RECOMB 2023 Proceedings

İstanbul, Türkiye, April 16-19, 2023.

PC Chair: Haixu Tang, Indiana University
Organization Committee: Can Alkan (co-chair), Attila Gürsoy (co-chair), Zülal Bingöl, A. Ercüment Çiçek, Tunca Doğan, Ezgi Ebren, Arzucan Özgür, Öznur Taştan
Keynote Speakers: İvet Bahar, Ewan Birney, Richard Durbin, Tuuli Lappalainen, Sohini Ramachandran, Fabian Theis

List of Publications

• VStrains: de novo reconstruction of viral strains via iterative path extraction from assembly graphs. Runpeng Luo, Yu Lin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 3-20, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_1
  • Preprint: bioRxiv 2022.10.21.513181
• Spectrum preserving tilings enable sparse and modular reference indexing. Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Robert Patro.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 21-40, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_2
  • Preprint: bioRxiv 2022.10.27.513881
• Statistically Consistent Rooting of Species Trees under the Multispecies Coalescent Model. Yasamin Tabatabaee, Sebastien Roch, Tandy Warnow.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 41-57, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_3
  • Preprint: bioRxiv 2022.10.26.513897
  • Journal: QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. Yasamin Tabatabaee, Sebastien Roch, Tandy Warnow. Journal of Computational Biology, 30(11): 1146–1181, 2023.
    • DOI: 10.1089/cmb.2023.0185
• Sequence to graph alignment using gap-sensitive co-linear chaining. Ghanshyam Chandra, Chirag Jain.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 58-73, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_4
  • Preprint: bioRxiv 2022.08.29.505691
  • Journal: Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs. Ghanshyam Chandra, Chirag Jain. Journal of Computational Biology, 30(11): 1182–1197, 2023.
    • DOI: 10.1089/cmb.2023.0186
• DM-Net: a dual-model network for automated biomedical image diagnosis. Xiaogen Zhou, Zhiqiang Li, Tong Tong.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 74-84, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_5
• MTGL-ADMET: A Novel Multi-Task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow. Bing-Xue Du, Yi Xu, Siu Ming Yiu, Hui Yu, Jian-Yu Shi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 85-103, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_6
• CDGCN: Conditional de novo Drug generative model using Graph Convolution Networks. Shikha Mallick, Sahely Bhadra.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 104-119, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_7
• Percolate: an exponential family JIVE model to design DNA-based predictors of drug response. Soufiane Mourragui, Marco Loog, Mirrelijn van Nee, Mark van de Wiel, Marcel Reinders, Lodewyk Wessels.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 120-138, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_8
  • Preprint: bioRxiv 2022.09.11.507473
• Translation rate prediction and regulatory motif discovery with multi-task learning. Weizhong Zheng, John H.C. Fong, Yuk Kei Wan, Athena H.Y. Chu, Yuanhua Huang, Alan S.L. Wong, Joshua Ho.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 139-154, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_9
  • Preprint: bioRxiv 2022.05.03.490410
• Computing shortest hyperpaths for pathway inference in cellular reaction networks. Spencer Krieger, John Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 155-173, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_10
  • Journal: Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference. Spencer Krieger, John Kececioglu. Journal of Computational Biology, 30(11): 1198–1225, 2023.
    • DOI: 10.1089/cmb.2023.0242
• T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy. Ziqi Chen, Martin Min, Hongyu Guo, Chao Cheng, Trevor Clancy, Xia Ning.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 174-192, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7_11
  • Preprint: arXiv:2303.02162
• TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees. Yunheng Han, Erin K. Molloy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 195-196, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.06.25.497608
  • Journal: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees. Yunheng Han, Erin K. Molloy. Genome Research, 33(7):1042-1052, 2023.
    • DOI: 10.1101/gr.277629.122
• mapquik: Efficient low-divergence mapping of long reads in minimizer space. Baris Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 197-199, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.12.23.521809
  • Journal: Efficient mapping of accurate long reads in minimizer space with mapquik. Baris Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi. Genome Research, 33(7): 1188-1197, 2023.
