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Evolutionary Bioinformatics

ISSN: 1176--9343
Publisher: Libertas Academica


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A Comprehensive Phylogenetic Analysis of Deadenylases

Author(s): Athanasia Pavlopoulou | Dimitrios Vlachakis | Nikolaos A.A. Balatsos | Sophia Kossida
Volume: 2013
Issue: 9
Year: 2013
EASER: Ensembl Easy Sequence Retriever

Author(s): Emanuel Maldonado | Imran Khan | Siby Philip | Vítor Vasconcelos | Agostinho Antunes
Volume: 2013
Issue: 9
Year: 2013
Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinofiagellate Alexandrium Tamarense

Author(s): Dahai Gao | Limei Qiu | Zhanhui Hou | Qingchun Zhang | Jianmin Wu | Qiang Gao | Linsheng Song
Volume: 2013
Issue: 9
Year: 2013
Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq

Author(s): Tae Young Yang | Seongmun Jeong
Volume: 2013
Issue: 9
Year: 2013
Identification of New Aquaporin Genes and Single Nucleotide Polymorphism in Bread Wheat

Author(s): B. Pandey | P. Sharma | D.M. Pandey | I. Sharma | R. Chatrath
Volume: 2013
Issue: 9
Year: 2013
PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics

Author(s): Kevin M. Kocot | Mathew R. Citarella | Leonid L. Moroz | Kenneth M. Halanych
Volume: 2013
Issue: 9
Year: 2013
Analysis of New Functional Profiles of Protein Isoforms Yielded by Ds Exonization in Rice

Author(s): Ting-Ying Chien | Li-yu Daisy Liu | Yuh-Chyang Charng
Volume: 2013
Issue: 9
Year: 2013
Prediction of Protein Essentiality by the Support Vector Machine with Statistical Tests

Author(s): Chiou-Yi Hor | Chang-Biau Yang | Zih-Jie Yang | Chiou-Ting Tseng
Volume: 2013
Issue: 9
Year: 2013
Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in Soybean

Author(s): Achal Neupane | Madhav P. Nepal | Sarbottam Piya | Senthil Subramanian | Jai S. Rohila | R. Neil Reese | Benjamin V. Benson
Volume: 2013
Issue: 9
Year: 2013
rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection

Author(s): Jan Irvahn | Sujay Chattopadhyay | Evgeni V. Sokurenko | Vladimir N. Minin
Volume: 2013
Issue: 9
Year: 2013
Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation

Author(s): Timothy D. O'Connor | Nicholas I. Mundy
Volume: 2013
Issue: 9
Year: 2013
Conserved Nonsense-Prone CpG Sites in Apoptosis-Regulatory Genes: Conditional Stop Signs on the Road to Cell Death

Author(s): Yongzhong Zhao | Richard J. Epstein
Volume: 2013
Issue: 9
Year: 2013
SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences

Author(s): Kirill S. Antonets | Anton A. Nizhnikov
Volume: 2013
Issue: 9
Year: 2013
Effective Encoding for DNA Sequence Visualization Based on Nucleotide’s Ring Structure

Author(s): A.T.M. Golam Bari | Mst. Rokeya Reaz | A.K.M. Tauhidul Islam | Ho-Jin Choi | Byeong-Soo Jeong
Volume: 2013
Issue: 9
Year: 2013
Molecular Evolution and Functional Divergence of Soluble Starch Synthase Genes in Cassava (Manihot Esculenta Crantz)

Author(s): Zefeng Yang | Yifan Wang | Shuhui Xu | Chenwu Xu | Changjie Yan
Volume: 2013
Issue: 9
Year: 2013
Comment on “The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway”

Author(s): David Alvarez-Ponce | Montserrat Aguadé | Julio Rozas
Volume: 2013
Issue: 9
Year: 2013
Analysis of Synonymous Codon Usage Patterns in Seven Different Citrus Species

Author(s): Chen Xu | Jing Dong | Chunfa Tong | Xindong Gong | Qiang Wen | Qiang Zhuge
Volume: 2013
Issue: 9
Year: 2013
Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology

Author(s): Dimitrios Vlachakis | Georgia Tsiliki | Athanasia Pavlopoulou | Maria G. Roubelakis | Spyridon Champeris Tsaniras | Sophia Kossida
Volume: 2013
Issue: 9
Year: 2013
Top-Down Clustering for Protein Subfamily Identification

Author(s): Eduardo P. Costa | Celine Vens | Hendrik Blockeel
Volume: 2013
Issue: 9
Year: 2013
A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests

Author(s): Chiou-Yi Hor | Chang-Biau Yang | Chia-Hung Chang | Chiou-Ting Tseng | Hung-Hsin Chen
Volume: 2013
Issue: 9
Year: 2013
Circulation of Human Respiratory Syncytial Virus Strains Among Hospitalized Children with Acute Lower Respiratory Infection in Malaysia

Author(s): Mohammad Reza Etemadi | Zamberi Sekawi | Norlijah Othman | Munn-Sann Lye | Faezeh Yazdani Moghaddam
Volume: 2013
Issue: 9
Year: 2013
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes

Author(s): Tanja Magoc | Derrick Wood | Steven L. Salzberg,
Volume: 2013
Issue: 9
Year: 2013
Design of Synthetic Genetic Oscillators Using Evolutionary Optimization

Author(s): Yen-Chang Chang | Chun-Liang Lin | Tanagorn Jennawasin
Volume: 2013
Issue: 9
Year: 2013
CMCpy: Genetic Code-Message Coevolution Models in Python

Author(s): Peter J. Becich | Brian P. Stark | Harish S. Bhat | David H. Ardell
Volume: 2013
Issue: 9
Year: 2013
A Proximity-Based Method to Identify Genomic Regions Correlated with a Continuously Varying Environmental Variable

Author(s): Cornelia Di Gaetano | Giuseppe Matullo | Alberto Piazza | Moreno Ursino | Mauro Gasparini
Volume: 2013
Issue: 9
Year: 2013
TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats

Author(s): Tomasz Gambin | Michał Startek | Krzysztof Walczak | Jarosław Paszek | Dariusz Grzebelus | Anna Gambin
Volume: 2013
Issue: 9
Year: 2013
The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway

Author(s): Minghui Wang | Qishan Wang | Zhen Wang | Qingping Wang | Xiangzhe Zhang | Yuchun Pan
Volume: 2013
Issue: 9
Year: 2013
Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus

Author(s): Ence Yang | Amanda M. Hulse | James J. Cai
Volume: 2012
Issue: 8
Year: 2012
A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence

Author(s): Eli Reuveni | Alessandro Giuliani
Volume: 2012
Issue: 8
Year: 2012
Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

Author(s): Payal Singh | Supratim Sengupta
Volume: 2012
Issue: 8
Year: 2012
Genome-Wide Survey of Ds Exonization to Enrich Transcriptomes and Proteomes in Plants

Author(s): Li-yu Daisy Liu | Yuh-Chyang Charng
Volume: 2012
Issue: 8
Year: 2012
Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana

Author(s): Wanjun Gu | Chuanying Zhai | Xiaofei Wang | Xueying Xie | Gurunadh Parinandi | Tong Zhou,
Volume: 2012
Issue: 8
Year: 2012
Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses

Author(s): Namrata Misra | Prasanna Kumar Panda | Bikram Kumar Parida | Barada Kanta Mishra
Volume: 2012
Issue: 8
Year: 2012
Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling

Author(s): Thomas Meinel | Antje Krause
Volume: 2012
Issue: 8
Year: 2012
Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups

Author(s): Julia Lambret-Frotté | Fernando Araújo Perini | Claudia Augusta de Moraes Russo
Volume: 2012
Issue: 8
Year: 2012
TreeCmp: Comparison of Trees in Polynomial Time

Author(s): Damian Bogdanowicz | Krzysztof Giaro | Borys Wróbel,
Volume: 2012
Issue: 8
Year: 2012
Inference of Self-Regulated Transcriptional Networks by Comparative Genomics

Author(s): Joseph P. Cornish | Fialelei Matthews | Julien R. Thomas | Ivan Erill
Volume: 2012
Issue: 8
Year: 2012
The Chordate Proteome History Database

Author(s): Anthony Levasseur | Julien Paganini | Jacques Dainat | Julie D. Thompson | Olivier Poch | Pierre Pontarotti | Philippe Gouret
Volume: 2012
Issue: 8
Year: 2012
PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Author(s): Runhua Lei | Thaine W. Rowley | Lifeng Zhu | Carolyn A. Bailey | Shannon E. Engberg | Mindy L. Wood | Mary C. Christman | George H. Perry | Edward E. Louis Jr | Guoqing Lu
Volume: 2012
Issue: 8
Year: 2012
Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX

Author(s): Julien Paganini | Philippe Gouret
Volume: 2012
Issue: 8
Year: 2012
Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species

Author(s): Shu-Hsi Lin | Miwa Yoshimoto | Ping-Chiang Lyu | Chuan-Yi Tang | Masanori Arita
Volume: 2012
Issue: 8
Year: 2012
Determinants of Exon-Level Evolutionary Rates in Arabidopsis Species

Author(s): Gideon C.-T. Wu | Feng-Chi Chen
Volume: 2012
Issue: 8
Year: 2012
AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots

Author(s): Muhammad Rashid | Guangyuan He | Yang Guangxiao | Javeed Hussain | Xu Yan
Volume: 2012
Issue: 8
Year: 2012
Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion

Author(s): Dapeng Wang | Yao Su | Xumin Wang | Hongxing Lei | Jun Yu
Volume: 2012
Issue: 8
Year: 2012
Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors

Author(s): Balasubramanian Nagarathnam, | Singaravelu Kalaimathy | Veluchamy Balakrishnan | Ramanathan Sowdhamini
Volume: 2012
Issue: 8
Year: 2012
MiIP: The Monomer Identification and Isolation Program

Author(s): Christopher Bun,§ | William Ziccardi | Jeffrey Doering | Catherine Putonti1–
Volume: 2012
Issue: 8
Year: 2012
Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns

Author(s): Jun Cao | Feng Shi
Volume: 2012
Issue: 8
Year: 2012
PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences

Author(s): Melissa M. Norström | Mattia C.F. Prosperi | Rebecca R. Gray | Annika C. Karlsson | Marco Salemi
Volume: 2012
Issue: 8
Year: 2012
Mitochondrial Genetic Differentiation of Spirlin (Actinopterigii: Cyprinidae) in the South Caspian Sea basin of Iran

Author(s): Mahvash Seifali | Aziz Arshad | Faezeh Yazdani Moghaddam | Hamid Reza Esmaeili | Bahram H. Kiabi | Siti Khalijah Daud | Mansour Aliabadian
Volume: 2012
Issue: 8
Year: 2012
Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets

Author(s): Carolina M. Voloch | Carlos G. Schrago
Volume: 2012
Issue: 8
Year: 2012
Efficient Feature Selection and Multiclass Classification with Integrated Instance and Model Based Learning

Author(s): Zhenqiu Liu | Halima Bensmail | Ming Tan
Volume: 2012
Issue: 8
Year: 2012
Promoter Sequences Prediction Using Relational Association Rule Mining

Author(s): Gabriela Czibula | Maria-Iuliana Bocicor | Istvan Gergely Czibula
Volume: 2012
Issue: 8
Year: 2012
A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment

Author(s): Valerio Freschi | Alessandro Bogliolo
Volume: 2012
Issue: 8
Year: 2012
Selection of Marker Genes Using Whole-Genome DNA Polymorphism Analysis

Author(s): Harry M. Bohle | Toni Gabaldón
Volume: 2012
Issue: 8
Year: 2012
Inferring the Phylogeny of Bovidae Using Mitochondrial DNA Sequences: Resolving Power of Individual Genes Relative to Complete Genomes

Author(s): Ibrahim A. Arif | Mohammad A. Bakir | Haseeb A. Khan
Volume: 2012
Issue: 8
Year: 2012
Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents

Author(s): Leticia Loss-Oliveira | Barbara O. Aguiar | Carlos G. Schrago*
Volume: 2012
Issue: 8
Year: 2012
Construction of a Pig Physical Interactome Using Sequence Homology and a Comprehensive Reference Human Interactome

Author(s): Felix Dreher | Atanas Kamburov | Ralf Herwig
Volume: 2012
Issue: 8
Year: 2012
Interkingdom Gene Transfer May Contribute to the Evolution of Phytopathogenicity in Botrytis Cinerea

Author(s): Bo Zhu | Qing Zhou | Guanlin Xie | Guoqing Zhang | Xiaowei Zhang | Yanli Wang | Gunchang Sun | Bin Li | Gulei Jin
Volume: 2012
Issue: 8
Year: 2012
Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group

Author(s): Nicolás Lavagnino | François Serra | Leonardo Arbiza | Hernán Dopazo | Esteban Hasson,
Volume: 2012
Issue: 8
Year: 2012
BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization

Author(s): Jing Hu | Xianghe Yan
Volume: 2012
Issue: 8
Year: 2012
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data

Author(s): Benjamin Linard | Ngoc Hoan Nguyen | Francisco Prosdocimi | Olivier Poch | Julie D. Thompson
Volume: 2012
Issue: 8
Year: 2011
SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis

Author(s): Dimosthenis Tsagrasoulis | Vasilis Danos, | Maria Kissa, | Philip Trimpalis, | V. Lila Koumandou | Amalia D. Karagouni | Athanasios Tsakalidis | Sophia Kossida
Volume: 2012
Issue: 8
Year: 2011
LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes

Author(s): Dapeng Wang | Yubin Zhang | Zhonghua Fan | Guiming Liu | Jun Yu
Volume: 2012
Issue: 8
Year: 2011
Species Delimitation and Global Biosecurity

Author(s): Laura M. Boykin | Karen F. Armstrong | Laura Kubatko | Paul De Barro
Volume: 2012
Issue: 8
Year: 2011
Cloud Computing for Comparative Genomics with Windows Azure Platform

Author(s): Insik Kim | Jae-Yoon Jung | Todd F. DeLuca | Tristan H. Nelson | Dennis P. Wall
Volume: 2012
Issue: 8
Year: 2012
Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method

Author(s): Abdelmonaem Messaoudi | Hatem Belguith | Jeannette Ben Hamida
Volume: 2011
Issue: 7
Year: 2011
Functional Evolution of BRCT Domains from Binding DNA to Protein

Author(s): Zi-Zhang Sheng | Yu-Qi Zhao | Jing-Fei Huang
Volume: 2011
Issue: 7
Year: 2011
How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling

Author(s): Sylvain Lespinats | Delphine Grando | Eric Maréchal | Mohamed-Ali Hakimi | Olivier Tenaillon | Olivier Bastien
Volume: 2011
Issue: 7
Year: 2011
Structurama: Bayesian Inference of Population Structure

Author(s): John P. Huelsenbeck | Peter Andolfatto | Edna T. Huelsenbeck
Volume: 2011
Issue: 7
Year: 2011
Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family

Author(s): V. Mallika | K.C. Sivakumar | E.V. Soniya
Volume: 2011
Issue: 7
Year: 2011
A Monte Carlo Method for Assessing the Quality of Duplication-Aware Alignment Algorithms

Author(s): Valerio Freschi | Alessandro Bogliolo
Volume: 2011
Issue: 7
Year: 2011
Phylogenomics-Based Reconstruction of Protozoan Species Tree

Author(s): Kary A.C.S. Ocaña | Alberto M.R. Dávila
Volume: 2011
Issue: 7
Year: 2011
A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses

Author(s): Grant Brammer | Seung-Jin Sul | Tiffani L. Williams
Volume: 2011
Issue: 7
Year: 2011
A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory

Author(s): Xingqin Qi | Qin Wu | Yusen Zhang | Eddie Fuller | Cun-Quan Zhang
Volume: 2011
Issue: 7
Year: 2011
Single-Domain Parvulins Constitute a Specific Marker for Recently Proposed Deep-Branching Archaeal Subgroups

Author(s): Christoph Lederer | Dominik Heider | Johannes van den Boom | Daniel Hoffmann | Jonathan W. Mueller | Peter Bayer
Volume: 2011
Issue: 7
Year: 2011
Characterization and Inference of Gene Gain/Loss Along Burkholderia Evolutionary History

Author(s): Bo Zhu | Shengli Zhou | Miaomiao Lou | Jun Zhu | Bin Li | Guanlin Xie | GuLei Jin | René De Mot
Volume: 2011
Issue: 7
Year: 2011
Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction

Author(s): Hafida Bouziane | Belhadri Messabih | Abdallah Chouarfia
Volume: 2011
Issue: 7
Year: 2011
Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of Oncidium Gower Ramsey

Author(s): Chen Xu | Xiaoning Cai | Quanzhan Chen | Hongxia Zhou | Yao Cai | Ailing Ben
Volume: 2011
Issue: 7
Year: 2011
ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications

Author(s): Sylvain Lespinats | Bernard Fertil
Volume: 2011
Issue: 7
Year: 2011
In Silico Prediction of Evolutionarily Conserved GC-Rich Elements Associated with Antigenic Proteins of Plasmodium falciparum

Author(s): Porkodi Panneerselvam, | Praveen Bawankar, | Surashree Kulkarni | Swati Patankar
Volume: 2011
Issue: 7
Year: 2011
Molecular Phylogeny of Edge Hill Virus Supports its Position in the Yellow Fever Virus Group and Identifies a New Genetic Variant

Author(s): Joanne Macdonald | Michael Poidinger | John S. Mackenzie | Richard C. Russell | Stephen Doggett | Annette K. Broom | Debra Phillips | Joseph Potamski | Geoff Gard | Peter Whelan | Richard Weir | Paul R. Young | Debra Gendle | Sheryl Maher | Ross T. Barnard | Roy A. Hall
Volume: 2010
Issue: 6
Year: 2010
Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference Versus Group-Specific Taxon Sampling

Author(s): Alexandros Stamatakis | Markus Göker | Guido W. Grimm
Volume: 2010
Issue: 6
Year: 2010
Comparative Molecular Evolution of Trichoderma Chitinases in Response to Mycoparasitic Interactions

Author(s): Katarina Ihrmark | Nashwan Asmail | Wimal Ubhayasekera | Petter Melin | Jan Stenlid | Magnus Karlsson
Volume: 2010
Issue: 6
Year: 2010
DNA Barcodes of Arabian Partridge and Philby's Rock Partridge: Implications for Phylogeny and Species Identification

Author(s): Haseeb Ahmad Khan | Ibrahim Abdulwahid Arif | Mohammad Shobrak
Volume: 2010
Issue: 6
Year: 2010
Computational Identification of Anthocyanin-Specific Transcription Factors using a Rice Microarray and Maximum Boundary Range Algorithm

Author(s): Chang Kug Kim | Shoshi Kikuchi | Jang Ho Hahn | Soo Chul Park | Yong Hwan Kim | Byun Woo Lee
Volume: 2010
Issue: 6
Year: 2010
Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias

Author(s): Soohyun Lee | Seyeon Weon | Sooncheol Lee | Changwon Kang
Volume: 2010
Issue: 6
Year: 2010
A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction

Author(s): Ra’ed M. Al-Khatib | Rosni Abdullah | Nur’aini Abdul Rashid
Volume: 2010
Issue: 6
Year: 2010
Identifying the Combinatorial Effects of Histone Modifications by Association Rule Mining in Yeast

Author(s): Jiang Wang | Xianhua Dai | Qian Xiang | Yangyang Deng | Jihua Feng | Zhiming Dai | Caisheng He
Volume: 2010
Issue: 6
Year: 2010
An Application of Supertree Methods to Mammalian Mitogenomic Sequences

Author(s): Véronique Campbell | François-Joseph Lapointe
Volume: 2010
Issue: 6
Year: 2010
Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup

Author(s): Parul Kudtarkar | Todd F. DeLuca | Vincent A. Fusaro | Peter J. Tonellato | Dennis P. Wall
Volume: 2010
Issue: 6
Year: 2010
PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

Author(s): Kessy Abarenkov | Leho Tedersoo | R. Henrik Nilsson | Kai Vellak | Irja Saar | Vilmar Veldre | Erast Parmasto | Marko Prous | Anne Aan | Margus Ots | Olavi Kurina | Ivika Ostonen | Janno Jõgeva | Siim Halapuu | Kadri Põldmaa | Märt Toots | Jaak Truu | Karl-Henrik Larsson | Urmas Kõljalg
Volume: 2010
Issue: 6
Year: 2010
Where Does the Alignment Score Distribution Shape Come from?

Author(s): Philippe Ortet | Olivier Bastien
Volume: 2010
Issue: 6
Year: 2010
EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics

Author(s): Michael S. Barker | Katrina M. Dlugosch | Louie Dinh | R. Sashikiran Challa | Nolan C. Kane | Matthew G. King | Loren H. Rieseberg
Volume: 2010
Issue: 6
Year: 2010
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

Author(s): Markus Göker | Guido W. Grimm | Alexander F. Auch | Ralf Aurahs | Michal Kučera
Volume: 2010
Issue: 6
Year: 2010
Clustering Protein Sequences Using Affinity Propagation Based on an Improved Similarity Measure

Author(s): Fan Yang | Qing-Xin Zhu | Dong-Ming Tang | Ming-Yuan Zhao
Volume: 2009
Issue: 5
Year: 2010
A Comprehensive Analysis of Gene Expression Evolution Between Humans and Mice

Author(s): Yupeng Wang | Romdhane Rekaya
Volume: 2009
Issue: 5
Year: 2009
Initial Implementation of a Comparative Data Analysis Ontology

Author(s): Francisco Prosdocimi | Brandon Chisham | Enrico Pontelli | Julie D. Thompson | Arlin Stoltzfus
Volume: 2009
Issue: 5
Year: 2009
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Author(s): Bastien Boussau | Laurent Guéguen | Manolo Gouy
Volume: 2009
Issue: 5
Year: 2009
Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates

Author(s): Amir Ali Abbasi | Debbie K. Goode | Saneela Amir | Karl-Heinz Grzeschik
Volume: 2009
Issue: 5
Year: 2009
REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

Author(s): Guy Leonard | Jamie R. Stevens | Thomas A. Richards
Volume: 2009
Issue: 5
Year: 2009
Snapshots of Tree Space

Author(s): Zheng Wang | Francesc López-Giráldez | Jeffrey P. Townsend
Volume: 2009
Issue: 5
Year: 2010
PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

Author(s): Robert C. Thomson
Volume: 2009
Issue: 5
Year: 2009
Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters

Author(s): Marc Thuillard | Didier Fraix-Burnet
Volume: 2009
Issue: 5
Year: 2009
Phylogenetic Analyses Reveal Monophyletic Origin of the Ergot Alkaloid Gene dmaW in Fungi

Author(s): Miao Liu | Daniel G. Panaccione | Christopher L. Schardl
Volume: 2009
Issue: 5
Year: 2009
Minimum Contradiction Matrices in Whole Genome Phylogenies

Author(s): Marc Thuillard
Volume: 4
Year: 2008
Estimation of Genetic Effects and Genotype-Phenotype Maps

Author(s): Arnaud Le Rouzic | José M. Álvarez-Castro
Volume: 4
Year: 2008
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

Author(s): R. Henrik Nilsson | Erik Kristiansson | Martin Ryberg | Nils Hallenberg | Karl ­Henrik Larsson
Volume: 4
Year: 2008
Fast Structural Search in Phylogenetic Databases

Author(s): Jason T. L. Wang | Huiyuan Shan | Dennis Shasha | William H. Piel
Volume: 1
Year: 2005
Phylogenetic biodiversity assessment based on systematic nomenclature

Author(s): Ross H Crozier | Lisa J Dunnett | Paul-Michael Agapow
Volume: 1
Year: 2005
ALFRED: An Allele Frequency Database for Microevolutionary Studies

Author(s): Haseena Rajeevan | Kei-Hoi Cheung | Rohit Gadagkar | Shannon Stein | Usha Soundararajan | Judith R Kidd | Andrew J Pakstis | Perry L Miller | Kenneth K Kidd
Volume: 1
Year: 2005
Arlequin (version 3.0): An integrated software package for population genetics data analysis

Author(s): Laurent Excoffier | Guillaume Laval | Stefan Schneider
Volume: 1
Year: 2005
Evolution of proteins and proteomes: a phylogenetics approach

Author(s): Toni Gabaldón
Volume: 1
Year: 2005
The identification of functional motifs in temporal gene expression analysis

Author(s): Jiuzhou Song | Jaime Bjarnason | Michael G. Surette
Volume: 1
Year: 2005
Why Bacteriophage Encode Exotoxins and other Virulence Factors

Author(s): Stephen T. Abedon | Jeffrey T. LeJeune
Volume: 1
Year: 2005
Finding common protein interaction patterns across organisms

Author(s): Mirco Gerke | Erich Bornberg-Bauer | Xiaoyi Jiang | Georg Fuellen
Volume: 2
Year: 2006
Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes

Author(s): Howard A. Ross | David C. Nickle | Yi Liu | Laura Heath | Mark A. Jensen | Allen G. Rodrigo | James I. Mullins
Volume: 2
Year: 2006
Positional Homology in Bacterial Genomes

Author(s): Ingrid J. Burgetz | Salimah Shariff | Andy Pang | Elisabeth R. M. Tillier
Volume: 2
Year: 2006
Functionality and the evolution of marginal stability in proteins: Inferences from lattice simulations

Author(s): Paul D. Williams | David D. Pollock | Richard A. Goldstein
Volume: 2
Year: 2006
3 UTR-located ALU Elements: Donors of Potetial miRNA Target Sites and Mediators of Network miRNA-based Regulatory Interactions

Author(s): Evelina Daskalova | Vesselin Baev | Ventsislav Rusinov | Ivan Minkov
Volume: 2
Year: 2006
A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis

Author(s): Abdoulaye Baniré Diallo | François-Joseph Lapointe | Vladimir Makarenkov
Volume: 2
Year: 2006
Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations

Author(s): Laurent Gatto | Daniele Catanzaro | Michel C. Milinkovitch
Volume: 2
Year: 2006
Modelling prokaryote gene content

Author(s): Matthew Spencer | Edward Susko | Andrew J. Roger
Volume: 2
Year: 2006
MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution

Author(s): James J. Cai | David K. Smith | Xuhua Xia | Kwok-yung Yuen
Volume: 2
Year: 2006
Examining Ancient Inter-domain Horizontal Gene Transfer

Author(s): Francisca C. Almeida | Magdalena Leszczyniecka | Paul B. Fisher | Rob DeSalle
Volume: 4
Year: 2008
Maximum Gene-Support Tree

Author(s): Yunfeng Shan
Volume: 4
Year: 2008
Dissection of Functional Residues in Receptor Activity-Modifying Proteins Through Phylogenetic and Statistical Analyses

Author(s): Alfonso Benítez-Páez | Sonia Cárdenas-Brito
Volume: 4
Year: 2008
Assessing the Evolution of Gene Expression Using Microarray Data

Author(s): Owen Z. Woody | Andrew C. Doxey | Brendan J. McConkey
Volume: 4
Year: 2008
Phylogenetic biodiversity assessment based on systematic nomenclature

Author(s): Ross H Crozier | Lisa J Dunnett | Paul-Michael Agapow
Volume: 2
Year: 2006
PIRSF Family Classification System for Protein Functional and Evolutionary Analysis

Author(s): Anastasia N. Nikolskaya | Cecilia N. Arighi | Hongzhan Huang | Winona C. Barker | Cathy H. Wu
Volume: 2
Year: 2006
Unravelling Selection Shifts Among Foot-and-Mouth Disease Virus (FMDV) Serotypes

Author(s): Damien C. Tully | Mario A. Fares
Volume: 2
Year: 2006
Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make

Author(s): Claudine Levasseur | François-Joseph Lapointe
Volume: 2
Year: 2006
Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype

Author(s): Xiang-Sun Zhang | Rui-Sheng Wang | Ling-Yun Wu | Wei Zhang
Volume: 2
Year: 2006
Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges

Author(s): Daniel P. Faith | Andrew M. Baker
Volume: 2
Year: 2006
A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

Author(s): Guido W. Grimm | Susanne S. Renner | Alexandros Stamatakis | Vera Hemleben
Volume: 2
Year: 2006
Co-evolutionary Rates of Functionally Related Yeast Genes

Author(s): Leonardo Mariño-Ramírez | Olivier Bodenreider | Natalie Kantz | I. King Jordan
Volume: 2
Year: 2006
A Fast and Specific Alignment Method for Minisatellite Maps

Author(s): Sèverine Bérard | François Nicolas | Jérôme Buard | Olivier Gascuel | Eric Rivals
Volume: 2
Year: 2006
Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations

Author(s): Tai-Sung Lee | Steven J. Potts | Matthew J. McGinniss | Charles M. Strom
Volume: 2
Year: 2006
Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction

Author(s): Michael Höhl | Isidore Rigoutsos | Mark A. Ragan
Volume: 2
Year: 2006
Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes

Author(s): Nadja Neumann | Daniel C. Jeffares | Anthony M. Poole
Volume: 2
Year: 2006
Improved Heuristics for Minimum-Flip Supertree Construction

Author(s): Duhong Chen | Oliver Eulenstein | David Fernández-Baca | J.Gordon Burleigh
Volume: 2
Year: 2006
MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes

Author(s): Srikrishna Putta | Jeramiah J. Smith | Chuck Staben | S. Randal Voss
Volume: 3
Year: 2007
Identification of Conflicting Selective Effects on Highly Expressed Genes

Author(s): Paul G. Higgs | Weilong Hao | G. Brian Golding
Volume: 3
Year: 2007
On the Adaptive Design Rules of Biochemical Networks in Evolution

Author(s): Bor-Sen Chen | Wan-Shian Wu | Wei-Sheng Wu | Wen-Hsiung Li
Volume: 3
Year: 2007
Mlcoalsim: Multilocus Coalescent Simulations

Author(s): Sebastian E. Ramos-Onsins | Thomas Mitchell-Olds
Volume: 3
Year: 2007
A Reduction Algorithm for Computing The Hybridization Number of Two Trees

Author(s): Magnus Bordewich | Simone Linz | Katherine St. John | Charles Semple
Volume: 3
Year: 2007
Fast Genes and Slow Clades: Comparative Rates of Molecular Evolution in Mammals

Author(s): Olaf R. P. Bininda-Emonds
Volume: 3
Year: 2007
Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes

Author(s): Nicola Vitulo | Alessandro Vezzi | Giulio Galla | Sandra Citterio | Giada Marino | Benedetto Ruperti | Monica Zermiani | Emidio Albertini | Giorgio Valle | Gianni Barcaccia
Volume: 3
Year: 2007
Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions

Author(s): Ekaterina Kotelnikova | Andrey Kalinin | Anton Yuryev | Sergei Maslov
Volume: 3
Year: 2007
Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians

Author(s): Sumiko Anno | Takashi Abe | Koichi Sairyo | Susumu Kudo | Takushi Yamamoto | Koretsugu Ogata | Vijay K. Goel
Volume: 3
Year: 2007
Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity

Author(s): Mike Steel | Aki Mimoto | Arne Ø. Mooers
Volume: 3
Year: 2007
Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

Author(s): Bor-Sen Chen | Wei-Sheng Wu
Volume: 3
Year: 2007
Phylogenomic Analysis Reveals Extensive Phylogenetic Mosaicism in the Human GPCR Superfamily

Author(s): Robin G. Allaby | Mathew Woodwark
Volume: 3
Year: 2007
Structural Evolution of the ABC Transporter Subfamily B

Author(s): Flanagan, J.U. | Huber, T.
Volume: 3
Year: 2007
Efficient Tree Searches with Available Algorithms

Author(s): Gonzalo Giribet
Volume: 3
Year: 2007
Phylogenetic Study of the Evolution of PEP-Carboxykinase

Author(s): Sanjukta Aich | Louis T.J. Delbaere
Volume: 3
Year: 2007
The 2006 NESCent Phyloinformatics Hackathon: A Field Report

Author(s): Hilmar Lapp | Sendu Bala | James P. Balhoff | Amy Bouck | Naohisa Goto | Mark Holder | Richard Holland | Alisha Holloway | Toshiaki Katayama | Paul O. Lewis | Aaron J. Mackey | Brian I. Osborne | William H. Piel | Sergei L. Kosakovsky Pond | Art F.Y. Poon | Wei-Gang Qiu | Jason E. Stajich | Arlin Stoltzfus | Tobias Thierer | Albert J. Vilella | Rutger A. Vos | Christian M. Zmasek | Derrick J. Zwickl | Todd J. Vision
Volume: 3
Year: 2007
SPR Distance Computation for Unrooted Trees

Author(s): Glenn Hickey | Frank Dehne | Andrew Rau-Chaplin | Christian Blouin
Volume: 4
Year: 2008
Why Should We Care About Molecular Coevolution?

