RECOMB-Seq 2023 Proceedings

İstanbul, Türkiye, April 14 - 15, 2023.

PC Chairs: Broňa Brejová, Comenius University in Bratislava; and A. Ercüment Çiçek, Bilkent University.
Keynote Speakers: Shilpa Garg and Gioele La Manno.

Full Papers

  • TreeTerminus - creating transcript trees using inferential replicate counts. Noor Pratap Singh, Michael I Love and Rob Patro. iScience, 26 (6): 106961, (2023)
  • DandD: efficient measurement of sequence growth and similarity. Jessica Bonnie, Omar Ahmed and Ben Langmead. iScience, 27 (3): 109054, (2024)
  • ADEPT: autoencoder with differentially expressed genes and imputation for a robust spatial transcriptomics clusterin. Yunfei Hu, Yuying Zhao, Curtis Schunk, Yingxiang Ma, Tyler Derr and Xin Maizie Zhou. iScience, 26 (6): 106792, (2023)
  • aKmerBroom: ancient oral DNA decontamination using Bloom filters on k-mer sets. Camila Duitama González, Riccardo Vicedomini, Hugues Richard and Rayan Chikhi. iScience, 26 (11): 108057, (2023)
  • Masked superstrings as a unified framework for textual k-mer set representations. Ondrej Sladky, Pavel Vesely and Karel Brinda. bioRxiv 2023.02.01.526717, (2023)
  • WGT: tools and algorithms for recognizing, visualizing and generating Wheeler graphs. Kuan-Hao Chao, Pei-Wei Chen, Sanjit A. Seshia and Ben Langmead. iScience, 26 (8): 107402, (2023)
  • Exploring high-quality microbial genomes by assembly of linked-reads with high barcode specificity using deep learning. Zhenmiao Zhang, Hongbo Wang, Chao Yang, Yufen Huang, Zhen Yue, Yang Chen, Lijuan Han, Aiping Lyu, Xiaodong Fang and Lu Zhang. overlay preprint
  • A safety framework for flow decomposition problems via integer linear programming. Fernando Hugo Cunha Dias, Manuel Caceres, Lucia Williams, Brendan Mumey and Alexandru I. Tomescu. overlay preprint
  • Coverage-preserving sparsification of overlap graphs for long-read assembly. Chirag Jain. overlay preprint
  • Predicting transcription factor activity using prior biological information. Joseph Estabrook, William Yashar, Hannah Holly, Julia Somers, Olga Nikolova, Ozgun Babur, Theodore Braun and Emek Demir. overlay preprint
  • On minimizers and convolutional filters: a partial justification for the effectiveness of CNNs in categorical sequence analysis. Yun William Yu. overlay preprint
  • TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering. Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan and Onur Mutlu. overlay preprint
  • An intrinsically interpretable neural network architecture for sequence to function learning. Ali Tugrul Balci, Mark Maher Ebeid, Panayiotis Benos, Dennis Kostka and Maria Chikina. overlay preprint
  • Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri Ghiasi and Onur Mutlu. overlay preprint

Short Talks Selected from Abstracts

  • TRIBAL: Tree inference of B cell clonal lineages. Leah Weber, Derek Reiman, Mohammed El-Kebir and Aly Khan.
  • A comprehensive analysis of the reusability of public omics data across 3.8 million research publications. Serghei Mangul, Mohammad Vahed, Nicholas Darci-Maher, Kerui Peng, Jaqueline Brito, JungHyun Jung, Anushka Rajesh, Andrew Smith, Reid F. Thompson, Casey Greene, Jonathan Jacobs, Dat Duong and Eleazar Eskin.
  • ClairS: accurate haplotype-aware long-read somatic variant calling using deep learning-based synthetic data learning. Zhenxian Zheng, Junhao Su, Tak-Wah Lam and Ruibang Luo.
  • A probabilistic framework for parametrizing RNA velocity fields with manifold-consistent cell cycle dynamics. Alex Lederer, Lorenzo Talamanca, Colas Droin, Maxine Leonardi, Irina Khven, Hugo Carvalho, Felix Naef and Gioele La Manno.
  • Pairwise sequence alignment with block and character edit operations. Ahmet Cemal Alıcıoğlu, Mahmud Sami Aydın and Can Alkan.
  • Genome misassembly detection using Stash: A data structure based on stochastic tile hashing. Armaghan Sarvar, Lauren Coombe, René Warren and Inanc Birol.
  • Sigmoni: efficient pangenome multi-classification of nanopore signal. Vikram Shivakumar, Omar Ahmed, Sam Kovaka, Mohsen Zakeri and Ben Langmead.
  • Panagram: alignment-free and interactive pan-genome visualization. Katharine Jenike, Sam Kovaka, Matthias Benoit, Srividya Ramakrishnan, Shujun Ou, James Saterlee, Stephan Hwang, Iacopo Gentile, Anat Hendelman, Michael Passalacqua, Xingang Wang, Michael Alonge, Hamsini Suresh, Ryan Santos, Blaine Fitzgerald, Gina Robitaille, Edeline Gagnon, Melissa Kramer, Sara Goodwin, W. Richard McCombie, Jaime Prohens, Tiina E. Särkinen, Amy Frary, Jesse Gillis, Joyce Van Eck, Ben Langmead, Zachary B. Lippman and Michael C. Schatz.
  • Integrating Hi-C sequencing data in verkko for gapless haplotype-resolved assembly. Dmitry Antipov, Shilpa Garg, Adam Phillippy and Sergey Koren.

