RECOMB 2021 Proceedings

Padova, Italy (virtual), August 29 – September 1, 2021

PC Chair: Jian Peng, University of Illinois at Urbana-Champaign
Organization Committee: Fabio Vandin (co-chair), Jian Ma (co-chair), Matteo Comin, Barbara Di Camillo, Leonardo Pellegrina, Cinzia Pizzi
Keynote Speakers: Trey Ideker, Ming Li, Katie Pollard, Aviv Regev, Marie-France Sagot, Mona Singh

List of Publications

  • Biobank-scale estimation of the proportion of trait variance explained by gene-environment interactions. Ali Pazokitoroudi, Andy Dahl, Noah Zaitlen, Saharon Rosset, Sriram Sankararaman.
    • Journal: A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits. Ali Pazokitoroudi, Zhengtong Liu, Andrew Dahl, Noah Zaitlen, Saharon Rosset, Sriram Sankararaman. American Journal of Human Genetics, 111(7): 1462-1480, 2024.
  • Fast Alignment-Free Similarity Estimation By Tensor Sketching. Amir Joudaki, Gunnar Ratsch, Andre Kahles.
  • Assembling Long Accurate Reads Using de Bruijn Graphs. Anton Bankevich, Andrey Bzikadze, Mikhail Kolmogorov, Pavel Pevzner.
    • Preprint: bioRxiv 2020.12.10.420448
    • Journal: Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads. Anton Bankevich, Andrey V. Bzikadze, Mikhail Kolmogorov, Dmitry Antipov, Pavel A. Pevzner. Nature Biotechnology, 40: 1075–1081, 2022.
  • Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms. Baraa Orabi, Brian McConeghy, Cedric Chauve, Faraz Hach.
    • Preprint: bioRxiv 2021.01.20.427493
    • Journal: Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing. Baraa Orabi, Ning Xie, Brian McConeghy, Xuesen Dong, Cedric Chauve, Faraz Hach. Nucleic Acids Research, 51(2):e11, 2023.
  • Minimizer-space de Bruijn Graphs. Barış Ekim, Bonnie Berger, Rayan Chikhi.
    • Preprint: bioRxiv 2021.06.09.447586
    • Journal: Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Barış Ekim, Bonnie Berger, Rayan Chikhi. Cell Systems, 12(10):958-968.e6, 2021.
  • SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity. Benjamin Chidester, Tianming Zhou, Jian Ma.
  • VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs. Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L Hamilton, Jerome Waldispuhl.
    • Preprint: arXiv:2009.00664
    • Journal: Vernal: a tool for mining fuzzy network motifs in RNA. Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L Hamilton, Jerome Waldispuhl. Bioinformatics, 38(4): 970-976, 2022.
  • RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer. Damian Wójtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim, Teresa M Przytycka.
    • Preprint: bioRxiv 2020.11.21.392878
    • Journal: RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer. Damian Wójtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim, Teresa M Przytycka. Cell Systems, 12(10):994-1003.e4, 2021.
  • SPRISS: Approximating Frequent k-mers by Sampling Reads, and Applications. Diego Santoro, Leonardo Pellegrina, Fabio Vandin.
    • Preprint: arXiv:2101.07117
    • Journal: SPRISS: approximating frequent k-mers by sampling reads, and applications. Diego Santoro, Leonardo Pellegrina, Matteo Comin, Fabio Vandin . Bioinformatics, 38(13):3343–3350, 2022.
  • Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert.
    • Preprint: bioRxiv 2020.10.08.330985
    • Journal: Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert. iScience, 24(7):102782, 2021.
  • DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution. Gryte Satas, Simone Zaccaria, Mohammed El-Kebir, Benjamin J Raphael.
    • Preprint: bioRxiv 2021.02.27.429196
    • Journal: DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Gryte Satas, Simone Zaccaria, Mohammed El-Kebir, Benjamin J Raphael. Cell Systems, 12(10): 1004-1018, 2021.
  • MoTSE: an interpretable task similarity estimator for small molecular property prediction tasks. Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Jianyang Zeng, Dan Zhao.
    • Preprint: bioRxiv 2021.01.13.426608
    • Journal: Improving molecular property prediction through a task similarity enhanced transfer learning strategy. Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao, Jianyang Zeng . iScience, 25(10): 105231, 2022.
  • An Unrolled Deep Learning Framework for Single Cell Gene Regulatory Networks. Harsh Shrivastava, Xiuwei Zhang, Srinivas Aluru, Le Song.
    • Preprint: bioRxiv 2020.04.23.058149
    • Journal: GRNUlar: A deep learning framework for recovering single-cell gene regulatory networks. Harsh Shrivastava , Xiuwei Zhang, Le Song, Srinivas Aluru. Journal of Computational Biology, 29(1):27-44, 2022.
  • Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA. Hua-Ting Yao, Jerome Waldispuhl, Yann Ponty, Sebastian Will.
  • Study of Real-Valued Distance Prediction For Protein Structure Prediction with Deep Learning. Jin Li, Jinbo Xu.
  • Strain Level Microbial Detection and Quantification with Applications to Single Cell Metagenomics. Kaiyuan Zhu, Welles Robinson, Alejandro Schaffer, Junyan Xu, Eytan Ruppin, Funda Ergun, Yuzhen Ye, S Cenk Sahinalp.
    • Preprint: bioRxiv 2020.06.12.149245
    • Journal: Strain level microbial detection and quantification with applications to single cell metagenomics. Kaiyuan Zhu, Alejandro A. Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, A. Funda Ergun, Yuzhen Ye, S. Cenk Sahinalp . Nature Communications, 13(1):6430, 2022.
  • Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling. Martin Grosshauser, Paul Zaharias, Tandy Warnow.
    • Journal: Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling. Paul Zaharias, Martin Grosshauser, Tandy Warnow . Journal of Computational Biology, 29(1):74-89, 2022.
  • Privacy-Preserving Genotype Imputation in a Trusted Execution Environment. Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, Xiaofeng Wang, S Cenk Sahinalp, Hyunghoon Cho.
    • Preprint: bioRxiv 2021.02.02.429428
    • Journal: Privacy-preserving genotype imputation in a trusted execution environment. Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, XiaoFeng Wang, S Cenk Sahinalp, Hyunghoon Cho . Cell Systems, 12(10):983-993.e7, 2021.
  • ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis. Nicholas Franzese, Jason Fan, Roded Sharan, Mark DM Leiserson.
    • Journal: ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis. Nicholas Franzese, Jason Fan, Roded Sharan, Mark D M Leiserson. Journal of Computational Biology, 29(1): 56-73, 2022.
  • Gromov-Wasserstein optimal transport to align single-cell multi-omics data. Pinar Demetci, Rebecca Santorella, Bjorn Sandstede, William Stafford Noble, Ritambhara Singh.
    • Preprint: bioRxiv 2020.04.28.066787
    • Journal: Gromov-Wasserstein optimal transport to align single-cell multi-omics data. Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh. Journal of Computational Biology, 29(1): 3-18, 2021.
  • Deep unfolding for non-negative matrix factorization with application to mutational signature analysis. Rami Nasser, Yonina Eldar, Roded Sharan.
    • Preprint: arXiv:2108.09138
    • Journal: Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis. Rami Nasser, Yonina C. Eldar, Roded Sharan. Journal of Computational Biology, 29(1):45-55, 2022.
  • Alignment and Integration of Spatial Transcriptomics Data. Ron Zeira, Max Land, Ben Raphael.
  • Towards the prediction of higher-order genetic interactions. Ruochi Zhang, Jianzhu Ma, Jian Ma.
    • Preprint: bioRxiv 2020.11.26.400739
    • Journal: Towards the prediction of higher-order genetic interactions. Ruochi Zhang, Jianzhu Ma, Jian Ma. Cell Systems, to appear, 2025.
  • Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model. Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger.
    • Preprint: bioRxiv 2021.01.22.427866
    • Journal: D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger. Cell Systems, 12(10):969-982.e6, 2021.
  • Robust Inference of Kinase Activity Using Functional Networks. Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A Ercument Cicek, Mark Chance, Mehmet Koyuturk.
