RECOMB-Seq 2021 Proceedings

Padova, Italy (virtual), August 27-28, 2021.

PC Chairs: Cinzia Pizzi, University of Padova; and Layla Oesper, Carleton College.
Keynote Speakers: Ben Langmead and Nadia Pisanti.

Full Papers

  • Dynamic partitioning of search patterns for approximate pattern matching using search schemes. Luca Renders, Kathleen Marchal and Jan Fostier. iScience, 24 (7): 102687, (2021)
  • Linearization of genome sequence graphs revisited. Anna Lisiecka and Norbert Dojer. iScience, 24 (7): 102755, (2021)
  • Pan-genomic matching statistics for targeted nanopore sequencing. Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael Schatz, Travis Gagie, Christina Boucher and Ben Langmead. iScience, 24 (6): 102696, (2021)
  • A molecular taxonomy of tumors independent of tissue-of-origin. Peter Nguyen, Simon Coetzee, Daniel Lakeland and Dennis Hazelett . iScience, 24 (10): 103084, (2021)
  • A reference-free approach for cell type classification with scRNA-seq. Qi Sun, Yifan Peng and Jinze Liu. iScience, 24 (8): 102855, (2021)
  • Accurate spliced alignment of long RNA sequencing reads. Kristoffer Sahlin and Veli Mäkinen. overlay preprint
  • Algorithms and complexity on indexing founder graphs. Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu and Veli Mäkinen. overlay preprint
  • HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery. Matthew Hayes, Angela Nguyen, Rahib Islam, Caryn Butler, Ethan Tran, Derrick Mullins and Chindo Hicks. overlay preprint
  • CONSULT: Accurate contamination removal usinglocality-sensitive hashing. Eleonora Rachtman, Vineet Bafna and Siavash Mirarab. overlay preprint
  • DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. Jiaxing Chen, Chinwang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lyu, William K Cheung and Lu Zhang. overlay preprint
  • Conditional resampling improves calibration and sensitivity in single-cell CRISPR screen analysis. Timothy Barry, Xuran Wang, Kathryn Roeder and Eugene Katsevich. overlay preprint
  • Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method. Yiqing Yan, Nimisha Chaturvedi and Raja Appuswamy. overlay preprint
  • BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data. Ziwei Chen, Fuzhou Gong, Lin Wan and Liang Ma. overlay preprint
  • Automated strain separation in low-complexity metagenomes using long reads. Riccardo Vicedomini, Christopher Quince, Aaron Darling and Rayan Chikhi. overlay preprint
  • Real-time, direct classification of nanopore signals with SquiggleNet. Yuwei Bao, Jack Wadden, John Erb-Downward, Piyush Ranjan, Robert Dickson, David Blaauw and Joshua Welch. overlay preprint
  • Population-scale detection of non-reference sequence variants using colored de Bruijn graphs. Thomas Krannich, W. Timothy J. White, Sebastian Niehus, Guillaume Holley, Bjarni V. Halldorsson and Birte Kehr. overlay preprint
  • Ariadne: barcoded linked-read deconvolution using de Bruijn graphs. Lauren Mak, Dmitry Meleshko, David C. Danko, Waris Barakzai, Natan Belchikov and Iman Hajirasouliha. overlay preprint
  • ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders. A. Ali Heydari, Oscar Davalos, Lihong Zhao, Katrina Hoyer and Suzanne Sindi. overlay preprint