Posters

  • SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger, Zülal Bingöl, Gurpreet Singh Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri Ghiasi, Gagandeep Singh, Juan Gómez Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose and Onur Mutlu.
  • Detection of large tandem duplications in HMPV isolates. Thomas Krannich, Stephan Fuchs and Sophie Köndgen.
  • Predicting the origin of soil samples - performance evaluation of a new targeted high-throughput sequencing metagenomic tool.. Kamila Marszałek, Michał B. Kowalski, Andrzej Ossowski, Rafał Płoski, Renata Zbieć Piekarska, Paweł P. Łabaj and Wojciech Branicki.
  • A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater. Viorel Munteanu, Khooshbu Kantibhai Patel, Nitesh Kumar Sharma, Sergey Knyazev and Serghei Mangul.
  • Rigorous benchmarking of HLA callers for RNA-seq data. Ram Ayyala, Dottie Yu, Sergey Knyazev and Serghei Mangul.
  • RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires in T cell rich tissues and certain repertoires. Serghei Mangul.
  • Machine learning enabled pattern discovery in large-scale spatial gene expression datasets. Reza Abbasi-Asl.
  • Assessing the completeness of immunogenetics databases across diverse populations. Yu-Ning Huang, Yiting Meng, Naresh Amrat Patel, Jay Himanshu Mehta, Brittney Hua, Marina Fayzullina, Houda Alachkar and Serghei Mangul.
  • The systematic assessment of completeness of public metadata accompanying omics studies. Yu-Ning Huang, Anushka Rajesh, Ram Ayyala, Aditya Sarkar, Ruiwei Guo, Irina Nakashidze, Shirley Monge, Dottie Yu, Qiushi Peng, Grace Scheg, Khooshbu Kantibhai Patel, Tejasvene Ramesh, Anushka Yadav, Fangyun Liu, Jay Himanshu Mehta and Serghei Mangul.
  • SurfR: Surfing the cells’ surfaceome. Aurora Maurizio, Anna Sofia Tascini and Marco Jacopo Morelli.
  • GoPeaks: histone modification peak calling for CUT&Tag. William Yashar, Garth Kong, Jake Vancampen, Brittany Curtiss, Daniel Coleman, Lucia Carbone, Galip Yardimci, Julia Maxson and Theodore Braun.
  • ClusterV: accurate detection of HIV quasispecies and drug resistance mutations using ONT sequencing data. Junhao Su, Tak-Wah Lam and Ruibang Luo.
  • Unikseq: unique region identification in genome sequences using a k-mer approach, to empower environmental DNA assay designs and comparative genomics studies. Rene Warren, Michael J Allison, M. Louie Lopez, Neha Acharya-Patel, Lauren Coombe, Cecilia L. Yang, Caren C Helbing and Inanc Birol.
  • ntHits: streaming through raw sequencing data to profile and filter k-mers with selected multiplicities. Parham Kazemi, Hamid Mohamadi, Justin Chu, Lauren Coombe, Rene L Warren and Inanc Birol.
  • Evaluating the Robustness and Reproducibility of RNA-Seq Quantification Tools. Fangyun Liu, Brian Nadel, Pelin Icer Baykal and Serghei Mangul.
  • Copy number estimation using Counting Bloom Filters in de novo assembled genomes. Klea Zambaku, Ricardo Roman-Brenes, Ömer Yavuz Öztürk, Can Alkan and Inanç Birol.
  • Improving functional annotation of bacterial genomes with COGtools. Karel Sedlar, Petra Polakovicova and Ralf Zimmer.
  • Orthanq: orthogonal evidence based haplotype quantification. Hamdiye Uzuner and Johannes Köster.
  • Minichain: a new method for pangenome graph construction. Ghanshyam Chandra and Chirag Jain.
  • ALIBI2: improved linearization of pangenome graphs. Anna Lisiecka and Norbert Dojer.
  • Characterization of alignment and search algorithms for short read, long read, and graph mappers. Ecem İlgün, Ömer Yavuz Öztürk, Klea Zambaku, Juan Gómez Luna, Mohammed Alser, Ricardo Roman-Brenes, Can Alkan and The Biopim Project.
  • Nanopore signal alignment, analysis, and visualization with Uncalled4. Sam Kovaka, Paul W. Hook, Vikram Shivakumar, Katharine M. Jenike, Luke Morina, Roham Razaghi, Winston Timp and Michael C. Schatz.
  • Mod.Plot: a rapid and interactive visualization of tandem repeats. Alexander Sweeten, Adam Phillippy and Michael Schatz.
  • Using minimizer interarrival distances for read-until human read detection from blood samples sequenced by Oxford Nanopore. Sina Barazandeh, Mahmud Sami Aydin, Berke Ucar, Can Alkan and Inanc Birol.