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Multiplex De Novo Sequencing of Peptide Antibiotics.
Hosein Mohimani, Wei Ting Liu, Yu Liang Yang, Susana Gaudencio, William Fenical, Pieter Dorrestein and Pavel Pevzner.

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model.
Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin and Tamir Tuller.

Recovering Key Biological Constituents through Sparse Representation of Gene Expression.
Yosef Prat, Menachem Fromer, Nathan Linial and Michal Linial.

Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals.
Xin Li and Jing Li.

PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling.
Jaebum Kim and Jian Ma.

Bacterial Community Reconstruction Using Compressed Sensing.
Amnon Amir and Or Zuk.

Causal reasoning on biological networks: Interpreting transcriptional changes.
Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel and Enoch Huang.

Metabolic Network Analysis Demystified.
Leonid Chindelevitch, Aviv Regev and Bonnie Berger.

A Probabilistic Model For Sequence Alignment with Context-Sensitive Indels.
Glenn Hickey and Mathieu Blanchette.

Variable Selection through Correlation Sifting.
Jim Huang and Nebojsa Jojic.

Pedigree Reconstruction using Identity by Descent.
Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp and Eran Halperin.

T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome.
Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Chin.

De novo Discovery of Mutated Driver Pathways in Cancer.
Fabio Vandin, Eli Upfal and Ben Raphael.

Increasing Power of Groupwise Association Test with Likelihood Ratio Test.
Jae Hoon Sul, Buhm Han and Eleazar Eskin.

Nonparametric combinatorial sequence models.
Fabian Wauthier, Michael Jordan and Nebojsa Jojic.

Simultaneous structural variation discovery in multiple paired-end sequenced genomes.
Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan Eichler and Cenk Sahinalp.

Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data.
Kerstin Scheubert, Franziska Hufsky, Florian Rasche and Sebastian Böcker.

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut.
Mark Leiserson, Diana Tatar, Lenore Cowen and Benjamin Hescott.

Experiment Specific Expression Patterns.
Tobias Petri, Robert Küffner and Ralf Zimmer.

Optimally Orienting Physical Networks.
Dana Silverbush, Michael Elberfeld and Roded Sharan.

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Jérôme Waldispühl and Yann Ponty.

Blocked Pattern Matching Problem and its Applications in Proteomics.
Julio Ng, Amihood Amir and Pavel Pevzner.

AREM: aligning short reads from ChIP-sequencing by expectation maximization.
Daniel Newkirk, Alvin Chon, Jacob Biesinger, Kyoko Yokomori and Xiaohui Xie.

A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs.
Jeffrey Martin, Anthony Yan, Chris Bailey-Kellogg, Pei Zhou and Bruce Donald.

Rich Parameterization Improves RNA Structure Prediction.
Shay Zakov, Yoav Goldberg, Michael Elhadad and Michal ziv-ukelson.

Algorithms for MDC-based Multi-locus Phylogeny Inference.
Yun Yu, Tandy Warnow and Luay Nakhleh.

Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks.
Sinan Erten, Gurkan Bebek and Mehmet Koyuturk.

Constrained De Novo Sequencing of Peptides with Application to Conotoxins.
Swapnil Bhatia, Yong Kil, Beatrix Ueberheide, Brian Chait, Lemmuel Tayo, Bingwen Lu, John Yates III and Marshall Bern.

Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm.
Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden and Bruce R. Donald.

Protein Loop Closure using Orientational Restraints from NMR Data.
Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou and Bruce Donald.

Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways.
Allison Heath, George Bennett and Lydia Kavraki.

An optimization-based sampling scheme for phylogenetic trees.
Navodit Misra, Guy Blelloch, R. Ravi and Russell Schwartz.

Hapsembler: An assembler for highly polymorphic genomes.
Nilgun Donmez and Michael Brudno.

Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction.
Emre Sefer and Carl Kingsford.

Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.
Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler and Pavel Pevzner.

Efficient traversal of protein folding pathways using ensemble models.
Solomon Shenker, Charles O'Donnell, Srinivas Devadas, Bonnie Berger and Jerome Waldispuhl.

Weighted genomic distance can hardly impose a bound on the proportion of transpositions.
Shuai Jiang and Max Alekseyev.

A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data.
Jianyang Zeng, Kyle Roberts, Pei Zhou and Bruce Donald.

Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.
Song Gao, Niranjan Nagarajan and Wing-Kin Sung.

IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly.
Wei Li, Jianxing Feng and Tao Jiang.

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs.
Tien-ho Lin, Ziv Bar-Joseph and Robert F. Murphy.

Optimization of combinatorial mutagenesis.
Andrew Parker, Karl Griswold and Chris Bailey-Kellogg.

Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-Loci and Algorithms for Optimal Tagging SNP Selection.
Ryan Tarpine, Fumei Lam and Sorin Istrail.





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