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HAPLOFREQ - Estimating Haplotype Frequencies
Efficiently
Authors: Eran Halperin, Elad Hazan |
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Reconstruction of Reticulate Networks from
Gene Trees
Authors: Daniel H. Huson, Tobias Kloepper, Pete J. Lockhart, Mike Steel |
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A Practical Approach to Significance
Assessment in Alignment with Gaps
Authors: Nicholas
Chia, Ralf Bundschuh |
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A Hidden Markov Model Based Scoring Function
for Mass Spectrometry Database Search
Authors: Yunhu Wan, Ting
Chen |
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EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
Authors:
Marshall Bern, David Goldberg |
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Avoiding Local Optima in Single Particle Reconstruction
Authors: Marshall Bern, Jindong (JD) Chen, H.
Chi Wong |
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Graph Theoretical Insights into Evolution of
Multidomain Proteins
Authors: Teresa Przytycka, George
Davis, Nan Song, Dannie Durand |
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Efficient Calculation of Interval Scores for
DNA Copy Number Data Analysis
Authors: Doron Lipson,
Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini |
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RNA-RNA Interaction Prediction and Antisense
RNA Target Search
Authors: Can Alkan, Emre Karakoç, Joe
Nadeau, S. Cenk Sahinalp, Kaizhong Zhang |
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The Factor Graph Network Model for Biological Systems
Authors: Irit Gat-Viks, Amos Tanay, Daniela
Raijman, Ron Shamir |
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Recognition of Binding Patterns Common to a
Set of Protein Structures
Authors: Maxim Shatsky,
Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson |
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Constructing a Smallest Refining Galled
Phylogenetic Network
Authors: Trinh N.D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung |
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On Sorting by Translocations
Authors: Anne Bergeron, Julia Mixtacki, Jens Stoye
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Modeling the Combinatorial Functions of Multiple Transcription Factors
Authors: Chen-Hsiang
Yeang, Tommi Jaakkola |
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RIBRA - An Error-Tolerant Algorithm for the NMR
Backbone Assignment Problem
Authors: Kuen-Pin Wu,
Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang
Huang, Ting-Yi Sung, Wen-Lian Hsu |
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Predicting Protein-Peptide Binding Affinity
by Learning Peptide-Peptide Distance Functions
Authors:
Chen Yanover, Tomer Hertz |
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Alignment of Optical
Maps
Authors: Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman |
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Rapid Protein Side-Chain Packing via Tree
Decomposition
Authors: Jinbo Xu |
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Segmentation Conditional Random Fields
(SCRFs): A New Approach for Protein Fold Recognition
Authors: Yan Liu, Jaime Carbonell, Peter Weigele,
Vanathi Gopalakrishnan, Jonathan King |
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Efficient Algorithms for Detecting Signaling
Pathways in Protein Interaction Networks
Authors: Jacob
Scott, Trey Ideker, Richard M. Karp, Roded Sharan |
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A Polynomial Time Solvable Formulation of Multiple Sequence Alignment
Authors: Sing-Hoi Sze, Yue
Lu, Qingwu Yang |
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A High-Throughput Approach for Associating
MicroRNAs with their Activity Conditions
Authors:
Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini |
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Information Theoretic Approaches to Whole
Genome Phylogenies
Authors: David Burstein, Igor
Ulitsky, Tamir Tuller, Benny Chor |
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Maximum Likelihood of Evolutionary Trees is
Hard
Authors: Benny Chor, Tamir Tuller |
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Improved Recombination Lower Bounds for
Haplotype Data
Authors: Vineet Bafna, Vikas
Bansal |
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Predicting Transcription Factor Binding Sites
Using Structural Knowledge
Authors: Tommy Kaplan, Nir
Friedman, Hanah Margalit |
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A Linear-Time Algorithm for the Perfect
Phylogeny Haplotyping (PPH) Problem
Authors: Zhihong
Ding, Vladimir Filkov, Dan Gusfield |
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Motif Discovery through Predictive Modeling of Gene Regulation
Authors: Manuel Middendorf, Anshul
Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina Leslie
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GenRate - A Generative Model that Finds and
Scores New Gene Structures in Genome-Wide Microarray Data
Authors: Brendan J. Frey, Quaid D. Morris, Naveed Mohammad,
Mark Robinson, Wen Zhang, Timothy R. Hughes |
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Consensus Folding of Unaligned RNA Sequences Revisited
Authors: Vineet Bafna, Haixu Tang, Shaojie
Zhang |
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A Fundamental Decomposition Theory for
Phylogenetic Networks and Incompatible Characters
Authors: Dan Gusfield, Vikas Bansal |
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Stability of Rearrangement Measures in the Comparison of Genome Sequences
Authors: David Sankoff,
Matthew Mazowita |
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Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution
Authors: Mehmet Koyutürk, Ananth Grama, Wojciech
Szpankowski |
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Towards an Integrated Protein-Protein
Interaction Network
Authors: Ariel Jaimovich, Gal
Elidan, Hanah Margalit, Nir Friedman |
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Learning Interpretable SVMs for Biological
Sequence Classification
Authors: Soren Sonnenburg,
Gunnar Rätsch, Christin Schäfer |
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Using Multiple Alignments to Improve Gene
Prediction
Authors: Samuel S. Gross, Michael R. Brent |
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A Hybrid Micro-Macroevolutionary Approach to
Gene Tree Reconstruction
Authors: Dannie Durand, Bjarni
Halldórsson, Benjamin Vernot |
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Efficient q-Gram Filters for Finding All
ε-Matches over a Given Length
Authors: Kim Roland
Rasmussen, Jens Stoye, Gene Myers |
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Peptide Sequence Tags for Fast Database
Search in Mass-Spectrometry
Authors: Ari Frank, Stephen
Tanner, Pavel Pevzner |
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