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ORCIDAlgorithms for Molecular Biology, Volume 8
Volume 8, 2013
- Shuai Cheng Li
:
The Difficulty Of Protein Structure Alignment Under The RMSD. 1 - Songjian Lu, Xinghua Lu:
Using graph model to find transcription factor modules: the hitting set problem and an exact algorithm. 2 - Daniele Catanzaro, Ramamoorthi Ravi, Russell Schwartz:
A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion. 3 - Beatriz Pontes, Raúl Giráldez, Jesús S. Aguilar-Ruiz:
Configurable pattern-based evolutionary biclustering of gene expression data. 4 - Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi, Ming Li:
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? 5 - Phillip E. C. Compeau:
DCJ-Indel sorting revisited. 6 - Alberto Apostolico, Matteo Comin, Andreas W. M. Dress, Laxmi Parida:
Ultrametric networks: a new tool for phylogenetic analysis. 7 - Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford:
Resolving spatial inconsistencies in chromosome conformation measurements. 8 - Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Edgar Wingender:
Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell. 9 - Yiannis Kourmpetis, Aalt D. J. van Dijk, Cajo J. F. ter Braak:
Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes. 10 - Brad Shutters, Sudheer Vakati, David Fernández-Baca:
Incompatible quartets, triplets, and characters. 11 - Thi Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Jean-Philippe Doyon, Vincent Berry:
Reconciliation and local gene tree rearrangement can be of mutual profit. 12 - Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson:
Unrooted unordered homeomorphic subtree alignment of RNA trees. 13 - Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen:
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. 14 - Mohd Saberi Mohamad, Sigeru Omatu, Safaai Deris, Michifumi Yoshioka, Afnizanfaizal Abdullah, Zuwairie Ibrahim:
An enhancement of binary particle swarm optimization for gene selection in classifying cancer classes. 15 - Alastair M. Kilpatrick, Bruce Ward, Stuart Aitken:
MCOIN: a novel heuristic for determining transcription factor binding site motif width. 16 - Bjarni V. Halldórsson, Dima Blokh, Roded Sharan:
Estimating population size via line graph reconstruction. 17 - Akshay Deepak, David Fernández-Baca, Michelle M. McMahon:
Extracting conflict-free information from multi-labeled trees. 18 - Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina:
MORPH-PRO: a novel algorithm and web server for protein morphing. 19 - Daniel Dexter, Daniel G. Brown:
Fast half-sibling population reconstruction: theory and algorithms. 20 - Poly H. da Silva, Raphael Machado, Simone Dantas, Marília D. V. Braga:
DCJ-indel and DCJ-substitution distances with distinct operation costs. 21 - Rayan Chikhi, Guillaume Rizk:
Space-efficient and exact de Bruijn graph representation based on a Bloom filter. 22 - Ilya E. Vorontsov, Ivan V. Kulakovskiy, Vsevolod J. Makeev:
Jaccard index based similarity measure to compare transcription factor binding site models. 23 - Peter Clote, Evangelos Kranakis, Danny Krizanc:
Asymptotic structural properties of quasi-random saturated structures of RNA. 24 - Sebastian Deorowicz, Szymon Grabowski:
Data compression for sequencing data. 25 - Alexandra Gavryushkina, David Welch, Alexei J. Drummond:
Recursive algorithms for phylogenetic tree counting. 26 - Tamar Pinhas, Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson:
Efficient edit distance with duplications and contractions. 27 - Ruchi Chaudhary, John Gordon Burleigh, David Fernández-Baca:
Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. 28 - Harry A. Stern, David H. Mathews:
Accelerating calculations of RNA secondary structure partition functions using GPUs. 29 - A. S. M. Sohidull Islam, Mohammad Sohel Rahman:
On the protein folding problem in 2D-triangular lattices. 30 - Witold Dyrka, Jean-Christophe Nebel, Malgorzata Kotulska:
Probabilistic grammatical model for helix-helix contact site classification. 31
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