No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects

A short history of RubisCO: the rise and fall (?) of Nature's predominant CO 2 fixing enzyme

(2018) Tobias J Erb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Protein synthesis controls phosphate homeostasis

(2018) Mauricio H. Pontes et al.   GENES & DEVELOPMENT

Identification of a metabolic disposal route for the oncometaboliteS-(2-succino)cysteine inBacillus subtilis

(2018) Thomas D. Niehaus et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bacterial RNA Biology on a Genome Scale

(2018) Jens Hör et al.   MOLECULAR CELL

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

The science of fake news

(2018) David M. J. Lazer et al.   SCIENCE

The fallacy of the average: on the ubiquity, utility and continuing novelty of Jensen's inequality

(2017) Mark Denny   JOURNAL OF EXPERIMENTAL BIOLOGY

A solution to the single-question crowd wisdom problem

(2017) Dražen Prelec et al.   NATURE

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

(2017) Karine Bastard et al.   Nature Chemical Biology

The European Nucleotide Archive in 2017

(2017) Nicole Silvester et al.   NUCLEIC ACIDS RESEARCH

DNA Data Bank of Japan: 30th anniversary

(2017) Yuichi Kodama et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

The lost language of the RNA World

(2017) James W. Nelson et al.   Science Signaling

Could a Neuroscientist Understand a Microprocessor?

(2017) Eric Jonas et al.   PLoS Computational Biology

Mycobacterium smegmatis PhoU Proteins Have Overlapping Functions in Phosphate Signaling and Are Essential

(2017) Alyssa M. Brokaw et al.   Frontiers in Microbiology

The lost language of the RNA World

(2017) James W. Nelson et al.   Science Signaling

Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota

(2017) Antoine Danchin et al.   Microbial Biotechnology

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement

(2017) Rainer Borriss et al.   Microbial Biotechnology

A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data

(2016) Fangfang Liu et al.   BIOINFORMATICS

Relative Rates of Surface and Volume Synthesis Set Bacterial Cell Size

(2016) Leigh K. Harris et al.   CELL

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

(2016) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

(2016) William R. Pearson et al.   NUCLEIC ACIDS RESEARCH

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins

(2016) Bijendra Khadka et al.   PHOTOSYNTHESIS RESEARCH

Hybrid promiscuous (Hypr) GGDEF enzymes produce cyclic AMP-GMP (3′, 3′-cGAMP)

(2016) Zachary F. Hallberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From membrane tension to channel gating: A principal energy transfer mechanism for mechanosensitive channels

(2016) Xuejun C. Zhang et al.   PROTEIN SCIENCE

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Reminder to deposit DNA sequences

(2016) M. Blaxter et al.   SCIENCE

A synthetic pathway for the fixation of carbon dioxide in vitro

(2016) Thomas Schwander et al.   SCIENCE

Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology

(2016) David T. Kysela et al.   PLOS BIOLOGY

What Is the Tree of Life?

(2016) W. Ford Doolittle et al.   PLoS Genetics

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

(2016) Yevgeny Nikolaichik et al.   PeerJ

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

(2016) Valerio Bianchi et al.   Frontiers in Genetics

Unknown unknowns: essential genes in quest for function

(2016) Antoine Danchin et al.   Microbial Biotechnology

Algebraic Dynamic Programming over general data structures

(2015) Christian zu Siederdissen et al.   BMC BIOINFORMATICS

Varieties of clinical reasoning

(2015) Jonathan W. Bolton   JOURNAL OF EVALUATION IN CLINICAL PRACTICE

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

(2015) Yi-Chien Chang et al.   NUCLEIC ACIDS RESEARCH

RNA catalysis—is that it?

(2015) Timothy J. Wilson et al.   RNA

Annotation inconsistencies beyond sequence similarity-based function prediction – phylogeny and genome structure

(2015) Vasilis J. Promponas et al.   Standards in Genomic Sciences

A Brief Review of Software Tools for Pangenomics

(2015) Jingfa Xiao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships

(2014) Shoshana D. Brown et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The ABC-F protein EttA gates ribosome entry into the translation elongation cycle

(2014) Grégory Boël et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Hydrodynamics and collective behavior of the tethered bacteriumThiovulum majus

(2014) Alexander Petroff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Paralogous metabolism: S-alkyl-cysteine degradation inBacillus subtilis

(2013) Che-Man Chan et al.   ENVIRONMENTAL MICROBIOLOGY

Comparing Medline citations using modified N-grams: Table 1

(2013) Rao Muhammad Adeel Nawab et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Multivariate meta-analysis of mixed outcomes: a Bayesian approach

(2013) Sylwia Bujkiewicz et al.   STATISTICS IN MEDICINE

Inverse probability weighting for covariate adjustment in randomized studies

(2013) Changyu Shen et al.   STATISTICS IN MEDICINE

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

(2012) Stefan Engelen et al.   BMC GENOMICS

Coordinated Regulation of Accessory Genetic Elements Produces Cyclic Di-Nucleotides for V. cholerae Virulence

(2012) Bryan W. Davies et al.   CELL

Identification of a novel nanoRNase in Bartonella

(2012) M. F. Liu et al.   MICROBIOLOGY-SGM

Facing growth in the European Nucleotide Archive

(2012) Guy Cochrane et al.   NUCLEIC ACIDS RESEARCH

Practical Guide to Understanding Multivariable Analyses

(2012) J. Gail Neely et al.   OTOLARYNGOLOGY-HEAD AND NECK SURGERY

Practical Guide to Understanding Multivariable Analyses, Part B

(2012) J. Gail Neely et al.   OTOLARYNGOLOGY-HEAD AND NECK SURGERY

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

(2012) Konstantinos Mavromatis et al.   PLoS One

From essential to persistent genes: a functional approach to constructing synthetic life

(2012) Carlos G. Acevedo-Rocha et al.   TRENDS IN GENETICS

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

(2012) Adam Alexander Thil Smith et al.   PLoS Computational Biology

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

(2010) Georg Fuchs   Annual Review of Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Genome (re-)annotation and open-source annotation pipelines

(2010) Roland J. Siezen et al.   Microbial Biotechnology

Cells need safety valves

(2009) Antoine Danchin   BIOESSAYS

Genomics of an extreme psychrophile, Psychromonas ingrahamii

(2009) Monica Riley et al.   BMC GENOMICS

Persistence drives gene clustering in bacterial genomes

(2008) Gang Fang et al.   BMC GENOMICS

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology