RECOMB 2020 Proceedings

Padova, Italy (virtual), June 22-25, 2020.

PC Chair: Russell Schwartz, Carnegie Mellon University
Organization Committee: Fabio Vandin (chair), Matteo Comin, Barbara Di Camillo, Leonardo Pellegrina, Cinzia Pizzi
Keynote Speakers: Manuela Helmer-Citterich, Michal Linial, Satoru Miyano, Pavel Pevzner, Eran Segal, Russ Altman

List of Publications

• Computing the Rearrangement Distance of Natural Genomes. Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 3-18, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_1
  • Preprint: arXiv:2001.02139
  • Journal: Computing the rearrangement distance of natural genomes. Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye. Journal of Computational Biology, 28(4): 410-431, 2021.
    • DOI: 10.1089/cmb.2020.0434
• Deep Large-Scale Multi-task Learning Network for Gene Expression Inference. Kamran Ghasedi Dizaji, Wei Chen, Heng Huang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 19-36, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_2
  • Journal: Deep Large-Scale Multitask Learning Network for Gene Expression Inference. Kamran Ghasedi Dizaji, Wei Chen, Heng Huang. Journal of Computational Biology, 28(5): 485-500, 2021.
    • DOI: 10.1089/cmb.2020.0438
• A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. Barış Ekim, Bonnie Berger, Yaron Orenstein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 37-53, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_3
  • Preprint: bioRxiv 2020.01.17.910513
• Multiple Competition-Based FDR Control and Its Application to Peptide Detection. Kristen Emery, Syamand Hasam, William Stafford Noble, Uri Keich.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 54-71, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_4
  • Preprint: arXiv:1907.01458
  • Journal: Competition-based control of the false discovery proportion. Dong Luo, Arya Ebadi, Kristen Emery, Yilun He, William Stafford Noble, Uri Keich. Biometrics, 79(4): 3472-3484, 2023.
    • DOI: 10.1111/biom.13830
• Supervised Adversarial Alignment of Single-Cell RNA-seq Data. Songwei Ge, Haohan Wang, Amir Alavi, Eric Xing, Ziv Bar-Joseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 72-87, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_5
  • Preprint: bioRxiv 2020.01.06.896621
  • Journal: Supervised Adversarial Alignment of Single-Cell RNA-seq Data. Songwei Ge, Haohan Wang, Amir Alavi, Eric Xing, Ziv Bar-Joseph. Journal of Computational Biology, 28(5): 501-513, 2021.
    • DOI: 10.1089/cmb.2020.0439
• Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction. Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 88-103, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_6
  • Journal: EPTool: a new enhancing PSSM tool for protein secondary structure prediction. Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang. Journal of Computational Biology, 28(4): 362-364, 2021.
    • DOI: 10.1089/cmb.2020.0417
• AStarix: Fast and Optimal Sequence-to-Graph Alignment. Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin Vechev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 104-119, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_7
  • Preprint: bioRxiv 2020.01.22.915496
• Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. Brandon Legried, Erin K. Molloy, Tandy Warnow, Sébastien Roch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 120-135, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_8
  • Preprint: bioRxiv 821439
  • Journal: Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss. Brandon Legried, Erin K. Molloy, Tandy Warnow, Sébastien Roch. Journal of Computational Biology, 28(5): 452-468, 2021.
    • DOI: 10.1089/cmb.2020.0424
• RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. Sneha Mitra, Jianling Zhong, David M. MacAlpine, Alexander J. Hartemink.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 136-151, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_9
  • Preprint: bioRxiv 2020.06.03.132001
  • Journal: RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Sneha Mitra, Jianling Zhong, TQ Tran, David M. MacAlpine, Alexander J. Hartemink. Nucleic Acids Research, 49(14): 7925-7938, 2021.
    • DOI: 10.1093/nar/gkab553
• Representation of k-mer Sets Using Spectrum-Preserving String Sets. Amatur Rahman, Paul Medvedev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 152-168, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_10
  • Preprint: bioRxiv 2020.01.07.896928
  • Journal: Representation of k-Mer Sets Using Spectrum-Preserving String Sets. Amatur Rahman, Paul Medvedev. Journal of Computational Biology, 28(4): 381-394, 2021.
    • DOI: 10.1089/cmb.2020.0431
• NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 169-185, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_11
  • Preprint: bioRxiv 2020.01.18.911438
  • Journal: NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael. Journal of Computational Biology, 28(5): 469–484, 2021.
    • DOI: 10.1089/cmb.2020.0435
• Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 186-201, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_12
  • Preprint: bioRxiv 834762
• Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. Hongyu Zheng, Carl Kingsford, Guillaume Marçais.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 202-217, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_13
  • Preprint: arXiv:2001.06550
  • Journal: Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. Hongyu Zheng, Carl Kingsford, Guillaume Marçais. Journal of Computational Biology, 28(4): 395-409, 2021.
    • DOI: 10.1089/cmb.2020.0432
• Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs. Jasmijn A. Baaijens, Leen Stougie, Alexander Schönhuth.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 221-222, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_14
  • Preprint: bioRxiv 645721
• Spectral Jaccard Similarity: A New Approach to Estimating Pairwise Sequence Alignments. Tavor Z. Baharav, Govinda M. Kamath, David N. Tse, Ilan Shomorony.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 223-225, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_15
  • Preprint: bioRxiv 800581
  • Journal: Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments. Tavor Z. Baharav, Govinda M. Kamath, David N. Tse, Ilan Shomorony. Patterns, 1(6), 100081, 2020.
    • DOI: 10.1016/j.patter.2020.100081
• MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads. Anton Bankevich, Pavel Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 226-228, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_16
  • Preprint: bioRxiv 2020.01.15.908285
• Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles. Nico Borgsmüller, Jose Bonet, Francesco Marass, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 229-230, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_17
  • Preprint: bioRxiv 2020.01.15.907345
  • Journal: BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. Nico Borgsmüller, Jose Bonet, Francesco Marass, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Niko Beerenwinkel. Bioinformatics, 36(19): 4854-4859, 2020.
    • DOI: 10.1093/bioinformatics/btaa599
• PaccMannRL: Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning. Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 231-233, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_18
  • Preprint: arXiv:1909.05114
  • Journal: PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning. Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez. iScience, 24(4):102269, 2021.
    • DOI: 10.1016/j.isci.2021.102269
• CluStrat: A Structure Informed Clustering Strategy for Population Stratification. Aritra Bose, Myson C. Burch, Agniva Chowdhury, Peristera Paschou, Petros Drineas.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 234-236, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_19
  • Preprint: bioRxiv 2020.01.15.908228
  • Journal: Structure-informed clustering for population stratification in association studies. Aritra Bose, Myson C. Burch, Agniva Chowdhury, Peristera Paschou, Petros Drineas. BMC Bioinformatics, 24(1): 411, 2023.
    • DOI: 10.1186/s12859-023-05511-w
• PWAS: Proteome-Wide Association Study. Nadav Brandes, Nathan Linial, Michal Linial.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 237-239, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_20
  • Preprint: bioRxiv 812289
  • Journal: PWAS: proteome-wide association study—linking genes and phenotypes by functional variation in proteins. Nadav Brandes, Nathan Linial, Michal Linial. Genome Biology, 21: 173, 2020.
    • DOI: 10.1186/s13059-020-02089-x
• Estimating the Rate of Cell Type Degeneration from Epigenetic Sequencing of Cell-Free DNA. Christa Caggiano, Barbara Celona, Fleur Garton, Joel Mefford, Brian Black, Catherine Lomen-Hoerth, Andrew Dahl, Noah Zaitlen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 240-242, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_21
  • Preprint: bioRxiv 2020.01.15.907022
  • Journal: Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Christa Caggiano, Barbara Celona, Fleur Garton, Joel Mefford, Brian Black, Robert Henderson, Catherine Lomen-Hoerth, Andrew Dahl, Noah Zaitlen. Nature Communications, 12: 2717, 2021.
    • DOI: 10.1038/s41467-021-22901-x
• Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. Gizem Caylak, A. Ercument Cicek.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 243-244, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_22
  • Preprint: bioRxiv 830216
  • Journal: Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. Gizem Caylak, Oznur Tastan, and A. Ercument Cicek. Journal of Computational Biology, 28(4): 365-377, 2021.
    • DOI: 10.1089/cmb.2020.0429
• Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 245-247, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_23
  • Preprint: bioRxiv 2020.01.16.909010; arXiv:1904.08747
  • Journal: Privacy-preserving biomedical database queries with optimal privacy-utility trade-offs. Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger. Cell Systems, 10(5): 408-416, 2020.
    • DOI: 10.1016/j.cels.2020.03.006
• Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning. Chao Gao, Joshua D. Welch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 248-250, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_24
  • Preprint: bioRxiv 2020.01.16.909861
  • Journal: Iterative single-cell multi-omic integration using online learning. Chao Gao, Jialin Liu, April R. Kriebel, Sebastian Preissl, Chongyuan Luo, Rosa Castanon, Justin Sandoval, Angeline Rivkin, Joseph R. Nery, Margarita M. Behrens, Joseph R. Ecker, Bing Ren, Joshua D. Welch. Nature Biotechnology, 39: 1000-1007, 2021.
    • DOI: 10.1038/s41587-021-00867-x
• A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New Information. Borislav H. Hristov, Bernard Chazelle, Mona Singh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 251-252, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_25
  • Preprint: arXiv:2001.06135
  • Journal: uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Borislav H. Hristov, Bernard Chazelle, Mona Singh. Cell Systems, 10(6): 470-479.e3, 2020.
