Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model

SAMSA2: a standalone metatranscriptome analysis pipeline

(2018) Samuel T. Westreich et al.   BMC BIOINFORMATICS

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition

(2018) Jennifer L. Pechal et al.   Scientific Reports

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

(2018) M. Eric Benbow et al.   ECOLOGICAL MONOGRAPHS

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Tracing the dynamics of gene transcripts after organismal death

(2017) Alex E. Pozhitkov et al.   Open Biology

Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition

(2017) Gulnaz T. Javan et al.   Frontiers in Microbiology

Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration

(2016) Z.M. Burcham et al.   FORENSIC SCIENCE INTERNATIONAL

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning

(2016) Manuel Delgado-Baquerizo et al.   JOURNAL OF ECOLOGY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Human Thanatomicrobiome Succession and Time Since Death

(2016) Gulnaz T. Javan et al.   Scientific Reports

Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing

(2016) Juanjuan Guo et al.   Scientific Reports

Estimating Time Since Death from Postmortem Human Gut Microbial Communities

(2015) Kathleen A. Hauther et al.   JOURNAL OF FORENSIC SCIENCES

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Microbial community assembly and metabolic function during mammalian corpse decomposition

(2015) J. L. Metcalf et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microbial communities associated with human decomposition and their potential use as postmortem clocks

(2014) Sheree J. Finley et al.   INTERNATIONAL JOURNAL OF LEGAL MEDICINE

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans

(2014) Ismail Can et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Mycobacterium ulcerans Fails to Infect through Skin Abrasions in a Guinea Pig Infection Model: Implications for Transmission

(2014) Heather R. Williamson et al.   PLoS Neglected Tropical Diseases

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing

(2013) Jennifer L. Pechal et al.   INTERNATIONAL JOURNAL OF LEGAL MEDICINE

Evaluation of Postmortem Bacterial Migration Using Culturing and Real-Time Quantitative PCR

(2013) Sari Tuomisto et al.   JOURNAL OF FORENSIC SCIENCES

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The Living Dead: Bacterial Community Structure of a Cadaver at the Onset and End of the Bloat Stage of Decomposition

(2013) Embriette R. Hyde et al.   PLoS One

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

(2013) Jessica L Metcalf et al.   eLife

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Postmortem Analyses of Intestinal Microbiota Changes and Bacterial Translocation in Human Flora Associated Mice

(2012) Markus M. Heimesaat et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS