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ORCIDAlgorithms for Molecular Biology, Volume 5
Volume 5, 2010
- Xiuwei Zhang, Bernard M. E. Moret
:
Refining transcriptional regulatory networks using network evolutionary models and gene histories. 1 - Jianrong Dong, David Fernández-Baca, Fred R. McMorris:
Constructing majority-rule supertrees. 2 - Peter Husemann, Jens Stoye:
Phylogenetic comparative assembly. 3 - Matthew Hansen, Logan Everett, Larry N. Singh, Sridhar Hannenhalli:
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. 4 - Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp:
Fast prediction of RNA-RNA interaction. 5 - Marta Gîrdea, Laurent Noé, Gregory Kucherov:
Back-translation for discovering distant protein homologies in the presence of frameshift mutations. 6 - Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane:
Linear-time protein 3-D structure searching with insertions and deletions. 7 - M. Shel Swenson, François Barbançon, Tandy J. Warnow, C. Randal Linder:
A simulation study comparing supertree and combined analysis methods using SMIDGen. 8 - Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen:
A tree-based method for the rapid screening of chemical fingerprints. 9 - Timothy Hancock, Hiroshi Mamitsuka:
A markov classification model for metabolic pathways. 10 - Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael:
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. 11 - Saeed Salem, Mohammed J. Zaki, Chris Bystroff:
FlexSnap: Flexible Non-sequential Protein Structure Alignment. 12 - Yelena Frid, Dan Gusfield:
A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup. 13 - Bangpeng Yao, Shao Li:
ANMM4CBR: a case-based reasoning method for gene expression data classification. 14 - Grégory Nuel, Leslie Regad, Juliette Martin, Anne-Claude Camproux:
Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data. 15 - Chris Conow, Daniel Fielder, Yaniv Ovadia, Ran Libeskind-Hadas:
Jane: a new tool for the cophylogeny reconstruction problem. 16 - Sandra Waaijenborg, Aeilko H. Zwinderman:
Association of repeatedly measured intermediate risk factors for complex diseases with high dimensional SNP data. 17 - Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca:
Robinson-Foulds Supertrees. 18 - Binh T. Nguyen, Andreas Spillner, Brent C. Emerson, Vincent Moulton:
Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity. 19 - Pierre-Yves Bourguignon, Areejit Samal, François Képès, Jürgen Jost, Olivier C. Martin:
Challenges in experimental data integration within genome-scale metabolic models. 20 - Gordon Blackshields, Fabian Sievers, Weifeng Shi, Andreas Wilm, Desmond G. Higgins:
Sequence embedding for fast construction of guide trees for multiple sequence alignment. 21 - Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen:
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. 22 - Burton Chia, R. Krishna Murthy Karuturi:
Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms. 23 - Darío Guerrero-Fernández, Rocío Bautista, David P. Villalobos, Francisco R. Cantón, M. Gonzalo Claros:
AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences. 24 - Christian Arnold, Peter F. Stadler:
Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. 25 - Kenneth Sundberg, Mark J. Clement, Quinn Snell:
On the use of cartographic projections in visualizing phylo-genetic tree space. 26 - James Z. M. Gao, Linda Y. M. Li, Christian M. Reidys:
Inverse folding of RNA pseudoknot structures. 27 - Hannes Planatscher, Jochen Supper, Oliver Poetz, Dieter Stoll, Thomas Joos, Markus F. Templin, Andreas Zell:
Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry. 28 - Pavel V. Mazin, Mikhail S. Gelfand, Andrey A. Mironov, Aleksandra B. Rakhmaninova, Anatoly R. Rubinov, Robert B. Russell, Olga V. Kalinina:
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. 29 - Zhenqiu Liu, Laurence S. Magder, Terry Hyslop, Li Mao:
Survival associated pathway identification with group Lp penalized global AUC maximization. 30 - Ivan Junier, Joan Hérisson, François Képès:
Periodic pattern detection in sparse boolean sequences. 31 - Ming Zheng, Guixia Liu, Chunguang Zhou, Yanchun Liang, Yan Wang:
Gravitation field algorithm and its application in gene cluster. 32 - Ye Tian, Christopher Deutsch, Bala Krishnamoorthy:
Scoring function to predict solubility mutagenesis. 33 - Ethan Kim, Ashish Sabharwal, Adrian Vetta, Mathieu Blanchette:
Predicting direct protein interactions from affinity purification mass spectrometry data. 34 - Andrew D. Fernandes, Benjamin P. Kleinstiver, David R. Edgell, Lindi M. Wahl, Gregory B. Gloor:
Estimating the evidence of selection and the reliability of inference in unigenic evolution. 35 - Gang Xu, Laura Bennett, Lazaros G. Papageorgiou, Sophia Tsoka:
Module detection in complex networks using integer optimisation. 36 - Anne Kupczok, Heiko A. Schmidt, Arndt von Haeseler:
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. 37 - Tin Yin Lam, Irmtraud M. Meyer:
Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training. 38 - Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp:
Sparsification of RNA structure prediction including pseudoknots. 39
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