    • DOI: 10.1101/gr.277679.123
• Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash. Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 200-202, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.01.11.475870
  • Journal: Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash. Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki. Genome Research, 33(7):1061-1068, 2023.
    • DOI: 10.1101/gr.277651.123
• Entropy predicts sensitivity of pseudo-random seeds. Benjamin Dominik Maier, Kristoffer Sahlin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 203-204, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.13.512198
  • Journal: Entropy predicts sensitivity of pseudorandom seeds. Benjamin Dominik Maier, Kristoffer Sahlin. Genome Research, 33(7): 1162-1174, 2023.
    • DOI: 10.1101/gr.277645.123
• Seed-chain-extend alignment is accurate and runs in close to O(m log n) time for similar sequences: a rigorous average-case analysis. Jim Shaw, Yun William Yu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 205-207, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.14.512303
  • Journal: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic. Jim Shaw, Yun William Yu. Genome Research, 33(7): 1175-1187, 2023.
    • DOI: 10.1101/gr.277637.122
• Extremely-fast construction and querying of compacted and colored de Bruijn graphs with GGCAT. Andrea Cracco, Alexandru I. Tomescu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 208-209, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.24.513174
  • Journal: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT. Andrea Cracco, Alexandru I. Tomescu. Genome Research, 33(7): 1198-1207, 2023.
    • DOI: 10.1101/gr.277615.122
• PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. Xinhao Liu, Ron Zeira, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 210-211, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.08.523162
  • Journal: Partial alignment of multislice spatially resolved transcriptomics data. Xinhao Liu, Ron Zeira, Benjamin J. Raphael. Genome Research, 33(7): 1124-1132, 2023.
    • DOI: 10.1101/gr.277670.123
• FastRecomb: Fast Inference of Genetic Recombination Rates in Biobank Scale Data. Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 212-213, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.09.523304
  • Journal: Fast inference of genetic recombination rates in biobank scale data. Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi. Genome Research, 33(7): 1015-1022, 2023.
    • DOI: 10.1101/gr.277676.123
• Efficient Taxa Identification Using a Pangenome Index. Omar Ahmed, Massimiliano Rossi, Christina Boucher, Ben Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 214-216, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Journal: Efficient taxa identification using a pangenome index. Omar Ahmed, Massimiliano Rossi, Christina Boucher, Ben Langmead. Genome Research, 33(7): 1069-1077, 2023.
    • DOI: 10.1101/gr.277642.123
• Vector-Clustering Multiple Sequence Alignment: Aligning into the Twilight Zone of Protein Sequence Similarity with Protein Language Models. Claire McWhite, Mona Singh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 217-218, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.21.513099
  • Journal: Leveraging protein language models for accurate multiple sequence alignments. Claire McWhite, Isabel Armour-Garb, Mona Singh. Genome Research, 33(7): 1145-1153, 2023.
    • DOI: 10.1101/gr.277675.123
• Single-Cell Methylation Sequencing Data Reveal Succinct Metastatic Migration Histories and Tumor Progression Models. Yuelin Liu, Xuan Cindy Li, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Maliki´ c, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 219-221, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2021.03.22.436475
  • Journal: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models. Yuelin Liu, Xuan Cindy Li, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Maliki´ c, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Sahinalp. Genome Research, 33(7): 1089-1100, 2023.
    • DOI: 10.1101/gr.277608.122
• Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multi-class Classification. Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 222-223, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: arXiv:2109.00582
  • Journal: Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li. Journal of Machine Learning Research, 23(341): 1-65, 2022.
    • DOI: NONE
• Efficient Minimizer Orders for Large Values of k Using Minimum Decycling Sets. David Pellow, Lianrong Pu, Baris Ekim, Lior Kotlar, Ron Shamir, Yaron Orenstein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 224-226, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.18.512682
  • Journal: Efficient minimizer orders for large values of k using minimum decycling sets. David Pellow, Lianrong Pu, Baris Ekim, Lior Kotlar, Bonnie Berger, Ron Shamir, Yaron Orenstein. Genome Research, 33(7): 1154-1161, 2023.
