RECOMB 2019 Proceedings

Washington, DC, United States, May 5-8, 2019.

PC Chair: Lenore J. Cowen
Organization Committee: Max Alekseyev (co-chair), Teresa Przytycka (co-chair), Pavel Avdeyev, Jan Hoinka, Chanson Benjamin, Damian Wojtowicz, Rebecca Sarto Basso, Alexander Hopkins-Ives
Keynote Speakers: Carlos D. Bustamante, Rachel Kolodny, Mihai Pop, Franziska Michor, Eytan Ruppin, Alfonso Valencia

• An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro.

List of Publications

• An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 1-18, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_1
  • Preprint: bioRxiv 464222
  • Journal: An efficient, scalable, and exact representation of high-dimensional color information enabled using de Bruijn graph search. Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro. Journal of Computational Biology, 27(4): 485-499, 2020.
    • DOI: 10.1089/cmb.2019.0322
• Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 19-34, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_2
  • Journal: Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning. Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno. JMIR Medical Informatics, 7(2): e12596, 2019.
    • DOI: 10.2196/12596
• ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. Philipp Benner, Martin Vingron.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 35-50, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_3
  • Journal: ModHMM: a modular supra-Bayesian genome segmentation method. Philipp Benner, Martin Vingron. Journal of Computational Biology, 27(4): 442-457, 2020.
    • DOI: 10.1089/cmb.2019.0280
• Learning Robust Multi-label Sample Specific Distances for Identifying HIV-1 Drug Resistance. Lodewijk Brand, Xue Yang, Kai Liu, Saad Elbeleidy, Hua Wang, Hao Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 51-67, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_4
  • Journal: Learning Robust Multilabel Sample Specific Distances for Identifying HIV-1 Drug Resistance. Lodewijk Brand, Xue Yang, Kai Liu, Saad Elbeleidy, Hua Wang, Hao Zhang, Feiping Nie. Journal of Computational Biology, 27(4): 655-672, 2020.
    • DOI: 10.1089/cmb.2019.0329
• MethCP: Differentially Methylated Region Detection with Change Point Models. Boying Gong, Elizabeth Purdom.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 68-84, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_5
  • Preprint: bioRxiv 265116
  • Journal: MethCP: differentially methylated region detection with change point models. Boying Gong, Elizabeth Purdom. Journal of Computational Biology, 27(4): 458-471, 2020.
    • DOI: 10.1089/cmb.2019.0326
• On the Complexity of Sequence to Graph Alignment. Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 85-100, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_6
  • Preprint: bioRxiv 522912
  • Journal: On the complexity of sequence-to-graph alignment. Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru. Journal of Computational Biology, 27(4): 640-654, 2020.
    • DOI: 10.1089/cmb.2019.0066
• Minimization-Aware Recursive K*(MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 101-119, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_7
  • Journal: *Minimization-Aware Recursive K: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape*. Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce R. Donald. *Journal of Computational Biology, 27(4): 550-564, 2020.
    • DOI: 10.1089/cmb.2019.0315
• Sparse Binary Relation Representations for Genome Graph Annotation. Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 120-135, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_8
  • Preprint: bioRxiv 468512
  • Journal: Sparse binary relation representations for genome graph annotation. Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles. Journal of Computational Biology, 27(4): 626-639, 2020.
    • DOI: 10.1089/cmb.2019.0324
• How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories. Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel, Govind Ramnarayan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 136-157, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_9
  • Preprint: arXiv:1811.03177
  • Journal: How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories. Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel, Govind Ramnarayan. Journal of Computational Biology, 27(4): 613-625, 2020.
    • DOI: 10.1089/cmb.2019.0318
• Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 158-173, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_10
  • Preprint: arXiv:1811.06933
  • Journal: Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini. Journal of Computational Biology, 27(4): 500-513, 2020.
    • DOI: 10.1089/cmb.2019.0309
• Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz .
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 174-189, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_11
  • Preprint: bioRxiv 519892
  • Journal: Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz. Journal of Computational Biology, 27(4): 565-598, 2020.
    • DOI: 10.1089/cmb.2019.0302
• OMGS: Optical Map-Based Genome Scaffolding. Weihua Pan, Tao Jiang, Stefano Lonardi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 190-207, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_12
  • Preprint: bioRxiv 585794