    • DOI: 10.1016/j.cels.2020.05.008
• A Scalable Method for Estimating the Regional Polygenicity of Complex Traits. Ruth Johnson, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, Sriram Sankararaman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 253-254, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_26
  • Preprint: bioRxiv 2020.01.15.908095
  • Journal: Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits. Ruth Johnson, Heather E. Wheeler, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, Sriram Sankararaman. PLOS Computational Biology, 17(10): e1009483, 2021.
    • DOI: 10.1371/journal.pcbi.1009483
• Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data. Tyler A. Joseph, Amey P. Pasarkar, Itsik Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 255-256, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_27
  • Preprint: bioRxiv 2020.01.10.902163
  • Journal: Efficient and Accurate Inference of Mixed Microbial Population Trajectories from Longitudinal Count Data. Tyler A. Joseph, Amey P. Pasarkar, Itsik Pe’er. Cell Systems, 10(6): 463-469.e6, 2020.
    • DOI: 10.1016/j.cels.2020.05.006
• Identifying Causal Variants by Fine Mapping Across Multiple Studies. Nathan LaPierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 257-258, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_28
  • Preprint: bioRxiv 2020.01.15.908517
  • Journal: Identifying causal variants by fine mapping across multiple studies. Nathan LaPierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari, Eleazar Eskin. PLOS Genetics, 17(9): e1009733, 2021.
    • DOI: 10.1371/journal.pgen.1009733
• MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and Proteins. Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 259-260, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_29
  • Preprint: bioRxiv 2019.12.30.891515
  • Journal: MONN: a Multi-Objective Neural Network for Predicting Compound-Protein Interactions and Affinities. Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng. Cell Systems, 10(4): 308-322.e11, 2020.
    • DOI: 10.1016/j.cels.2020.03.002
• Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering. Yunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu, Wesley Wei Qian, Huimin Zhao,Jian Peng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 261-263, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_30
  • Preprint: bioRxiv 2020.01.16.908509
  • Journal: ECNet is an evolutionary context-integrated deep learning framework for protein engineering. Yunan Luo, G Jiang, T Yu, Y Liu, Lam Vo, Hantian Ding, Yufeng Su, Wesley Wei Qian, Huimin Zhao, Jian Peng. Nature Communications, 12(1): 5743, 2021.
    • DOI: 10.1038/s41467-021-25976-8
• Log Transformation Improves Dating of Phylogenies. Uyen Mai, Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 264-265, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_31
  • Preprint: bioRxiv 2019.12.20.885582
  • Journal: Log Transformation Improves Dating of Phylogenies. Uyen Mai, Siavash Mirarab. Molecular Biology and Evolution, 38(3): 1151-1167, 2021.
    • DOI: 10.1093/molbev/msaa222
• Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores. Brooks Paige, James Bell, Aurélien Bellet, Adrià Gascón, Daphne Ezer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 266-268, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_32
  • Preprint: bioRxiv 2020.01.15.907808
  • Journal: Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores. Brooks Paige, James Bell, Aurélien Bellet, Adrià Gascón, Daphne Ezer. Journal of Computational Biology, 28(5): 435-451, 2021.
    • DOI: 10.1089/cmb.2020.0445
• d-PBWT: Dynamic Positional Burrows-Wheeler Transform. Ahsan Sanaullah, Degui Zhi, Shaojie Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 269-270, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_33
  • Preprint: bioRxiv 2020.01.14.906487
  • Journal: d-PBWT: dynamic positional Burrows–Wheeler transform. Ahsan Sanaullah, Degui Zhi, Shaojie Zhang. Bioinformatics, 37(16): 2390-2397, 2021.
    • DOI: 10.1093/bioinformatics/btab117
• A Mixture Model for Signature Discovery from Sparse Mutation Data. Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 271-272, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_34
  • Journal: A mixture model for signature discovery from sparse mutation data. Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan. Genome Medicine, 13(1): 1-12, 2021.
    • DOI: 10.1186/s13073-021-00988-7
• Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 273-273, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_35
  • Preprint: bioRxiv 840355
  • Journal: SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael. Cell Systems, 10(4): 323-332.e8, 2020.
    • DOI: 10.1016/j.cels.2020.04.001
• Reconstruction of Gene Regulatory Networks by Integrating Biological Model and a Recommendation System. Yijie Wang, Justin M. Fear, Isabelle Berger, Hangnoh Lee, Brian Oliver, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 274-275, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_36
  • Preprint: bioRxiv 2020.01.07.898031
  • Journal: NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks. Yijie Wang, Hangnoh Lee, Justin M. Fear, Isabelle Berger, Brian Oliver, Teresa M. Przytycka. Communications Biology, 5, 1282, 2022.
    • DOI: 10.1038/s42003-022-04226-7
• Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. Ruochi Zhang, Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 276-277, Springer, Cham.
    • DOI: 10.1007/978-3-030-45257-5_37
  • Preprint: bioRxiv 2020.01.22.916171
  • Journal: MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. Ruochi Zhang, Jian Ma. Cell Systems, 10(5): 397-407, 2020.
    • DOI: 10.1016/j.cels.2020.04.004