Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

(2015) Lars Barquist et al.   Annual Review of Genetics

Deletion of the Sm1 encoding motif in the lsm gene results in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells

(2015) Lisa-Katharina Maier et al.   BIOCHIMIE

Quantitative bacterial transcriptomics with RNA-seq

(2015) James P Creecy et al.   CURRENT OPINION IN MICROBIOLOGY

Found in translation: functions and evolution of a recently discovered alternative proteome

(2015) Christian R Landry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The oxidative pentose phosphate pathway in the haloarchaeonHaloferax volcaniiinvolves a novel type of glucose-6-phosphate dehydrogenase - The archaeal Zwischenferment

(2015) Andreas Pickl et al.   FEBS LETTERS

Post-transcriptional inducible gene regulation by natural antisense RNA

(2015) Mikio Nishizawa   Frontiers in Bioscience-Landmark

Neighboring Gene Regulation by Antisense Long Non-Coding RNAs

(2015) Victoria Villegas et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

(2015) José Vicente Gomes-Filho et al.   RNA Biology

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

(2015) Jie Li et al.   Scientific Reports

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

(2015) Scarlet S. Shell et al.   PLoS Genetics

Archaeal type IV pili and their involvement in biofilm formation

(2015) Mechthild Pohlschroder et al.   Frontiers in Microbiology

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

READemption--a tool for the computational analysis of deep-sequencing-based transcriptome data

(2014) K. U. Forstner et al.   BIOINFORMATICS

ReadXplorer—visualization and analysis of mapped sequences

(2014) Rolf Hilker et al.   BIOINFORMATICS

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

(2014) Dominik Jäger et al.   BMC GENOMICS

Differential RNA-seq: the approach behind and the biological insight gained

(2014) Cynthia M Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti

(2014) Arjan de Groot et al.   Genome Biology and Evolution

Natural antisense transcripts

(2014) O. Khorkova et al.   HUMAN MOLECULAR GENETICS

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

Physiological roles of small RNA molecules

(2014) C. Michaux et al.   MICROBIOLOGY-SGM

Generation and Phenotyping of a Collection of sRNA Gene Deletion Mutants of the Haloarchaeon Haloferax volcanii

(2014) Katharina Jaschinski et al.   PLoS One

Haloferax volcanii, a Prokaryotic Species that Does Not Use the Shine Dalgarno Mechanism for Translation Initiation at 5′-UTRs

(2014) Piet Kramer et al.   PLoS One

Small non-coding RNAs in streptomycetes

(2014) Nona Heueis et al.   RNA Biology

Riboregulation in plant-associated α-proteobacteria

(2014) Anke Becker et al.   RNA Biology

Small regulatory RNAs in Archaea

(2014) Julia Babski et al.   RNA Biology

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

(2014) W. Shao et al.   mBio

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

(2014) Erin A. Becker et al.   PLoS Genetics

The regulatory potential of upstream open reading frames in eukaryotic gene expression

(2014) Klaus Wethmar   Wiley Interdisciplinary Reviews-RNA

Structural and biochemical properties of an extreme ‘salt-loving’ proteasome activating nucleotidase from the archaeon Haloferax volcanii

(2013) Laurence Prunetti et al.   EXTREMOPHILES

Accelerated growth in the absence of DNA replication origins

(2013) Michelle Hawkins et al.   NATURE

RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri

(2013) Andreas A. H. Su et al.   NUCLEIC ACIDS RESEARCH

Essential requirements for the detection and degradation of invaders by theHaloferax volcaniiCRISPR/Cas system I-B

(2013) Lisa-Katharina Maier et al.   RNA Biology

RNA at 92°C

(2013) Claire Toffano-Nioche et al.   RNA Biology

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

N-glycosylation in Haloferax volcanii: adjusting the sweetness

(2013) Jerry Eichler et al.   Frontiers in Microbiology

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

An Archaeal Immune System Can Detect Multiple Protospacer Adjacent Motifs (PAMs) to Target Invader DNA

(2012) Susan Fischer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

(2012) Erin A. Lynch et al.   PLoS One

High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments inHaloferax volcanii

(2012) Ruth Heyer et al.   RNA Biology

Flowering time control: another window to the connection between antisense RNA and chromatin

(2012) Robert Ietswaart et al.   TRENDS IN GENETICS

RNA processing in the minimal organism Nanoarchaeum equitans

(2012) Lennart Randau   GENOME BIOLOGY

Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

(2011) Kounthéa Phok et al.   BMC GENOMICS

Selective Translation of Leaderless mRNAs by Specialized Ribosomes Generated by MazF in Escherichia coli

(2011) Oliver Vesper et al.   CELL

A conserved regulatory role for antisense RNA in meiotic gene expression in yeast

(2011) Huei-Mei Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Phenotyping in the archaea: optimization of growth parameters and analysis of mutants of Haloferax volcanii

(2011) Katharina Jantzer et al.   FEMS MICROBIOLOGY LETTERS

cis-Antisense RNA, Another Level of Gene Regulation in Bacteria

(2011) J. Georg et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeonHaloferax volcanii

(2011) Julia Babski et al.   RNA Biology

Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology ofHaloferax volcanii

(2011) Jörg Soppa   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Improved Strains and Plasmid Vectors for Conditional Overexpression of His-Tagged Proteins in Haloferax volcanii

(2010) T. Allers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

(2010) Amber L. Hartman et al.   PLoS One

Small RNAs in Haloarchaea: Identification, differential expression and biological function

(2010) Julia Straub et al.   RNA Biology

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

An Unexpected Type of Ribosomes Induced by Kasugamycin: A Look into Ancestral Times of Protein Synthesis?

(2009) Anna Chao Kaberdina et al.   MOLECULAR CELL

A novel mechanism for translation initiation operates in haloarchaea

(2009) Oliver Hering et al.   MOLECULAR MICROBIOLOGY

Prevalence of transcription promoters within archaeal operons and coding sequences

(2009) Tie Koide et al.   Molecular Systems Biology

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

(2009) Alfredo Mendoza-Vargas et al.   PLoS One

Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability

(2009) D. Jager et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Characterization of a Haloferax volcanii member of the enolase superfamily: deletion mutant construction, expression analysis, and transcriptome comparison

(2008) Michael Dambeck et al.   ARCHIVES OF MICROBIOLOGY

Genome information management and integrated data analysis with HaloLex

(2008) Friedhelm Pfeiffer et al.   ARCHIVES OF MICROBIOLOGY