  • Journal: OMGS: Optical Map-Based Genome Scaffolding. Weihua Pan, Tao Jiang, Stefano Lonardi. Journal of Computational Biology, 27(4): 519-533, 2020.
    • DOI: 10.1089/cmb.2019.0310
• Fast Approximation of Frequent k-mers and Applications to Metagenomics. Leonardo Pellegrina, Cinzia Pizzi, Fabio Vandin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 208-226, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_13
  • Preprint: arXiv:1902.10168
  • Journal: Fast approximation of frequent k-mers and applications to metagenomics. Leonardo Pellegrina, Cinzia Pizzi, Fabio Vandin. Journal of Computational Biology, 27(4): 534-549, 2020.
    • DOI: 10.1089/cmb.2019.0314
• De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm. Kristoffer Sahlin, Paul Medvedev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 227-242, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_14
  • Preprint: bioRxiv 463463
  • Journal: De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm. Kristoffer Sahlin, Paul Medvedev. Journal of Computational Biology, 27(4): 472-484, 2020.
    • DOI: 10.1089/cmb.2019.0313
• A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. Itay Sason, Damian Wojtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 243-255, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_15
  • Journal: A sticky multinomial mixture model of strand-coordinated mutational processes in cancer. Itay Sason, Damian Wojtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan. iScience, 23(3): 100900, 2020.
    • DOI: 10.1016/j.isci.2020.100900
• Disentangled Representations of Cellular Identity. Ziheng Wang, Grace H. T. Yeo, Richard Sherwood, David Gifford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 256-271, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_16
• RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature. Ye Wu, Ruibang Luo, Henry C. M. Leung, Hing-Fung Ting, Tak-Wah Lam.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 272-284, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7_17
• APPLES: Fast Distance-Based Phylogenetic Placement. Metin Balaban, Shahab Sarmashghi, Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 287-288, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 475566
  • Journal: APPLES: Scalable distance-based phylogenetic placement with or without alignments. Metin Balaban, Shahab Sarmashghi, Siavash Mirarab. Systematic Biology, 69(3): 566-578, 2020.
    • DOI: 10.1093/sysbio/syz063
• De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments. Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 289-291, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 521872
  • Journal: De novo peptide sequencing reveals a vast cyclopeptidome in human gut and other environments. Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner. Cell Systems, 10(1): 99-108, 2020.
    • DOI: 10.1016/j.cels.2019.11.007
• Biological Sequence Modeling with Convolutional Kernel Networks. Dexiong Chen, Laurent Jacob, Julien Mairal.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 292-293, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 217257
  • Journal: Biological sequence modeling with convolutional kernel networks. Dexiong Chen, Laurent Jacob, Julien Mairal. Bioinformatics, 35(18): 3294-3302, 2019.
    • DOI: 10.1093/bioinformatics/btz094
• Dynamic Pseudo-time Warping of Complex Single-Cell Trajectories. Van Hoan Do, Mislav Blažević, Pablo Monteagudo, Luka Borozan, Khaled Elbassioni, Sören Laue, Francisca Rojas Ringeling, Domagoj Matijević, Stefan Canzar.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 294-296, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 522672
• netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data. Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 297-298, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 544346
  • Journal: netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael. Genome Research, 30(2): 195-204, 2020.
    • DOI: 10.1101/gr.251603.119
• Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. Brian Hie, Hyunghoon Cho, Benjamin DeMeo, Bryan Bryson, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 299-301, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 536730
  • Journal: Geometric sketching compactly summarizes the single-cell transcriptomic landscape. Brian Hie, Hyunghoon Cho, Benjamin D. DeMeo, Bryan Bryson, Bonnie Berger. Cell Systems, 8(6): 483-493.e7, 2019.
    • DOI: 10.1016/j.cels.2019.05.003
• Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M. Oguzhan Kulekci, David P. Woodruff, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 302-304, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 468355
  • Journal: Sketching algorithms for genomic data analysis and querying in a secure enclave. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M. Oguzhan Kulekci, David P. Woodruff, S. Cenk Sahinalp. Nature Methods, 17(3): 295-301, 2020.
    • DOI: 10.1038/s41592-020-0761-8
• Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 305-307, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 519413
• Efficient Estimation and Applications of Cross-Validated Genetic Predictions. Joel Mefford, Danny Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Paivi Pajukanta, Jian Yang, John Witte, Noah Zaitlen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 308-310, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 517821
