Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

Library construction for ancient genomics: Single strand or double strand?

(2016) E. Andrew Bennett et al.   BIOTECHNIQUES

Dramatic reduction of sequence artefacts from DNA isolated from formalin-fixed cancer biopsies by treatment with uracil-DNA glycosylase.

(2015) Hongdo Do et al.   Oncotarget

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

(2014) Adam L. Bazinet et al.   SYSTEMATIC BIOLOGY

Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues

(2013) Stefan Paireder et al.   ANALYTICAL BIOCHEMISTRY

De novotranscriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set

(2013) Sonal Singhal   Molecular Ecology Resources

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes, chimeras, and a novel phylogenetic hypothesis

(2012) Robert G. Moyle et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons

(2011) Tara L. Fulton et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

(2011) Martin Kerick et al.   BMC Medical Genomics

Illumina whole-genome complementary DNA–mediated annealing, selection, extension and ligation platform: assessing its performance in formalin-fixed, paraffin-embedded samples and identifying invasion pattern–related genes in oral squamous cell carcinoma

(2011) Olivier Loudig et al.   HUMAN PATHOLOGY

Museum genomics: low-cost and high-accuracy genetic data from historical specimens

(2011) KEVIN C. ROWE et al.   Molecular Ecology Resources

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Major global radiation of corvoid birds originated in the proto-Papuan archipelago

(2011) K. A. Jonsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA

(2009) M. Stiller et al.   GENOME RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Explosive avian radiations and multi-directional dispersal across Wallacea: Evidence from the Campephagidae and other Crown Corvida (Aves)

(2008) Knud A. Jønsson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION