RECOMB 2015 Proceedings

Warsaw, Poland, April 12-15, 2015

PC Chair: Teresa M. Przytycka
Organization Committee: Jerzy Tiuryn (cochair), Bartek Wilczyński (co-chair), Paweł Bednarz, Agata Charzyńska, Norbert Dojer, Anna Gambin, Paweł Górecki, Ilona Grabowicz, Julia Herman-Iżycka, Aleksander Jankowski, Agnieszka Mykowiecka, Ewa Szczurek, Irina Tuszyńska, Damian Wójtowicz, Rafał Zaborowski
Keynote Speakers: Madan Babu, Bonnie Berger, M. Magda Konarska, Michael Levitt, Bas van Steensel, Wacław Szybalski

List of Publications

• Efficient Alignment Free Sequence Comparison with Bounded Mismatches. Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 1-12, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_1
• DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes. Naama Amir, Dan Cohen, Haim J. Wolfson.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 13-15, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_2
• CRISPR Detection from Short Reads Using Partial Overlap Graphs. Ilan Ben-Bassat and Benny Chor.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 16-27, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_3
• HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. Emily Berger, Deniz Yorukoglu, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 28-29, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_4
• Read Clouds Uncover Variation in Complex Regions of the Human Genome. Alex Bishara, Yuling Liu, Dorna Kashef-Haghighi, Ziming Weng, Daniel E. Newburger, Robert West, Arend Sidow, Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 30-31, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_5
• Learning Microbial Interaction Networks from Metagenomic Count Data. Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 32-43, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_6
• Immunoglobulin Classification Using the Colored Antibody Graph. Stefano R. Bonissone and Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 44-59, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_7
• CIDANE: Comprehensive Isoform Discovery and Abundance Estimation. Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 60-61, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_8
• Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. Hyunghoon Cho, Bonnie Berger, Jian Peng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 62-64, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_9
• Fragmentation Trees Reloaded. Kai Dührkop and Sebastian Böcker.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 65-79, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_10
• KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids. Rasmus Fonseca, Henry van den Bedem, Julie Bernauer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 80-95, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_11
• Locating a Tree in a Phylogenetic Network in Quadratic Time. Philippe Gambette, Andreas D.M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 96-107, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_12
• Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 108-121, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_13
• COMETS (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. Mark A. Hallen and Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 122-135, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_14
• Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure. Jong Wha J. Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Aldons J. Lusis, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 136-153, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_15
• *BWM: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design **. Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 154-166, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_16
• An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations. Seunghak Lee, Aurélie Lozano, Prabhanjan Kambadur, Eric P. Xing.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 167-187, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_17
• Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models. Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 188-201, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_18
• CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer. Mark D.M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 202-204, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_19
• Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 205-217, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_20
• Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 218-221, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_21
• ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching. Igor Mandric and Alex Zelikovsky.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 222-223, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_22
• A Symmetric Length-Aware Enrichment Test. David Manescu and Uri Keich.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 224-242, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_23
• Functional Alignment of Metabolic Networks. Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 243-255, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_24
• Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. Andrew McPherson, Andrew Roth, Cedric Chauve, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 256-258, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_25
• Ultra-Large Alignments Using Ensembles of Hidden Markov Models. Nam Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy Warnow.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 259-260, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_26
• Topological Signatures for Population Admixture. Laxmi Parida, Filippo Utro, Deniz Yorukoglu, Anna Paola Carrieri, David Kuhn, Saugata Basu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 261-275, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_27
• Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele. Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 276-280, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_28
• Gap Filling as Exact Path Length Problem. Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 281-292, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_29
• Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. Emre Sefer, Geet Duggal, Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 293-308, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_30
• A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. Mingfu Shao and Bernard M.E. Moret.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 309-322, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_31
• Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions. Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 323-325, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_32
• On the Sample Complexity of Cancer Pathways Identification. Fabio Vandin, Benjamin J. Raphael, Eli Upfal.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 326-337, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_33
• A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks. Roni Wilentzik and Irit Gat-Viks.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 338-339, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_34
• Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. Shuo Yang, Shai Carmi, Itsik Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 340-353, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_35
• Computational Protein Design Using AND/OR Branch-and-Bound Search. Yichao Zhou, Yuexin Wu, Jianyang Zeng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 354-366, Springer, Cham.
    • DOI: 10.1007/978-3-319-16706-0_36