RECOMB 2019

Registration

Registration

Opening and Welcome Remarks

Keynote

The Landscape of Disease Comorbidities

Alfonso Valencia

9:00 AM - 10:00 AM

Chair: Martin Vingron (Max Planck Institute for Molecular Genetics)

GENETICS AND ASSOCIATION STUDIES

Interpretable deep learning modeling embedding gene regulatory network for understanding functional genomics in neuropsychiatric disorders [Highlight]

Scalable multi-component linear mixed models with application to SNP heritability estimation

Fast estimation of genetic correlation for Biobank-scale data

Coffee Break

SEQUENCING I

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

Assembly of a pan-genome from deep sequencing of 910 humans of African descent [Highlight]

Lunch Break

Keynote

Evolutionary mathematical modeling enables optimization of glioblastoma treatment strategies

Franziska Michor

1:30 PM - 2:30 PM

Chair: Teresa Przytycka (NIH)

CANCER I

Inferring tumor evolution from longitudinal samples

A sticky multinomial mixture model of strand-coordinated mutational processes in cancer

Coffee Break

REGULATORY GENOMICS

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map [Highlight]

MethCP: Differentially Methylated Region Detection with Change Point Models

Distinguishing biological from technical sources of variation by leveraging multiple methylation datasets

STATISTICAL FOUNDATIONS

AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing [Highlight]

A Note on Computing Interval Overlap Statistics

Efficient estimation and applications of cross-validated genetic predictions

How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories

RECOMB Business Meeting

Keynote

Harnessing genetic interactions to advance whole-exome precision cancer treatment

Eytan Ruppin

9:00 AM - 10:00 AM

Chair: Cenk Sahinalp (Indiana University)

Venue: Lisner Auditorium

CANCER II

Mutational interactions define novel cancer subgroups [Highlight]

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data

Coffee Break

SINGLE CELL I

Geometric sketching of single-cell data preserves transcriptional structure

Dynamic pseudo-time warping of complex single-cell trajectories

Accurate sub-population detection and mapping across single cell experiments with PopCorn

Lunch Break

Keynote

Evolution-CSI: hunting for evidence in the protein universe

Rachel Kolodny

1:30 PM - 2:30 PM

Chair: Lenore Cowen (Tufts University)

Venue: Lisner Auditorium

PROTEIN STRUCTURE

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning

Distance-based Protein Folding Powered by Deep Learning

Minimization-Aware Recursive K* (MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the Energy Landscape

Coffee Break

SINGLE CELL II

netNMF: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

Disentangled Representations of Cellular Identity

Towards a post-clustering test for differential expression

TEXT MINING

RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature

Identifying clinical terms in free-text notes using ontology-guided machine learning

Break

Poster Session and Reception

6:00 PM - 8:00 PM

Venue: Marvin Center, Grand Ballroom

Keynote

Innovating in Biomedical Data Science for Precision Health

Carlos Bustamante

9:00 AM - 10:00 AM

Chair: Bonnie Berger (MIT)

Venue: Lisner Auditorium

GENOMIC PRIVACY

Identity inference of genomic data using long-range familial searches [Highlight]

Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave

Realizing private and practical pharmacological collaboration [Highlight]

Coffee Break

Special Panel Session on Genomic Privacy

11:20 AM - 12:30 PM

Chair: Bonnie Berger

Lunch Break

PROTEOMICS

Venue: Lisner Auditorium

De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments

Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry [Highlight]

GENOME ORGANIZATION

Comparing 3D Genome Organization in Multiple Species using Phylo-HMRF

ModHMM: A modular supra-Bayesian genome segmentation method

Coffee Break

SEQUENCING II

An Efficient and Scalable Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

Sparse Binary Relation Representations for Genome Graph Annotation

De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm

OMGS: Optical Map-based Genome Scaffolding

Depart for Social Event

Keynote

Uncovering heterogeneity in microbial communities

Mihai Pop

9:00 AM - 10:00 AM

Chair: Tandy Warnow (UIUC)

Venue: Lisner Auditorium

METAGENOMICS

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics [Highlight]

Fast Approximation of Frequent k-mers and Applications to Metagenomics

Coffee Break

PANEL WITH NSF AND NIH PROGRAM DIRECTORS

11:00 AM - 12:00 PM

Lunch Break

NETWORKS AND PATHWAY ANALYSIS

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data [Highlight]

GRep: Gene Set Representation via Gaussian Embedding

The Distance Precision Matrix: computing networks from non-linear relationships [Highlight]

Coffee Break

ALGORITHMIC FOUNDATIONS

APPLES: Fast Distance Based Phylogenetic Placement

On the Complexity of Sequence to Graph Alignment

SEQUENCE LEARNING

Learning Robust Multi-Label Sample Specific Distances for Identifying HIV-1 Drug Resistance

Biological Sequence Modeling with Convolutional Kernel Networks

CONFERENCE CLOSING AND AWARDS CEREMONY

4:10 PM - 5:00 PM