All Stories

  1. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics
  2. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing
  3. A new molecular phylogeny-based taxonomy of parasitic barnacles (Crustacea: Cirripedia: Rhizocephala)
  4. Claw asymmetry in crabs: approaching an old issue from a new point of view
  5. Evaluation of haplotype callers for next-generation sequencing of viruses
  6. Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
  7. Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus
  8. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
  9. Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis
  10. Baseline human gut microbiota profile in healthy people and standard reporting template
  11. Towards a barnacle tree of life: integrating diverse phylogenetic efforts into a comprehensive hypothesis of thecostracan evolution
  12. Machine learning approaches to predict lupus disease activity from gene expression data
  13. Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health
  14. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
  15. Transcriptome patterns in hidradenitis suppurativa: support for the role of antimicrobial peptides and interferon pathways in disease pathogenesis
  16. Aegla chilota, new species of anomuran freshwater crab from Chiloé Island, western Patagonia
  17. A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans
  18. Baseline human gut microbiota profile in healthy people and standard reporting template
  19. Invasion by non-indigenous freshwater decapods of Malta and Sicily, central Mediterranean Sea
  20. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
  21. The Evolution of Gene Expression Underlying Vision Loss in Cave Animals
  22. Systematic pan-cancer analysis of somatic allele frequency
  23. Earth BioGenome Project: Sequencing life for the future of life
  24. More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae)
  25. Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end
  26. Transcriptomic effects of dispersed oil in a non-model decapod crustacean
  27. Transcriptomic effects of dispersed oil in a non-model decapod crustacean
  28. DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants
  29. Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma
  30. Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)
  31. Corrigendum to: Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)
  32. Faculty of 1000 evaluation for GenVisR: Genomic Visualizations in R.
  33. Collecting and processing freshwater crayfishes
  34. Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children
  35. Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies
  36. Faculty of 1000 evaluation for Prediction of missing sequences and branch lengths in phylogenomic data.
  37. Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology
  38. Global Diversity and Conservation of Freshwater Crayfish (Crustacea: Decapoda: Astacoidea)
  39. Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America
  40. Three new species of Aeglidae ( AeglaLeach, 1820) from Paraná State, Brazil
  41. Synthesis of phylogeny and taxonomy into a comprehensive tree of life
  42. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls
  43. Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities
  44. Phylogenetic Estimate of the Freshwater Crayfish (Decapoda: Astacidea) using Morphology and Molecules
  45. Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma
  46. Concordance and discordance of sequence survey methods for molecular epidemiology
  47. Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)
  48. A synthetic phylogeny of freshwater crayfish: insights for conservation
  49. Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency
  50. Molecular phylogeny, systematics and morphological evolution of the acorn barnacles (Thoracica: Sessilia: Balanomorpha)
  51. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms
  52. Characteristics of equipartition for RNA structure
  53. Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia
  54. The native South American crayfishes (Crustacea, Parastacidae): state of knowledge and conservation status
  55. Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data
  56. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes
  57. Status, distribution, and genetics of Blair's fencing crayfish,Faxonella blairi(Decapoda: Cambaridae)
  58. Epidemiological and Evolutionary Dynamics of Pathogens
  59. Biodiversity only makes sense in the light of evolution
  60. Life in extreme environments: microbial diversity in Great Salt Lake, Utah
  61. The Emergence of Lobsters: Phylogenetic Relationships, Morphological Evolution and Divergence Time Comparisons of an Ancient Group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida)
  62. Characteristics and Prediction of RNA Structure
  63. On stabilising the names of the infraorders of thalassinidean shrimps, Axiidea de Saint Laurent, 1979 and Gebiidea de Saint Laurent, 1979 (Decapoda)
  64. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples
  65. Lost Branches on the Tree of Life
  66. Failed species, innominate forms, and the vain search for species limits: cryptic diversity in dusky salamanders (Desmognathus ) of eastern Tennessee
  67. Pathoscope: Species identification and strain attribution with unassembled sequencing data
  68. Failed species, innominate forms, and the vain search for species limits: cryptic diversity in dusky salamanders (Desmognathus) of eastern Tennessee
  69. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology
  70. Molecular phylogenetics of the burrowing crayfish genusFallicambarus(Decapoda: Cambaridae)
  71. A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda)
  72. Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada
  73. Phylogeny and Evolutionary Patterns in the Dwarf Crayfish Subfamily (Decapoda: Cambarellinae)
  74. Molecular phylogeny and character evolution of the chthamaloid barnacles (Cirripedia: Thoracica)
  75. A new species of burrowing crayfish,Virilastacus jarai(Crustacea, Decapoda, Parastacidae) from central-southern Chile
  76. Testing Phylogenetic Hypotheses of the Subgenera of the Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)
  77. Phylogenetics links monster larva to deep-sea shrimp
  78. A Genomic Island in Salmonella enterica ssp. salamae Provides New Insights on the Genealogy of the Locus of Enterocyte Effacement
  79. Conflicting Evolutionary Patterns Due to Mitochondrial Introgression and Multilocus Phylogeography of the Patagonian Freshwater Crab Aegla neuquensis
  80. All the better to see you with: a review of odonate color vision with transcriptomic insight into the odonate eye
  81. Deep Phylogeny and Character Evolution in Thecostraca (Crustacea: Maxillopoda)
  82. Genetic diversity and molecular epidemiology of HIV transmission
  83. Population Genomics and Phylogeography of an Australian Dairy Factory Derived Lytic Bacteriophage
  84. The evolution of HIV: Inferences using phylogenetics
  85. Three new species of Aegla (Anomura) freshwater crabs from the upper Uruguay River hydrographic basin in Brazil
  86. Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)
  87. Population structure of two crayfish with diverse physiological requirements
  88. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics
  89. Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea)
  90. Phylodynamics of HIV-1 from a Phase III AIDS Vaccine Trial in Bangkok, Thailand
  91. HIV-1 infected monozygotic twins: a tale of two outcomes
  92. Multilocus Sequence Typing of Pathogens
  93. Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage
  94. Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV)
  95. Gondwanan radiation of the Southern Hemisphere crayfishes (Decapoda: Parastacidae): evidence from fossils and molecules
  96. Cryptic genetic divergence in the giant Tasmanian freshwater crayfish Astacopsis gouldi (Decapoda: Parastacidae): implications for conservation
  97. Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda)
  98. Evolution of Picornaviridae: An examination of phylogenetic relationships and cophylogeny
  99. Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans
  100. Population dynamics of Neisseria gonorrhoeae in Shanghai, China: a comparative study
  101. EVOLUTIONARY BIOLOGY IN BIODIVERSITY SCIENCE, CONSERVATION, AND POLICY: A CALL TO ACTION
  102. Ongoing Phenotypic and Genotypic Diversification in Adaptively Radiated Freshwater Crabs from Jamaica
  103. New Species and New Records of Endemic Freshwater Crabs from the Atlantic Forest in Southern Brazil (Anomura: Aeglidae)
  104. Phylogeography’s past, present, and future: 10 years after Avise, 2000
  105. DNA EVIDENCE FOR NONHYBRID ORIGINS OF PARTHENOGENESIS IN NATURAL POPULATIONS OF VERTEBRATES
  106. Phylodynamics of HIV-1 from a Phase-III AIDS Vaccine Trial in North America
  107. Expanding the toolbox for phylogeographic analysis
  108. Decapod Crustacean Phylogenetics
  109. Decapod Phylogenetics and Molecular Evolution
  110. Phylogenetic Inference Using Molecular Data
  111. The Timing of the Diversification of the Freshwater Crayfishes
  112. Conservation Assessment of Southern South American Freshwater Ecoregions on the Basis of the Distribution and Genetic Diversity of Crabs from the GenusAegla
  113. Remarkable convergent evolution in specialized parasitic Thecostraca (Crustacea)
  114. A multifaceted approach to species conservation
  115. Pleistocene glaciation leaves deep signature on the freshwater crabAegla alacalufiin Chilean Patagonia
  116. Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson
  117. Phylogenetic Relationships and Molecular Adaptation Dynamics of Human Rhinoviruses
  118. Similarity Searching Using BLAST
  119. Phylogenetic relationships between spiny, slipper and coral lobsters (Crustacea, Decapoda, Achelata)
  120. Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial
  121. Taxonomic Revision of Cave Crayfish in the Genus Cambarus, Subgenus Aviticambarus (Decapoda: Cambaridae) with Descriptions of Two New Species, C. Speleocoopi and C. Laconensis, Endemic to Alabama, U.S.A.
