RECOMB-SEQ will be held at the Faculty Center on UCLA campus: 480 Charles E Young Dr E, Los Angeles, CA 90095.


Parking information for visitors:


Saturday, April 16

8:30am – Breakfast
UCLA Faculty Center [view on UCLA map]
480 Charles E Young Dr E, Los Angeles, CA 90095


8:50 – 9:00 a.m. – Opening remarks by organizing committee


9:00 – 9:50 a.m. – KEYNOTE: Jared Simpson


9:55 – 10:35 a.m. – Contributed Talks:


Leena Salmela, Riku Walve, Eric Rivals and Esko Ukkonen. Accurate self correction of errors in long reads using de Bruijn graphs


Joaquín Ezpeleta, Flavia J. Krsticevic, Pilar Bulacio and Elizabeth Tapia. Designing robust watermark barcodes for multiplex long-read sequencing


10:35 – 10:50 a.m. – Coffee break


10:50 – 11:15 a.m. – Contributed Talks:

Lorenzo Calviello, Neelanjan Mukherjee, Emanuel Wyler, Henrik Zauber, Antje Hirsekorn, Matthias Selbach, Markus Landthaler, Benedikt Obermayer and Uwe Ohler. Detecting actively translated open reading frames in ribosome profiling data.


11:15 – 12:15 p.m. – Poster Flash Talks


12:15 – 2:00 p.m. – Lunch & posters


2:00 – 3:00 p.m. – Contributed talks:


Yang Lu, Ting Chen, Jed Fuhrman and Fengzhu Sun. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge

Roye Rozov, Aya Brown Kav, David Bogumil, Itzhak Mizrahi, Eran Halperin and Ron Shamir. Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Dmitry Antipov, Nolan Hartwick, Max Shen, Michael Rayko, Alla Lapidus and Pavel Pevzner. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data


3:00 – 3:15 p.m. – Coffee break


3:15 – 4:05 p.m. – KEYNOTE: Christina Curtis, PhD
Stanford University School of Medicine, Departments of Medicine and Genetics

Quantifying the evolutionary dynamics of human tumor growth and progression

Genetic diversification and clonal selection underlie tumor progression and resistance,
but their dynamics are poorly characterized. Although direct observations of human
tumor growth are impractical, tumors faithfully record their ancestries in the form of
somatic alterations acquired during cell division such that the resultant patterns of intratumor
heterogeneity can be exploited through multi-region sequencing to infer the
evolutionary history of the tumor. Recently, we described a novel ‘Big Bang’ model of
primary human colorectal tumor growth, whereby after transformation, the neoplasm
grows predominantly as a single terminal expansion producing numerous intermixed
sub-clones that are not subject to stringent selection and where both public and most
detectable private alterations arise early during growth. Hence, in this model, the timing
of a mutation is the fundamental determinant of its frequency in the final tumor. Through
spatial computational modeling and statistical inference we verify that the majority of
detectable intra-tumor heterogeneity occurs during the earliest stages of tumor growth.
This new model is compatible with effectively neutral evolution and provides a
framework for quantifying the dynamics of tumor growth with fundamental implications
for earlier detection, therapeutic resistance and metastasis. I will describe extensions of
our computational models to delineate mechanisms of disease progression and discuss
the importance of accounting for tumor growth dynamics when interpreting cancer
genomic data.


4:05 – 4:25 – Coffee break


4:25 – 5:30 – Joint Contributed Talks:


Nisha Rajagopal, Sharanya Srinivasan, Kameron Kooshesh, Yuchun Guo, Matthew Edwards, Budhaditya Banerjee, Tahin Syed, Bart Emons, David Gifford and Richard Sherwood. High-throughput mapping of regulatory DNA

Avi Srivastava, Hirak Sarkar, Laraib Malik and Robert Patro. Fast, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes

Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp and Pavel Pezvner. Single-Molecule Protein Identification by Sub-Nanopore Sensors



Sunday April 17th

8:30am – Breakfast
UCLA Faculty Center [view on UCLA map]
480 Charles E Young Dr E, Los Angeles, CA 90095


9:00 – 9:50 a.m. – Keynote Speaker: Christina Boucher. Systematic Surveillance of the Resistome in Food Production

The World Health Organization describes antimicrobial resistance (AMR) as “an increasingly serious threat to global public health.” This threat has prompted the President of the United States to issue an executive order initiating the National Action Plan for Combating Antibiotic-Resistant Bacteria. The fifth goal of this action plan is to: “improve international collaboration and capacities for antibiotic-resistance prevention, surveillance, control, and antibiotic research and development.” This plan also recognizes that humans, animals, and the environment can be sources of AMR, and calls for a “One-Health approach to disease surveillance.” However, despite the growing concern with antibiotic use in agriculture, there are very few computational methods to measure, quantify, and track the AMR genes within a food production system. In this talk, we present a computational framework that will detect, quantify, and track AMR agents contained in, and around, a food production facility.

Our approach focuses on the systematic surveillance of the microbiome—or more specifically the resistome—within a food production system through the analysis of high throughput sequence data. The computational methods that are part of this approach rely on the use of succinct data structures that dramatically reduce the amount of memory required to store and use the de Bruijn graph. Thus, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible, such as the widespread surveillance of the resistome. In addition to surveillance, we present tools to compare the resistome of different agricultural production systems to identify possible sources of AMR within these systems. Although our methods are developed for the study of the resistome in food production, our methods are generalizable to other agricultural or human settings.


9:50 – 10:50 a.m. – Contributed Talks:

Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze and Yana Safonova. IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction

Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford and Rob Patro. Efficient Index Maintenance Under Dynamic Genome Modification

Sunyoung Kwon, Gyuwan Kim, Byunghan Lee, Sungroh Yoon and Young-Han Kim. NASCUP: Nucleic Acid Sequence Classification by Universal Probability


10:50 – 11:05 a.m. – Coffee break


11:05 – 12:05 p.m. – Panel of Journal Editors
12:05 p.m. – End of Program