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WEMSA2024: Workshop on Emerging Methods for Sequence Analysis

The Center for Computational Biology and Bioinformatics at Penn State will host a one-day workshop on emerging methods for sequence analysis on August 9, 2024. The workshop will feature a mix of invited speakers and talks selected from submitted abstracts. We thank Zhiping Weng (University of Massachusetts) and Ben Raphael (Princeton University) for accepting our invitation as keynote speakers! To participate in the workshop please fill the registration form below. Registration is free.

The conference will be held in Agricultural Sciences and Industries Building. You can find its location on the map below along with other State College locations of interest.

CONFERENCE MAP

Topics of interest include, but are not limited to:

  • data structures and algorithms for indexing, searching, sketching, assembling, and comparing sequencing data
  • theoretical analysis on abstracted mathematical formulations
  • statistical inference and association studies with sequencing data
  • methods for analyzing omics data, e.g., single-cell, transcriptomic, or proteogenomic data

Key Dates

  • July 06: Abstract submission deadline
  • July 08: Abstract notification deadline
  • July 15: Registration deadline. Registrations after this deadline are space permitting, on a first-come first-serve basis.
  • July 20: Late poster submission deadline
  • Aug 09 : Day of workshop

Schedule

Session Time Speaker Title Full-Author List
Breakfast, poster setup, registration 8:30 AM
Morning keynote 9:00 AM Zhiping Weng Using a Comprehensive Atlas and Predictive Models to Reveal the Complexity and Evolution of cis-Regulatory Elements
Session 1 10:00 AM Md Hasin Abrar PLA-index: A k-mer Index Exploiting Rank Curve Linearity Md. Hasin Abrar, Paul Medvedev
10:15 AM Adam Park The Procrustean Graph: A breakthrough in rapid k-mer exploration across varying orders Adam Park, David Koslicki
Morning coffee break with posters 10:30 AM
Session 2 11:00 AM Stephen Hwang MEM-based pangenome indexing for k-mer queries Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine Jenike; Sam Kovaka; Michael C. Schatz, Ben Langmead
11:15 AM Yun William Yu On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis
11:30 AM Guillaume Marçais Designing robust sketching methods Guillaume Marçais, C.S. Elder, Carl Kingsford
11:45 AM Ke Chen Sequence similarity estimation by random subsequence embedding Vinamratha Pattar, Ke Chen, Mingfu Shao
Lunch break (lunch provided) and poster session 12:00 PM
Session 3 1:30 PM Omar Ahmed Cliffy: robust 16S rRNA classification based on a compressed LCA index Omar Ahmed, Christina Boucher, Ben Langmead
1:45 PM Alex Sweeten Alignment-Free Annotation of Satellite DNA Alex Sweeten, Adam Phillippy, Michael Schatz
2:00 PM Sina Majidian Orthology inference at scale with FastOMA Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy, Stefano Pascarelli, David Moi, Natasha Glover, Adrian Altenhoff, Christophe Dessimoz
2:15 PM Mariia Pospelova Comparative analysis of adaptive immune receptor loci in mammalian species Maria Pospelova, Anton Zamyatin, Yixin Zhu, Katalin Voss, Corey T. Watson, Klaus-Peter Koepfli, Matt Pennell, Anton Bankevich, Yana Safonova
2:30 PM Hyuntae Na Reproducing the polarity characteristics of amino acids in the atomic level by coarse-graining waters and predicting the interactions between protein atoms and waters.
Afternoon coffee break with posters 2:45 PM
Session 4 3:15 PM Justin Silverman The First Software for Differential Expression/Abundance Analysis that is Actually Robust to Sequencing Depth Artifacts. Justin D. Silverman, Michelle Nixon, Greg Gloor
3:30 PM Qunhua Li Linkreg: a statistical framework for linking genome-wide candidate cis-regulatory elements to target genes Qiuhai Zeng, Guanjue Xiang, Ross Hardison, Xiang Zhu, and Qunhua Li
Afternoon keynote 3:45 PM Ben Raphael TBA
Closing remarks 4:45 PM

Accepted posters

  • Xiaofei Carl Zang. Anchorage accurately assembles anchor-flanked synthetic long reads
  • Vikram Shivakumar. Mumemto: efficient maximal matching across multiple genomes
  • Ke Chen Heuristic. minimum flow decomposition for general graphs
  • Carina Howell. The Power of Community of Practice (CoP) in Implementing Classroom Undergraduate Research Experiences (CUREs)
  • Juan Cerda. Genome evolution in parasitic plants; Insights from the first chromosome assemblies in Cuscuta
  • Raul A. Gonzalez-Pech. A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change
  • Zhezheng Song. Accurate detection of tandem repeat in error-prone long reads
  • Alan Brown. Integrative Analysis of Histone Modifications, TF Binding, and Gene Expression in Plasmodium falciparum
  • Lucia Williams. Multi-strain viral assembly and quantification using fractional flows
  • Aaryan Mahesh. Sarnaik A SAT Approach for Faster Computation of DCJ Distance in Genomes with Duplicate Genes
  • Kerim Heber. StrainR2 accurately deconvolutes strain-level abundance in synthetic microbial communities
  • Xiang Li. Efficient Seeding for Error-Prone Sequences with SubseqHash2
  • Chen Xue. Detection of Differential Chromatin Interactions
  • Ilia Minkin. Conservation assessment of human splice site annotation based on a 470-genome alignment
  • Amatur Rahman. Efficient computation of EHH-based statistics

Organizers

Previous workshops

Funding

This workshop is funded with the generous support of the Huck Institutes for the Life Sciences.