| scholarly article | Q13442814 |
| P2093 | author name string | David S Holmes | |
| Carolina González | |||
| Marcelo Lazcano | |||
| Jorge Valdés | |||
| P2860 | cites work | A simple, fast, and accurate method of phylogenomic inference | Q21184110 |
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| Response of Acidithiobacillus caldus toward suboptimal pH conditions | Q43018478 | ||
| A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment | Q43693420 | ||
| Physiological Characteristics of a New Thermophilic Obligately Chemolithotrophic Thiobacillus Species, Thiobacillus tepidarius | Q45310784 | ||
| Definitive assignment by multigenome analysis of the gammaproteobacterial genus Thermithiobacillus to the class Acidithiobacillia | Q45841016 | ||
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| Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream | Q46760771 | ||
| Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. | Q46844784 | ||
| Insights into the pathways of iron- and sulfur-oxidation, and biofilm formation from the chemolithotrophic acidophile Acidithiobacillus ferrivorans CF27. | Q46848038 | ||
| Protein Identification and Analysis Tools on the ExPASy Server | Q56880448 | ||
| 2020 visions | Q57141170 | ||
| The RAST Server: rapid annotations using subsystems technology | Q21263157 | ||
| The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes | Q21284200 | ||
| The evolutionary origin of orphan genes | Q22122002 | ||
| The origin of new genes: glimpses from the young and old | Q22122023 | ||
| MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform | Q24540347 | ||
| Gapped BLAST and PSI-BLAST: a new generation of protein database search programs | Q24545170 | ||
| Using pyrosequencing to shed light on deep mine microbial ecology | Q24548757 | ||
| MAFFT version 5: improvement in accuracy of multiple sequence alignment | Q24556683 | ||
| MUSCLE: multiple sequence alignment with high accuracy and high throughput | Q24613456 | ||
| Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm | Q24618007 | ||
| The Pfam protein families database | Q24619716 | ||
| Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus | Q24631130 | ||
| Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions | Q24645090 | ||
| The TIGRFAMs database of protein families | Q24681677 | ||
| SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB | Q24685829 | ||
| Evidence for symmetric chromosomal inversions around the replication origin in bacteria | Q24791763 | ||
| Computational Identification of Novel Genes: Current and Future Perspectives | Q26738988 | ||
| MrBayes 3: Bayesian phylogenetic inference under mixed models | Q26778438 | ||
| Ligand-induced conformational changes in a thermophilic ribose-binding protein | Q27652936 | ||
| New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 | Q27860476 | ||
| Profile hidden Markov models | Q27860536 | ||
| MRBAYES: Bayesian inference of phylogenetic trees | Q27860538 | ||
| Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes | Q27860838 | ||
| A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood | Q27861000 | ||
| Artemis: sequence visualization and annotation | Q27861024 | ||
| PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization | Q28139371 | ||
| Prediction of protein subcellular localization | Q28244166 | ||
| Life in acid: pH homeostasis in acidophiles | Q28290891 | ||
| TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases | Q28710519 | ||
| Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation | Q28828755 | ||
| jModelTest 2: more models, new heuristics and parallel computing | Q29546516 | ||
| Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB | Q29547254 | ||
| The Ribosomal Database Project: improved alignments and new tools for rRNA analysis | Q29547434 | ||
| Community structure and metabolism through reconstruction of microbial genomes from the environment | Q29547528 | ||
| progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement | Q29616598 | ||
| Shifting the genomic gold standard for the prokaryotic species definition | Q29616599 | ||
| DNA-DNA hybridization values and their relationship to whole-genome sequence similarities | Q29617100 | ||
| PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments | Q29617502 | ||
| Activities at the Universal Protein Resource (UniProt) | Q29617787 | ||
| Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees | Q30000954 | ||
| Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. | Q30455097 | ||
| DNAPlotter: circular and linear interactive genome visualization | Q30850857 | ||
| Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications | Q33392439 | ||
| Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans | Q33474603 | ||
| Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus | Q33484077 | ||
| Finding families for genomic ORFans | Q33875139 | ||
| Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. | Q33897615 | ||
| Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences | Q34046549 | ||
| Identification of steroid sulfate transport processes in the human mammary gland | Q34221995 | ||
| Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria | Q34323505 | ||
| Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. | Q34335104 | ||
| The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences | Q34336945 | ||
| IMG 4 version of the integrated microbial genomes comparative analysis system | Q34380660 | ||
| The genome portal of the Department of Energy Joint Genome Institute: 2014 updates | Q34384748 | ||
| Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l | Q34631305 | ||
| Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups | Q35023038 | ||
| Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. | Q35046577 | ||
| RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes | Q35065741 | ||
| Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics | Q35392870 | ||
| Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin | Q35502575 | ||
| Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage | Q35533051 | ||
| Metagenomic biomarker discovery and explanation | Q35557728 | ||
| Chromosomal "stress-response" domains govern the spatiotemporal expression of the bacterial virulence program. | Q35620180 | ||
| Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle | Q35673712 | ||
| The replication-related organization of bacterial genomes. | Q35796723 | ||
| Periplasmic binding proteins: a versatile superfamily for protein engineering | Q35863927 | ||
| Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs? | Q36035025 | ||
| Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. | Q36068973 | ||
| Prediction of lipoprotein signal peptides in Gram-negative bacteria | Q36572165 | ||
| Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? | Q36958151 | ||
| Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms. | Q36970743 | ||
| Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes | Q37129701 | ||
| Analytical tools and databases for metagenomics in the next-generation sequencing era | Q37223525 | ||
| The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae | Q37274005 | ||
| Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile. | Q37377814 | ||
| Application of 'next-generation' sequencing technologies to microbial genetics | Q37415296 | ||
| Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms | Q37490244 | ||
| IMG/M 4 version of the integrated metagenome comparative analysis system | Q37661739 | ||
| The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). | Q37661996 | ||
| Draft Genome Sequence of the Extremophile Acidithiobacillus thiooxidans A01, Isolated from the Wastewater of a Coal Dump | Q37683224 | ||
| RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans. | Q38382312 | ||
| Microbial diversity and metabolic networks in acid mine drainage habitats. | Q38527803 | ||
| Detection, identification and typing of Acidithiobacillus species and strains: a review | Q38862022 | ||
| Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review | Q38891055 | ||
| Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans | Q39764461 | ||
| FtsL, an essential cytoplasmic membrane protein involved in cell division in Escherichia coli | Q39939982 | ||
| Draft genome sequence of Acidithiobacillus ferrooxidans YQH-1. | Q40178243 | ||
| PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. | Q41126055 | ||
| IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. | Q41282214 | ||
| PhyloSift: phylogenetic analysis of genomes and metagenomes | Q41882289 | ||
| AlterORF: a database of alternate open reading frames | Q42007168 | ||
| Sulfur oxidation genes in diverse deep-sea viruses | Q42220895 | ||
| Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3. | Q42849911 | ||
| P921 | main subject | bioinformatics | Q128570 |
| Acidithiobacillus | Q142671 | ||
| transcriptome | Q252857 | ||
| metagenomics | Q903778 | ||
| P304 | page(s) | 2035 | |
| P577 | publication date | 2016-12-27 | |
| P1433 | published in | Frontiers in Microbiology | Q27723481 |
| P1476 | title | Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation | |
| P478 | volume | 7 |
| Q33790049 | Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes |
| Q50868052 | In a quest for engineering acidophiles for biomining applications: challenges and opportunities. |
| Q90044972 | Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C |
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