    • Preprint: bioRxiv 2020.05.01.062802
    • Journal: Robust inference of kinase activity using functional networks. Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A Ercument Cicek, Mark Chance, Mehmet Koyuturk. Nature Communications, 12(1):1177, 2021.
  • Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna.
    • Preprint: bioRxiv 2021.01.28.428636
    • Journal: Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna. PLOS Computational Biology, 17(11):e1009449, 2021.
  • FaNDOM: Fast Nested Distance-based seeding of Optical Maps. Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna.
    • Journal: FaNDOM: Fast nested distance-based seeding of optical maps. Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna. Patterns, 2(5):100248, 2021.
  • scDesign2: an interpretable simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li.
    • Preprint: bioRxiv 2020.11.17.387795
    • Journal: scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li. Genome Biology, 22: 163, 2021.
  • scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. Wei Vivian Li, Yanzeng Li.
    • Preprint: bioRxiv 2020.09.19.304956
    • Journal: scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data. Wei Vivian Li, Yanzeng Li . Genomics, Proteomics & Bioinformatics, 19(3):475–492, 2021.
  • scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Ching-Hsing Luo, Yuedong Yang.
    • Preprint: bioRxiv 2021.01.18.427083
    • Journal: scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang. Briefings in Bioinformatics, 22(6):bbab281, 2021.
  • Variational Inference Using Approximate Likelihood Under the Coalescent With Recombination. Xinhao Liu, Huw A Ogilvie, Luay Nakhleh.
    • Preprint: bioRxiv 2020.08.19.258137
    • Journal: Variational inference using approximate likelihood under the coalescent with recombination. Xinhao Liu, Huw A Ogilvie, Luay Nakhleh. Genome Research, 31(11): 2107-2119, 2021.
  • DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning. Yuepeng Jiang, Stefano Rensi, Sheng Wang, Russ Altman.
  • DEPP: Deep Learning Enables Extending Species Trees using Single Genes. Yueyu Jiang, Metin Balaban, Siavash Mirarab.
  • ProALIGN: directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs. Lupeng Kong, Fusong Ju, Wei-mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu.
    • Preprint: bioRxiv 2020.12.28.424539
    • Journal: ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. Lupeng Kong, Fusong Ju, Wei-mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu . Journal of Computational Biology, 29(2): 92-105, 2022.
  • HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression. Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, Fengzhu Sun.
    • Preprint: bioRxiv 2021.03.01.433489
    • Journal: Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, Fengzhu Sun. Journal of Computational Biology, 29(2): 106-120, 2022.
  • Deriving Ranges of Optimal Estimated Transcript Expression due to Non-identifiability. Hongyu Zheng, Cong Ma, Carl Kingsford.
    • Preprint: bioRxiv 2019.12.13.875625
    • Journal: Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability. Hongyu Zheng, Cong Ma, Carl Kingsford. Journal of Computational Biology, 29(2): 121-139, 2022.
  • Set-Min sketch: a probabilistic map for power-law distributions with application to k-mer annotation. Yoshihiro Shibuya, Djamal Belazzougui, Gregory Kucherov.
    • Preprint: bioRxiv 2020.11.14.382713
    • Journal: Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation. Yoshihiro Shibuya, Djamal Belazzougui, Gregory Kucherov. Journal of Computational Biology, 29(2): 140-154, 2022.
  • The statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches. Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev.
    • Preprint: bioRxiv 2021.01.15.426881
    • Journal: The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev. Journal of Computational Biology, 29(2): 155-168, 2022.
  • MONI: A Pangenomics Index for Finding MEMs. Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher.
    • Preprint: bioRxiv 2021.07.06.451246
    • Journal: MONI: A Pangenomic Index for Finding Maximal Exact Matches. Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher. Journal of Computational Biology, 29(2): 169-187, 2022.
  • Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing. Jim Shaw, Yun William Yu.
    • Preprint: bioRxiv 2020.11.06.371799
    • Journal: flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning. Jim Shaw, Yun William Yu. Journal of Computational Biology, 29(2): 195-211, 2022.