    • DOI: 10.1101/gr.277644.123
• Dashing 2: Genomic Sketching with Multiplicities and Locality-Sensitive Hashing. Daniel N. Baker, Ben Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 227-228, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.16.512384
  • Journal: Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2. Daniel N. Baker, Ben Langmead. Genome Research, 33(7): 1218-1227, 2023.
    • DOI: 10.1101/gr.277655.123
• Startle: A Star Homoplasy Approach for CRISPR-Cas9 Lineage Tracing. Palash Sashittal, Henri Schmidt, Michelle Chan, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 229, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.12.18.520935
  • Journal: Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing. Palash Sashittal, Henri Schmidt, Michelle Chan, Benjamin J. Raphael. Cell Systems, 14(12): 1113-1121.e9, 2023.
    • DOI: 10.1016/j.cels.2023.11.005
• A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 230-232, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: arXiv:2301.00992
  • Journal: A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu. Genome Research, 33(7): 1053-1060, 2023.
    • DOI: 10.1101/gr.277669.123
• Aligning Distant Sequences to Graphs using Long Seed Sketches. Amir Joudaki, Alexandru Meterez, Harun Mustafa, Ragnar Groot Koerkamp, André Kahles, Gunnar Rätsch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 233-235, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.26.513890
  • Journal: Aligning distant sequences to graphs using long seed sketches. Amir Joudaki, Alexandru Meterez, Harun Mustafa, Ragnar Groot Koerkamp, André Kahles, Gunnar Rätsch. Genome Research, 33(7): 1208-1217, 2023.
    • DOI: 10.1101/gr.277659.123
• MD-Cat: Phylogenetic Dating under a Flexible Categorical Model using Expectation-Maximization. Uyen Mai, Eduardo Charvel, Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 236-238, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.06.511147
  • Journal: Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model. Uyen Mai, Eduardo Charvel, Siavash Mirarab. Systematic Biology, 73(5): 823-838, 2024.
    • DOI: 10.1093/sysbio/syae034
• Phenotypic subtyping via contrastive learning. Aditya Gorla, Sriram Sankararaman, Esteban Burchard, Jonathan Flint, Noah Zaitlen, Elior Rahmani.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 239-240, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.05.522921
• HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2. Sara C. Schulte, Alexander Dilthey, Gunnar W. Klau.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 241-243, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.09.523288
  • Journal: HOGVAX: Exploiting epitope overlaps to maximize population coverage in vaccine design with application to SARS-CoV-2. Sara C. Schulte, Alexander Dilthey, Gunnar W. Klau. Cell Systems, 14(12): 1122-1130, 2023.
    • DOI: 10.1016/j.cels.2023.11.001
• Ultra-fast genome-wide inference of pairwise coalescence times (Final version). Regev Schweiger, Richard Durbin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 244-246, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.06.522935
  • Journal: Ultrafast genome-wide inference of pairwise coalescence times. Regev Schweiger, Richard Durbin. Genome Research, 33(7): 1023-1031, 2023.
    • DOI: 10.1101/gr.277665.123
• Leveraging family data to design Mendelian Randomization that is provably robust to population stratification. Nathan LaPierre, Boyang Fu, Steven Turnbull, Eleazar Eskin, Sriram Sankararaman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 247-248, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.05.522936
  • Journal: Leveraging family data to design Mendelian randomization that is provably robust to population stratification. Nathan LaPierre, Boyang Fu, Steven Turnbull, Eleazar Eskin, Sriram Sankararaman. Genome Research, 33(7): 1032-1041, 2023.
    • DOI: 10.1101/gr.277664.123
• Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model. Ahsan Sanaullah, Degui Zhi, Shaojie Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 249-250, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.04.522803
  • Journal: Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model. Ahsan Sanaullah, Degui Zhi, Shaojie Zhang. Genome Research, 33(7): 1007-1014, 2023.
    • DOI: 10.1101/gr.277673.123
• Cell segmentation for high-resolution spatial transcriptomics. Hao Chen, Dongshunyi Li, Ziv Bar-Joseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 251-253, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.11.523658
  • Journal: SCS: cell segmentation for high-resolution spatial transcriptomics. Hao Chen, Dongshunyi Li, Ziv Bar-Joseph. Nature Methods, 20(8): 1237-1243, 2023.