Author(s): Francisco M. Codoñer | Mario A. Fares
Volume: 4
Year: 2008
How to Summarize Estimates of Ancestral Divergence Times

Author(s): David A. Morrison
Volume: 4
Year: 2008
Expected Anomalies in the Fossil Record

Author(s): Mareike Fischer | Mike Steel
Volume: 4
Year: 2008
Identifying Coevolving Partners from Paralogous Gene Families

Author(s): Chen-Hsiang Yeang
Volume: 4
Year: 2008
A Comprehensive Analysis of Gene Expression Evolution Between Humans and Mice

Author(s): Yupeng Wang | Romdhane Rekaya
Volume: 5
Year: 2009
Initial Implementation of a comparative Data Analysis Ontology

Author(s): Francisco Prosdocimi | Brandon Chisham | Enrico Pontelli | Julie D. Thompson | Arlin Stoltzfus
Volume: 5
Year: 2009
Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates

Author(s): Amir Ali Abbasi | Debbie K. Goode | Saneela Amir | Karl-Heinz Grzeschik
Volume: 5
Year: 2009
REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

Author(s): Guy Leonard | Jamie R. Stevens | Thomas A. Richards
Volume: 5
Year: 2009
The Austronesian Basic Vocabulary Database: From Bioinformatics to Lexomics

Author(s): Simon J. Greenhill | Robert Blust | Russell D. Gray
Volume: 4
Year: 2008
Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence

Author(s): R.S. Ross | J. Verbeeck | S. Viazov | P. Lemey | M. Van Ranst | M. Roggendorf
Volume: 4
Year: 2008
Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

Author(s): Haseeb A. Khan | Ibrahim A. Arif | Ali H. Bahkali | Ahmad H. Al Farhan | Ali A. Al Homaidan
Volume: 4
Year: 2008
Electrostatic and Functional Analysis of the Seven-Bladed WD β-Propellers

Author(s): Najl V. Valeyev | A. Kristina Downing | John Sondek | Charlotte Deane
Volume: 4
Year: 2008
Estimation of Phylogeny Using a General Markov Model

Author(s): Vivek Jayaswal | Lars S. Jermiin | John Robinson
Volume: 1
Year: 2005
MySSP: Non-stationary evolutionary sequence simulation, including indels

Author(s): Michael S. Rosenberg
Volume: 1
Year: 2005
Coevolution of exploiter specialization and victim mimicry can be cyclic and saltational

Author(s): Niclas Norrström | Wayne M. Getz | Noél M.A. Holmgren
Volume: 2
Year: 2006
CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies

Author(s): Chunghau Lee | Sigal Blay | Arne Ø. Mooers | Ambuj Singh | Todd H. Oakley
Volume: 2
Year: 2006
Gaussian Quadrature Formulae for Arbitrary Positive Measures

Author(s): Andrew D. Fernandes | William R. Atchley
Volume: 2
Year: 2006
Choosing and Using Introns in Molecular Phylogenetics

Author(s): Simon Creer
Volume: 3
Year: 2007
Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution

Author(s): Agostinho Antunes | Maria João Ramos
Volume: 3
Year: 2007
Identifcation of Novel Retroid Agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis

Author(s): Holly A. Basta | Alex J. Buzak | Marcella A. McClure
Volume: 3
Year: 2007
Evolution of the Influenza A Virus: Some New Advances

Author(s): Raul Rabadan | Harlan Robins
Volume: 3
Year: 2007
Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

Author(s): Anthony Levasseur | Pierre Pontarotti | Olivier Poch | Julie D. Thompson
Volume: 4
Year: 2008
The ABCs of MGR with DCJ

Author(s): Zaky Adam | David Sankoff
Volume: 4
Year: 2008
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny

Author(s): Tanja Gernhard | Daniel Ford | Rutger Vos | Mike Steel
Volume: 2
Year: 2006
Genome Halving with an Outgroup

Author(s): Chunfang Zheng | Qian Zhu | David Sankoff
Volume: 2
Year: 2006
Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup

Author(s): Ludovic Orlando | Catherine Hänni | Christophe J. Douady
Volume: 3
Year: 2007
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Author(s): Bastien Boussau | Laurent Guéguen | Manolo Gouy
Volume: 5
Year: 2009
Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters

Author(s): Marc Thuillard | Didier Fraix-Burnet
Volume: 5
Year: 2009
Phylogenetic Analyses Reveal Monophyletic Origin of the Ergot Alkaloid Gene dmaW in Fungi

Author(s): Miao Liu | Daniel G. Panaccione | Christopher L. Schardl
Volume: 5
Year: 2009
Evolution, Bioinformatics and Evolutionary Bioinformatics Online

Author(s): Mark Pagel
Volume: 2
Year: 2006
Minimizing Contradictions on Circular Order of Phylogenic Trees

Author(s): Marc Thuillard
Volume: 3
Year: 2007
An Improved Implementation of Codon Adaptation Index

Author(s): Xuhua Xia
Volume: 3
Year: 2007
Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens

Author(s): Wendy Mok | Kelly Seto | Jon Stone
Volume: 3
Year: 2007
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