RECOMB 2018 Proceedings

Paris, France, April 21-24, 2018

PC Chair: Benjamin J. Raphael
Organization Committee: Yann Ponty (co-chair), Mireille Regnier (co-chair), Alessandra Carbone, Celine Scornavacca, Eric Tannier, Hélène Touzet, Stéphane Vialette
Keynote Speakers: Peter Campbell, Ron Shamir, Sarah Teichmann, Nevan Krogan, Francois Spitz, Tandy Warnow

List of Publications

• Long Reads Enable Accurate Estimates of Complexity of Metagenomes. Anton Bankevich and Pavel Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 1-20, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_1
• Chromatyping: Reconstructing Nucleosome Profiles from NOME Sequencing Data. Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 21-36, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_2
  • Journal: Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz. Journal of Computational Biology, 27(3):330-341, 2020.
    • DOI: 10.1089/cmb.2019.0457
• GTED: Graph Traversal Edit Distance. Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, S. Cenk Sahinalp, Hamidreza Chitsaz.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 37-53, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_3
• Statistical Inference of Peroxisome Dynamics. Cyril Galitzine, Pierre M. Jean Beltran, Ileana M. Cristea, Olga Vitek.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 54-74, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_4
• Loss-Function Learning for Digital Tissue Deconvolution. Franziska Görtler, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Rainer Spang, Michael Altenbuchinger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 75-89, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_5
• Inference of Population Structure from Ancient DNA. Tyler A. Joseph and Itsik Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 90-104, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_6
• Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru Tomescu, Veli Mäkinen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 105-121, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_7
• Modeling Dependence in Evolutionary Inference for Proteins. Gary Larson, Jeffrey L. Thorne, Scott Schmidler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 122-137, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_8
• Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry. Sujun Li, Alex DeCourcy, Haixu Tang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 138-153, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_9
• Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. Yaron Orenstein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 154-166, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_10
• Circular Networks from Distorted Metrics. Sebastien Roch and Kun-Chieh Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 167-176, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_11
• A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 177-193, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_12
  • Journal: A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl. Journal of Computational Biology, 27(3):390-402, 2020.
    • DOI: 10.1089/cmb.2019.0401
• Context-Specific Nested Effects Models. Yuriy Sverchkov, Yi-Hsuan Ho, Audrey Gasch, Mark Craven.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 194-210, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_13
• Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 211-224, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_14
• Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes. Zhemin Zhou, Nina Luhmann, Nabil-Fareed Alikhan, Christopher Quince, Mark Achtman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 225-242, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9_15
• Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR. Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 243-244, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs. Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 245-247, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Journal: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J. Noble, Bonnie Berger. Nature Methods, 16:1153–1160, 2018.
    • DOI: 10.1038/s41592-019-0575-8
• Designing RNA Secondary Structures Is Hard. Édouard Bonnet, Paweł Rzążewski, Florian Sikora.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 248-250, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Preprint: arXiv:1710.11513 [cs.DS]
  • Journal: Designing RNA Secondary Structures Is Hard. Édouard Bonnet, Paweł Rzążewski, Florian Sikora. Journal of Computational Biology, 27(3):302-316, 2020.
    • DOI: 10.1089/cmb.2019.0420
• Generalizable Visualization of Mega-Scale Single-Cell Data. Hyunghoon Cho, Bonnie Berger, Jian Peng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 251-253, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis. G. Durif, L. Modolo, J. E. Mold, S. Lambert-Lacroix, F. Picard.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 254-255, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Journal: Probabilistic count matrix factorization for single cell expression data analysis. Ghislain Durif, Laurent Modolo, Jeff E Mold, Sophie Lambert-Lacroix, Franck Picard. Bioinformatics, 35(20):4011-4019, 2019.
    • DOI: 10.1093/bioinformatics/btz177
• Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 256-258, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Contribution of Structural Variation to Genome Structure: TAD Fusion Discovery and Ranking. Linh Huynh and Fereydoun Hormozdiari.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 259-260, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Assembly of Long Error-Prone Reads Using Repeat Graphs. Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 261-262, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• A Multi-species Functional Embedding Integrating Sequence and Network Structure. Mark D. M. Leiserson, Jason Fan, Anthony Cannistra, Inbar Fried, Tim Lim, Thomas Schaffner, Mark Crovella, Benjamin Hescott.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 263-265, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Deciphering Signaling Specificity with Deep Neural Networks. Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 266-268, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. Salem Malikic, Katharina Jahn, Jack Kuipers, S. Cenk Sahinalp, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 269-270, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 271-273, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Tensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies. Elior Rahmani, Regev Schweiger, Saharon Rosset, Sriram Sankararaman, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 274-275, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 276-277, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Journal: Skmer: assembly-free and alignment-free sample identification using genome skims. Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab. Genome Biology, 20(1):34, 2019.
    • DOI: 10.1186/s13059-019-1632-4
• Efficient Algorithms to Discover Alterations with Complementary Functional Association in Cancer. Rebecca Sarto Basso, Dorit S. Hochbaum, Fabio Vandin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 278-279, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Journal: Efficient algorithms to discover alterations with complementary functional association in cancer. Rebecca Sarto Basso, Dorit S. Hochbaum, Fabio Vandin. PLOS Computational Biology, 15(5):e1006802, 2019.
    • DOI: 10.1371/journal.pcbi.1006802
• Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. Ariya Shajii, Ibrahim Numanagić, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 280-282, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules.. Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 283-284, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Preprint: bioRxiv 288399
• SCIO: Single-Cell Mutation Identification via Phylogenetic Inference. Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 285-286, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• AptaBlocks: Accelerating the Design of RNA-Based Drug Delivery Systems. Yijie Wang, Jan Hoinka, Piotr Swiderski, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 287-288, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Journal: AptaBlocks: Accelerating the Design of RNA-based Drug Delivery Systems. Yijie Wang, Jan Hoinka, Yong Liang, Tomasz Adamus, Piotr Swiderski, and Teresa M. Przytycka. Nucleic Acids Research, 46(16):8133-8142, 2018.
    • DOI: 10.1093/nar/gky696
• A Unifying Framework for Summary Statistic Imputation. Yue Wu, Eleazar Eskin, Sriram Sankararaman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 289-290, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data. Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 291-292, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
• Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.. Yang Yang, Quanquan Gu, Takayo Sasaki, Julianna Crivello, Rachel O’Neill, David M. Gilbert, Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 293-294, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9
  • Journal: Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. Yang Yang, Quanquan Gu, Yang Zhang, Takayo Sasaki, Julianna Crivello, Rachel J. O’Neill, David M. Gilbert, Jian Ma. Cell Systems, 7(2):208-218.e11, 2018.
    • DOI: 10.1016/j.cels.2018.05.022
• Deep Learning Reveals Many More Inter-protein Residue-Residue Contacts than Direct Coupling Analysis. Tian-Ming Zhou, Sheng Wang, Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812, pp 295-296, Springer, Cham.
    • DOI: 10.1007/978-3-319-89929-9