  122. Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change
  123. The evolution of foot-and-mouth disease virus: Impacts of recombination and selection
  124. Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfishEngaeus sericatusClark (Decapoda: Parastacidae)
  125. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
  126. Publication in the Journal of Crustacean Biology
  127. A Comparison of Phylogenetic Network Methods Using Computer Simulation
  128. Characterization of the Follicular Dendritic Cell Reservoir of Human Immunodeficiency Virus Type 1
  129. Avoidance of extinction through nonexistence: the use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater crayfish
  130. Disease progression and evolution of the HIV-1 env gene in 24 infected infants
  131. Incorporating gaps as phylogenetic characters across eight DNA regions: Ramifications for North American Psoraleeae (Leguminosae)
  132. Algorithms in Bioinformatics
  133. Methods for Analyzing Viral Evolution
  134. The tempo and mode of barnacle evolution
  135. Calculating expected DNA remnants from ancient founding events in human population genetics
  136. Taxonomic Revision of Cave Crayfishes in the Genus Orconectes, Subgenus Orconectes (Decapoda: Cambaridae) along the Cumberland Plateau, Including a Description of a New Species, Orconectes Barri
  137. Interspecies physiological variation as a tool for cross-species assessments of global warming-induced endangerment: validation of an intrinsic determinant of macroecological and phylogeographic structure
  138. Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae––Decapoda) in freshwater
  139. Global diversity of crabs (Aeglidae: Anomura: Decapoda) in freshwater
  140. Living with the genetic signature of Miocene induced change: Evidence from the phylogeographic structure of the endemic angulate tortoise Chersina angulata
  141. Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizardXantusia vigilisspecies complex (Squamata: Xantusiidae)
  142. Assessing the conservation status of the land snail Oreohelix peripherica wasatchensis (Family Oreohelicidae)
  143. The ecology and conservation status of Madagascar's endemic freshwater crayfish (Parastacidae; Astacoides)
  144. Human Immunodeficiency Viruses (HIV)
  145. Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy
  146. Testing hypotheses of population structuring in the Northeast Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis
  147. Temporal trends in gonococcal population genetics in a high prevalence urban community
  148. Molecular taxonomy in the dark: Evolutionary history, phylogeography, and diversity of cave crayfish in the subgenus Aviticambarus, genus Cambarus
  149. A New Species of Burrowing Crayfish Virilastacus Retamali (Decapoda: Parastacidae) from the Southern Chile Peatland
  150. New methods for inferring population dynamics from microbial sequences
  151. Cryptic diversity inEngaeusErichson,GeocharaxClark andGramastacusRiek (Decapoda : Parastacidae) revealed by mitochondrial 16S rDNA sequences
  152. Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis
  153. Surface to subsurface freshwater connections: phylogeographic and habitat analyses of Cambarus tenebrosus, a facultative cave-dwelling crayfish
  154. Molecular Characterization of Crustacean Visual Pigments and the Evolution of Pancrustacean Opsins
  155. Longitudinal Population Analysis of Dual Infection with Recombination in Two Strains of HIV Type 1 Subtype B in an Individual from a Phase 3 HIV Vaccine Efficacy Trial
  156. Nested clade analysis statistics
  157. Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes) reveals the signature of historical climatic oscillations
  158. Advocacy dressed up as scientific critique
  159. Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence
  160. Somatic Mitochondrial DNA Mutations in Prostate Cancer and Normal Appearing Adjacent Glands in Comparison to Age-Matched Prostate Samples without Malignant Histology
  161. Taxonomic subdivisions within the fossorial skink subfamily Acontinae (Squamata: Scincidae) reconsidered: a multilocus perspective
  162. Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts
  163. Isolation and characterization of di- and tetranucleotide microsatellite loci in the yellow-spotted night lizard Lepidophyma flavimaculatum (Squamata: Xantusiidae)
  164. On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy
  165. Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data
  166. Recombination Estimation Under Complex Evolutionary Models with the Coalescent Composite-Likelihood Method
  167. APPLICATIONS OF PHYLOGENETICS TO ISSUES IN FRESHWATER CRAYFISH BIOLOGY
  168. Jumpstarting phylogenetic analysis
  169. A new species of burrowing crayfish, Virilastacus rucapihuelensis (Crustacea: Decapoda: Parastacidae), from southern Chile
  170. Model-based multi-locus estimation of decapod phylogeny and divergence times
  171. Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes
  172. Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA
  173. Empirical tests for ecological exchangeability
  174. Population Genetics of Neisseria gonorrhoeae in a High-Prevalence Community Using a Hypervariable Outer Membrane porB and 13 Slowly Evolving Housekeeping Genes
  175. Unraveling evolutionary lineages in the limbless fossorial skink genus Acontias (Sauria: Scincidae): are subspecies equivalent systematic units?
  176. A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints
  177. EVOLUTION: Genomic Databases and the Tree of Life
  178. Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigaster
  179. Molecular Systematics and Biogeography of the Southern South American Freshwater “Crabs” Aegla (Decapoda: Anomura: Aeglidae) Using Multiple Heuristic Tree Search Approaches
  180. Testing Species Boundaries in an Ancient Species Complex with Deep Phylogeographic History: Genus Xantusia (Squamata: Xantusiidae)
  181. The Impact of Species Concept on Biodiversity Studies
  182. Evaluating the performance of likelihood methods for detecting population structure and migration
  183. Unraveling the Evolutionary Radiation of the Thoracican Barnacles Using Molecular and Morphological Evidence: A Comparison of Several Divergence Time Estimation Approaches
  184. Beyond FST: Analysis of population genetic data for conservation
  185. The causes and consequences of HIV evolution
  186. Lost along the way: the significance of evolution in reverse
  187. LINEAR HABITATS AND THE NESTED CLADE ANALYSIS: AN EMPIRICAL EVALUATION OF GEOGRAPHIC VERSUS RIVER DISTANCES USING AN OZARK CRAYFISH (DECAPODA: CAMBARIDAE)
  188. TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees
  189. LINEAR HABITATS AND THE NESTED CLADE ANALYSIS: AN EMPIRICAL EVALUATION OF GEOGRAPHIC VERSUS RIVER DISTANCES USING AN OZARK CRAYFISH (DECAPODA: CAMBARIDAE)
  190. Recombination in Evolutionary Genomics
  191. Conservation phylogenetics of Chilean freshwater crabs Aegla (Anomura, Aeglidae): assigning priorities for aquatic habitat protection
  192. The Effect of Recombination on the Accuracy of Phylogeny Estimation
  193. Phylogenetic Approaches to Molecular Epidemiology
  194. Phylogenetics of HIV
  195. Phylogenetic Position of the Freshwater Anomuran Family Aeglidae
  196. Phylogenetic Relationships among the Species of Aegla (Anomura: Aeglidae) Freshwater Crabs from Chile
  197. Molecular Population Genetics: Coalescent Methods Based on Summary Statistics
  198. TCS: estimating gene genealogies
  199. Human Immunodeficiency Viruses (HIV)
  200. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
