’ErInference of population structure from ancient DNA
• Yue Wu, Eleazar Eskin and Sriram SankararamanA unifying framework for summary statistics imputation
• Elior Rahmani, Regev Schweiger, Saharon Rosset, Sriram Sankararaman and Eran HalperinTensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies
• Tyler Cowman and Mehmet Koyuturk[Highlight] Prioritizing Tests of Epistasis Through Hierarchical Representation of Genomic Redundancies

Session 11 – Single-cell Analysis

Chair: Bonnie Berger
• Hyunghoon Cho, Bonnie Berger and Jian PengGeneralizable visualization of mega-scale single-cell data
• Ghislain Durif, Laurent Modolo, Jeff E. Mold, Sophie Lambert-Lacroix and Franck PicardProbabilistic Count Matrix Factorization for Single Cell Expression Data Analysis

Session 12 – Metagenomics and Microbiome

Chair: Fereydoun Hormozdiari
• Anton Bankevich and Pavel PevznerLong Reads Enable Accurate Estimates Of Complexity Of Metagenomes
• Zhemin Zhou, Nina Luhmann, Nabil-Fareed Alikhan, Christopher Quince and Mark AchtmanAccurate Reconstruction of Microbial Strains Using Representative Reference Genomes
• Jasmijn Baaijens, Zine El Aabidine Amal, Eric Rivals and Alexander Schoenhuth[Highlight] De Novo Viral Quasispecies Assembly using Overlap Graphs

Session 13 – Functional Genomics and Metagenomics

Chair: Alex Schoenhuth
• Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna and Siavash MirarabAssembly-free and alignment-free barcoding from genome skims
• Naomi Yamada, William K.M. Lai, Nina Farrell, B. Franklin Pugh and Shaun MahonyCharacterizing protein-DNA binding event subtypes in ChIP-exo data
• Shounak Chakraborty, Stefan Canzar, Tobias Marschall and Marcel H. SchulzChromatyping: Reconstructing nucleosome profiles from NOMe sequencing data
• Jingyi Jessica Li, Guo-Liang Chew and Mark D. Biggin[Highlight] Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them

Session 14 – Learning and Inference

Chair: Fabio Vandin
• Yuriy Sverchkov, Yi-Hsuan Ho, Audrey Gasch and Mark CravenContext-Specific Nested Effects Models
• Cyril Galitzine, Pierre Jean Beltran, Ileana Cristea and Olga VitekStatistical inference of peroxisome dynamics
• Franziska Görtler, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Rainer Spang and Michael AltenbuchingerLoss-function learning for digital tissue deconvolution
• Nima Aghaeepour, Edward Ganio, David McIlwain, Amy Tsai, Martha Tingle, Sofie Van Gassen, Dyani Gaudilliere, Quantin Baca, Leslie McNeil, Robin Okada, Mohammad Sajjad Ghaemi, David Furman, Ronald Wong, Virginia Wingg, Maurice Druzin, Yasser El-Sayed, Cecele Quaintance, Ronald Gibbs, Gary Darmstadt, Gary Shaw, David Stevenson, Robert Tibshirani, Garry Nolan, David Lewis, Martin Ansgt and Brice Gaudilliere[Highlight] An Immune Clock of Human Pregnancy

Session 15 – RNA

Chair: Mireille Regnier
• Stefan Hammer, Yann Ponty, Wei Wang and Sebastian WillFixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures
• Yijie Wang, Jan Hoinka, Piotr Swiderski and Teresa PrzytyckaAptaBlocks: Accelerating the Design of RNA-based Drug Delivery Systems
• Antoine Soulé, Jean-Marc Steyaert and Jerome WaldispuhlA nested 2-level cross-validation ensemble learning pipeline suggests a negative pressure against crosstalk snoRNA-mRNA interactions in Saccharomyces Cerevisae
• Edouard Bonnet, Paweł Rzążewski and Florian SikoraDesigning RNA Secondary Structures is Hard

Social event

Our social event will be held at Musée Montmartre and gardens of Renoir, a meeting place for many artists including Auguste Renoir and Suzanne Paladin.

Starting from 7 PM, we will enjoy the Van Dongen Exhibition, a cocktail for all tastes, including a wine tasting accompanied by smoked salmon appetizers starting.

To get there, take the metro line 10 at Jussieu towards Boulogne/Pont de Saint-Cloud, and get off at Sèvres-Babylone. Switch to line 12 towards Front Populaire, and get off at Lamarck-Caulaincourt. Then walk 7 minutes un-til the 12 rue Cortot. Remember to buy your train tickets in advance to avoid queuing at the ticket machine with around 400 other scientists!