WABI 2017 August 21-23, 2017 - Boston, MA, USA

17th International Workshop on Algorithms in Bioinformatics (WABI 2017)



Russell Schwartz and Knut Reinert (Eds.)
ISBN 978-3-95977-050-7, LIPICS Vol. 88 ISSN 1868-8969
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Authors
  • Abramova, Anastasiia
  • Alipanahi, Bahar
  • Almirantis, Yannis
  • Almodaresi, Fatemeh
  • Altschul, Stephen F.
  • Bayegan, Amir H.
  • Bayzid, Md. Shamsuzzoha
  • Boucher, Christina
  • Bravo, Héctor Corrada
  • Brubach, Brian
  • Bunnik, Evelien M.
  • Charalampopoulos, Panagiotis
  • Christensen, Sarah
  • Ciach, Michal Aleksander
  • Clote, Peter
  • Comin, Matteo
  • Cornwell, Steffen
  • Crochemore, Maxime
  • Ebert, Peter
  • El-Mabrouk, Nadia
  • Francisco, Alexandre P.
  • Frank, Yves
  • Górecki, Pawel
  • Gao, Jia
  • Geiß, Manuela
  • Ghurye, Jay
  • Girotto, Samuele
  • Gunady, Mohamed K.
  • Hasan, Md. Abid
  • Hellmuth, Marc
  • Holub, Jan
  • Hruz, Tomas
  • Hu, Chenyue W.
  • Iliopoulos, Costas S.
  • Jabbari, Hosna
  • Kannan, Sreeram
  • Kim, Jongkyu
  • Korobeynikov, Anton
  • Le Roch, Karine
  • Li, Hanyang
  • Lonardi, Stefano
  • Mao, Shunfu
  • Merkle, Daniel
  • Mohajer, Soheil
  • Mohamed, Manal
  • Molloy, Erin K.
  • Montemagno, Carlo
  • Mount, Stephen M.
  • Muggli, Martin
  • Muszewska, Anna
  • Nikumbh, Sarvesh
  • Nojgaard, Nikolai
  • Ouangraoua, Aïda
  • Pan, Weihua
  • Pandey, Prashant
  • Patro, Rob
  • Pfeifer, Nico
  • Pissis, Solon P.
  • Pizzi, Cinzia
  • Polishko, Anton
  • Polychronopoulos, Dimitris
  • Pop, Mihai
  • Procházka, Petr
  • Puglisi, Simon J.
  • Quedenfeld, Jens
  • Qutub, Amina A.
  • Rahmann, Sven
  • Ramachandran, Kannan
  • Reinert, Knut
  • Roayaei Ardakany, Abbas
  • Salmela, Leena
  • Schwartz, Russell
  • Shah, Nidhi
  • Simonaitis, Pijus
  • Srinivasan, Aravind
  • Stadler, Peter F.
  • Swenson, Krister M.
  • Taipale, Jussi
  • Toivonen, Jarkko
  • Tschager, Thomas
  • Tse, David
  • Ukkonen, Esko
  • Vachaspati, Pranjal
  • Vaz, Cátia
  • Venzin, Valentin
  • Wark, Ian
  • Warnow, Tandy
  • Wieseke, Nicolas
  • Will, Sebastian

  •   
    Front Matter, Table of Contents, Preface, List of Authors
    Authors: Schwartz, Russell ; Reinert, Knut

    Abstract | Document (282 KB) | BibTeX

    Disentangled Long-Read De Bruijn Graphs via Optical Maps
    Authors: Alipanahi, Bahar ; Salmela, Leena ; Puglisi, Simon J. ; Muggli, Martin ; Boucher, Christina

    Abstract | Document (656 KB) | BibTeX

    Gene Tree Parsimony for Incomplete Gene Trees
    Authors: Bayzid, Md. Shamsuzzoha ; Warnow, Tandy

    Abstract | Document (490 KB) | BibTeX

    Better Greedy Sequence Clustering with Fast Banded Alignment
    Authors: Brubach, Brian ; Ghurye, Jay ; Pop, Mihai ; Srinivasan, Aravind

    Abstract | Document (858 KB) | BibTeX

    Optimal Computation of Overabundant Words
    Authors: Almirantis, Yannis ; Charalampopoulos, Panagiotis ; Gao, Jia ; Iliopoulos, Costas S. ; Mohamed, Manal ; Pissis, Solon P. ; Polychronopoulos, Dimitris

    Abstract | Document (709 KB) | Document 2 (655 KB) | BibTeX

    Detecting Locus Acquisition Events in Gene Trees
    Authors: Ciach, Michal Aleksander ; Muszewska, Anna ; Górecki, Pawel

    Abstract | Document (2,602 KB) | BibTeX

    An IP Algorithm for RNA Folding Trajectories
    Authors: Bayegan, Amir H. ; Clote, Peter

    Abstract | Document (889 KB) | BibTeX

    Fast Spaced Seed Hashing
    Authors: Girotto, Samuele ; Comin, Matteo ; Pizzi, Cinzia

    Abstract | Document (653 KB) | BibTeX

    A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation
    Authors: El-Mabrouk, Nadia ; Ouangraoua, Aïda

    Abstract | Document (659 KB) | BibTeX

    Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time
    Authors: Crochemore, Maxime ; Francisco, Alexandre P. ; Pissis, Solon P. ; Vaz, Cátia

    Abstract | Document (1,498 KB) | BibTeX

    Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification
    Authors: Gunady, Mohamed K. ; Cornwell, Steffen ; Mount, Stephen M. ; Bravo, Héctor Corrada

    Abstract | Document (1,353 KB) | BibTeX

    Shrinkage Clustering: A Fast and Size-Constrained Algorithm for Biomedical Applications
    Authors: Hu, Chenyue W. ; Li, Hanyang ; Qutub, Amina A.

    Abstract | Document (624 KB) | BibTeX

    Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice
    Authors: Jabbari, Hosna ; Wark, Ian ; Montemagno, Carlo ; Will, Sebastian

    Abstract | Document (709 KB) | BibTeX

    Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence
    Authors: Kim, Jongkyu ; Reinert, Knut

    Abstract | Document (1,318 KB) | BibTeX

    Assessing the Significance of Peptide Spectrum Match Scores
    Authors: Abramova, Anastasiia ; Korobeynikov, Anton

    Abstract | Document (488 KB) | BibTeX

    abSNP: RNA-Seq SNP Calling in Repetitive Regions via Abundance Estimation
    Authors: Mao, Shunfu ; Mohajer, Soheil ; Ramachandran, Kannan ; Tse, David ; Kannan, Sreeram

    Abstract | Document (1,037 KB) | BibTeX

    All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels
    Authors: Nikumbh, Sarvesh ; Ebert, Peter ; Pfeifer, Nico

    Abstract | Document (1,101 KB) | BibTeX

    Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps
    Authors: Nojgaard, Nikolai ; Geiß, Manuela ; Merkle, Daniel ; Stadler, Peter F. ; Wieseke, Nicolas ; Hellmuth, Marc

    Abstract | Document (504 KB) | BibTeX

    Rainbowfish: A Succinct Colored de Bruijn Graph Representation
    Authors: Almodaresi, Fatemeh ; Pandey, Prashant ; Patro, Rob

    Abstract | Document (534 KB) | BibTeX

    ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks
    Authors: Polishko, Anton ; Hasan, Md. Abid ; Pan, Weihua ; Bunnik, Evelien M. ; Le Roch, Karine ; Lonardi, Stefano

    Abstract | Document (2,999 KB) | BibTeX

    Byte-Aligned Pattern Matching in Encoded Genomic Sequences
    Authors: Procházka, Petr ; Holub, Jan

    Abstract | Document (653 KB) | BibTeX

    Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping
    Authors: Quedenfeld, Jens ; Rahmann, Sven

    Abstract | Document (520 KB) | BibTeX

    Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps
    Authors: Roayaei Ardakany, Abbas ; Lonardi, Stefano

    Abstract | Document (568 KB) | BibTeX

    Outlier Detection in BLAST Hits
    Authors: Shah, Nidhi ; Altschul, Stephen F. ; Pop, Mihai

    Abstract | Document (1,210 KB) | BibTeX

    Finding Local Genome Rearrangements
    Authors: Simonaitis, Pijus ; Swenson, Krister M.

    Abstract | Document (891 KB) | BibTeX

    Seed-driven Learning of Position Probability Matrices from Large Sequence Sets
    Authors: Toivonen, Jarkko ; Taipale, Jussi ; Ukkonen, Esko

    Abstract | Document (583 KB) | BibTeX

    Improved De Novo Peptide Sequencing using LC Retention Time Information
    Authors: Frank, Yves ; Hruz, Tomas ; Tschager, Thomas ; Venzin, Valentin

    Abstract | Document (658 KB) | BibTeX

    Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL
    Authors: Christensen, Sarah ; Molloy, Erin K. ; Vachaspati, Pranjal ; Warnow, Tandy

    Abstract | Document (658 KB) | BibTeX

      




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