    • DOI: 10.1038/s41592-023-01939-3
• Unsupervised Deep Peak Caller for ATAC-seq. Yudi Zhang, Ha Vu, Geetu Tuteja, Karin Dorman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 254-256, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.07.523108
  • Journal: Unsupervised contrastive peak caller for ATAC-seq. Ha T.H. Vu, Yudi Zhang, Geetu Tuteja, Karin Dorman. Genome Research, 33(7): 1133-1144, 2023.
    • DOI: 10.1101/gr.277677.123
• Unraveling causal gene regulation from the RNA velocity graph using Velorama. Rohit Singh, Alexander Wu, Anish Mudide, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 257-258, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.10.18.512766
  • Journal: Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors. Rohit Singh, Alexander Wu, Anish Mudide, Bonnie Berger. Cell Systems, 15(5):462-474, 2024.
    • DOI: 10.1016/j.cels.2024.04.005
• PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks. Vitalii Stebliankin, Azam Shirali, Prabin Baral, Prem Chapagain, Giri Narasimhan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 259-261, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.01.03.522623
  • Journal: Evaluating protein binding interfaces with transformer networks. Vitalii Stebliankin, Azam Shirali, Prabin Baral, Jimeng Shi, Prem Chapagain, Kalai Mathee, Giri Narasimhan. Nature Machine Intelligence, 5: 1042–1053, 2023.
    • DOI: 10.1038/s42256-023-00715-4
• DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 262-264, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: arXiv:2107.05556
  • Journal: A Framework for Improving the Generalizability of Drug–Target Affinity Prediction Models. Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli. Journal of Computational Biology, 30(11): 1226–1239, 2023.
    • DOI: 10.1089/cmb.2023.0208
• Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning. Zhihang Hu, Qinze Yu, Yucheng Guo, Taifeng Wang, Irwin King, Xin Gao, Le Song, Yu Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 265-267, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: arXiv:2301.05931
• Pisces: a cross-modal contrastive learning approach to synergistic drug combination prediction. Jiacheng Lin, Hanwen Xu, Addie Woicik, Jianzhu Ma, Sheng Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 268-270, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.11.21.517439
  • Journal: Pisces: A multi-modal data augmentation approach for drug combination synergy prediction. Hanwen Xu, Jiacheng Lin, Addie Woicik, Zixuan Liu, Jianzhu Ma, Sheng Zhang, Hoifung Poon, Liewei Wang, Sheng Wang. Cell Genomics, 5(7): 100892, 2025.
    • DOI: 10.1016/j.xgen.2025.100892
• Modeling and Predicting Cancer Clonal Evolution with Reinforcement Learning. Stefan Ivanovic, Mohammed El-Kebir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 271-273, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2022.12.11.519917
  • Journal: Modeling and predicting cancer clonal evolution with reinforcement learning. Stefan Ivanovic, Mohammed El-Kebir. Genome Research, 33(7): 1078-1088, 2023.
    • DOI: 10.1101/gr.277672.123
• Enabling Trade-offs in Privacy and Utility in Genomic Data Beacons and Summary Statistics. Rajagopal Venkatesaramani, Zhiyu Wan, Brad Malin, Yevgeniy Vorobeychik.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 274-276, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: arXiv:2302.01763
  • Journal: Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics. Rajagopal Venkatesaramani, Zhiyu Wan, Brad Malin, Yevgeniy Vorobeychik. Genome Research, 33(7): 1113-1123, 2023.
    • DOI: 10.1101/gr.277674.123
• Accurate evaluation of transcriptomic re-identification risks using discriminative sequence models. Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 277-279, Springer, Cham.
    • DOI: 10.1007/978-3-031-29119-7
  • Preprint: bioRxiv 2023.04.13.536784
  • Journal: Assessing transcriptomic reidentification risks using discriminative sequence models. Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho. Genome Research, 33(7):1101–1112, 2023.
    • DOI: 10.1101/gr.277699.123