  201. Cryptic species of Clavelina (Ascidiacea) in two different habitats: harbours and rocky littoral zones in the northwestern Mediterranean
  202. Selecting the Best-Fit Model of Nucleotide Substitution
  203. Selecting the Best-Fit Model of Nucleotide Substitution
  204. Gene flow estimates in Utah's cougars imply management beyond Utah
  205. Intraspecific gene genealogies: trees grafting into networks
  206. Human Immunodeficiency Virus Type 1 Quasi Species That Rebound after Discontinuation of Highly Active Antiretroviral Therapy Are Similar to the Viral Quasi Species Present before Initiation of Therapy
  207. Limited Heterogeneity of HIV Type 1 in Infected Mothers Correlates with Lack of Vertical Transmission
  208. TCS: a computer program to estimate gene genealogies
  209. Considering evolutionary processes in conservation biology
  210. HTLV Type I/II in British Columbia Amerindians: A Seroprevalence Study and Sequence Characterization of an HTLV Type IIa Isolate
  211. Biogeographic regionalization of Australia: assigning conservation priorities based on endemic freshwater crayfish phylogenetics
  212. Biogeographic regionalization of Australia: assigning conservation priorities based on endemic freshwater crayfish phylogenetics
  213. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes
  214. PCR Detection of Host and HIV-1 Sequences from Archival Brain Tissue
  215. Phylogeny of the Thoracican Barnacles Based on 18S rDNA Sequences
  216. Systematics of the European Endangered Crayfish Species Austropotamobius Pallipes (Decapoda: Astacidae)
  217. On the Phylogenetic Positioning of the South American Freshwater Crayfish Genera (Decapoda: Parastacidae)
  218. Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus
  219. Effective population sizes: missing measures and missing concepts
  220. Effective population sizes: missing measures and missing concepts
  221. Different Models, Different Trees: The Geographic Origin of PTLV-I
  222. Independent Evolution of HIV Type 1 in Different Brain Regions
  223. The Zoogeography and Centers of Origin of the Crayfish Subgenus Procericambarus (Decapoda: Cambaridae)
  224. Conservation phylogenetics of Ozark crayfishes: Assigning priorities for aquatic habitat protection
  225. Cocaine abuse and HIV-1 infection: Epidemiology and neuropathogenesis
  226. Testing Species Boundaries in Biodiversity Studies
  227. The Molecular Evolution of Visual Pigments of Freshwater Crayfishes (Decapoda: Cambaridae)
  228. PHYLOGENY ESTIMATION AND HYPOTHESIS TESTING USING MAXIMUM LIKELIHOOD
  229. "Call of the wild"
  230. Multiple and Ancient Origins of the Domestic Dog
  231. Rhodopsin evolution in the dark
  232. Crayfish Molecular Systematics: Using a Combination of Procedures to Estimate Phylogeny
  233. Identifying Links Between Genotype and Phenotype Using Marker Loci and Candidate Genes
  234. Molecular Markers, Natural History and Evolution.
  235. Opsin Phylogeny and Evolution: A Model for Blue Shifts in Wavelength Regulation
  236. J. Avise., Molecular Markers, Natural History and Evolution
  237. Intraspecific Cladogram Estimation: Accuracy at Higher Levels of Divergence
  238. Intraspecific Cladogram Estimation: Accuracy at Higher Levels of Divergence
  239. Book reviews
  240. Molecular phylogenetics for conservation biology
  241. Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae—Decapoda) in freshwater
  242. Crayfish in the decapod lineage, their natural distribution and their threatened status
  243. Global diversity of crabs (Aeglidae: Anomura: Decapoda) in freshwater
  244. Infraorder Astacidea Latreille, 1802 p.p.: the freshwater crayfish
  245. Phylogenomics and Molecular Evolution of Polyomaviruses
  246. Nested clade phylogeographic analysis for conservation genetics