  • Journal: Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models. Joel Mefford, Danny Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Päivi Pajukanta, Jian Yang, John Witte, Noah Zaitlen. Journal of Computational Biology, 27(4): 550-564, 2020.
    • DOI: 10.1089/cmb.2019.0315
• Inferring Tumor Evolution from Longitudinal Samples. Matthew A. Myers, Gryte Satas, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 311, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 526814
  • Journal: CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. Matthew A. Myers, Gryte Satas, Benjamin J. Raphael. Cell Systems, 8(6): 514–522.e5, 2019.
    • DOI: 10.1016/j.cels.2019.05.010
• Scalable Multi-component Linear Mixed Models with Application to SNP Heritability Estimation. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Bogdan Pasaniuc, Sriram Sankararaman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 312-313, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 522003
  • Journal: Efficient variance components analysis across millions of genomes. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Aaron Zhou, Bogdan Pasaniuc & Sriram Sankararaman. Nature Communications, 11(1): 4020, 2020.
    • DOI: 10.1038/s41467-020-17576-9
• A Note on Computing Interval Overlap Statistics. Shahab Sarmashghi and Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 314-315, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 517987
  • Journal: Computing the Statistical Significance of Overlap between Genome Annotations with iStat. Shahab Sarmashghi and Vineet Bafna. Cell Systems, 8(6): p523-529.e4, 2019.
    • DOI: 10.1016/j.cels.2019.05.006
• Distinguishing Biological from Technical Sources of Variation Using a Combination of Methylation Datasets. Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 316-317, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 521146
  • Journal: CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets. Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani & Eran Halperin. Genome Biology, 20(1): 138, 2019.
    • DOI: 10.1186/s13059-019-1743-y
• GRep: Gene Set Representation via Gaussian Embedding. Sheng Wang, Emily Flynn, Russ B. Altman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 318-319, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 519033
  • Journal: Gaussian embedding for large-scale gene set analysis. Sheng Wang, Emily R. Flynn & Russ B. Altman. Nature Machine Intelligence, 2(7): 387–395, 2020.
    • DOI: 10.6084/m9.figshare.11341181.v1
• Accurate Sub-population Detection and Mapping Across Single Cell Experiments with PopCorn. Yijie Wang, Jan Hoinka, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 320-3321, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 485979
  • Journal: Subpopulation Detection and Their Comparative Analysis across Single-Cell Experiments with scPopCorn. Yijie Wang ∙ Jan Hoinka ∙ Teresa M. Przytycka. Cell Systems, 8(6): 506–513.e5, 2019.
    • DOI: 10.1016/j.cels.2019.05.007
• Fast Estimation of Genetic Correlation for Biobank-Scale Data. Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, Sriram Sankararaman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 322-323, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 525055
  • Journal: Fast estimation of genetic correlation for biobank-scale data. Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, Sriram Sankararaman. American Journal of Human Genetics, 109(1): 24-32, 2022.
    • DOI: 10.1016/j.ajhg.2021.11.015
• Distance-Based Protein Folding Powered by Deep Learning. Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 324-325, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: arXiv:1811.03481
  • Journal: Distance-based protein folding powered by deep learning. Jinbo Xu. Proceedings of the National Academy of Sciences, 116(34): 16856-16865, 2019.
    • DOI: 10.1073/pnas.1821309116
• Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Yang Yang, Yang Zhang, Bing Ren, Jesse Dixon, Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 326-327, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 552505
  • Journal: Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma. Cell Systems, 8(6): 494-505.e14, 2019.
    • DOI: 10.1016/j.cels.2019.05.011
• Towards a Post-clustering Test for Differential Expression. Jesse M. Zhang, Govinda M. Kamath, David N. Tse.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 328-329, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 463265
  • Journal: Valid Post-clustering Differential Analysis for Single-Cell RNA-Seq. Jesse M. Zhang, Govinda M. Kamath, David N. Tse. Cell Systems, 9(4): 383-392.e6, 2019.
    • DOI: 10.1016/j.cels.2019.07.012
• AdaFDR: A Fast, Powerful and Covariate-Adaptive Approach to Multiple Hypothesis Testing. Martin J. Zhang, Fei Xia, James Zou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467, pp 330-333, Springer, Cham.
    • DOI: 10.1007/978-3-030-17083-7
  • Preprint: bioRxiv 496372
  • Journal: Fast and covariate-adaptive method amplifies detection power in large-scale multiple hypothesis testing. Martin J. Zhang, Fei Xia, James Zou. Nature Communications, 10(1): 3433, 2019.
    • DOI: 10.1038/s41467-019-11247-0