High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic

Pandemic influenza - including a risk assessment of H5N1

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In vivo evaluation of pathogenicity and transmissibility of influenza A(H1N1)pdm09 hemagglutinin receptor binding domain 222 intrahost variants isolated from a single immunocompromised patient

(2012) Matthew J. Memoli et al.   VIROLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

ECHO: A reference-free short-read error correction algorithm

(2011) W.-C. Kao et al.   GENOME RESEARCH

Clinical and virological course of infection with haemagglutinin D222G mutant strain of 2009 pandemic influenza A (H1N1) virus

(2011) Paul K.S. Chan et al.   JOURNAL OF CLINICAL VIROLOGY

Paraffin Embedding Contributes to RNA Aggregation, Reduced RNA Yield, and Low RNA Quality

(2011) David L. Evers et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Diagnosis of Influenza from Respiratory Autopsy Tissues

(2011) Amy M. Denison et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The Effect of Formaldehyde Fixation on RNA

(2011) David L. Evers et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue

(2011) Lorenza Mittempergher et al.   PLoS One

Mutation Analysis of 2009 Pandemic Influenza A(H1N1) Viruses Collected in Japan during the Peak Phase of the Pandemic

(2011) Jean-Étienne Morlighem et al.   PLoS One

Distinguishing Characteristics between Pandemic 2009–2010 Influenza A (H1N1) and Other Viruses in Patients Hospitalized with Respiratory Illness

(2011) Philip A. Chan et al.   PLoS One

Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak

(2011) Z.-M. Sheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights on influenza pathogenesis from the grave

(2011) Jeffery K. Taubenberger et al.   VIRUS RESEARCH

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

Influenza Virus Evolution, Host Adaptation, and Pandemic Formation

(2010) Jeffery K. Taubenberger et al.   Cell Host & Microbe

Hospitalized Patients with 2009 Pandemic Influenza A (H1N1) Virus Infection in the United States—September–October 2009

(2010) Jacek Skarbinski et al.   CLINICAL INFECTIOUS DISEASES

Prior infection with classical swine H1N1 influenza viruses is associated with protective immunity to the 2009 pandemic H1N1 virus

(2010) John C. Kash et al.   Influenza and Other Respiratory Viruses

Lung abscess and pleuritis caused by Lactobacillus rhamnosus in an immunocompetent patient

(2010) Hisashi Shoji et al.   JOURNAL OF INFECTION AND CHEMOTHERAPY

Deep Sequencing Reveals Mixed Infection with 2009 Pandemic Influenza A (H1N1) Virus Strains and the Emergence of Oseltamivir Resistance

(2010) Elodie Ghedin et al.   JOURNAL OF INFECTIOUS DISEASES

Pandemic Swine-Origin H1N1 Influenza A Virus Isolates Show Heterogeneous Virulence in Macaques

(2010) D. Safronetz et al.   JOURNAL OF VIROLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

(2010) Henry M. Wood et al.   NUCLEIC ACIDS RESEARCH

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

Genomic Signature and Mutation Trend Analysis of Pandemic (H1N1) 2009 Influenza A Virus

(2010) Chungen Pan et al.   PLoS One

Complete-Proteome Mapping of Human Influenza A Adaptive Mutations: Implications for Human Transmissibility of Zoonotic Strains

(2010) Olivo Miotto et al.   PLoS One

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans

(2009)   NEW ENGLAND JOURNAL OF MEDICINE

Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

(2009) Shota Nakamura et al.   PLoS One

Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis

(2009) Michal R. Schweiger et al.   PLoS One

The Feasibility of Using High Resolution Genome Sequencing of Influenza A Viruses to Detect Mixed Infections and Quasispecies

(2009) Muthannan A. Ramakrishnan et al.   PLoS One

Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples

(2009) Craig April et al.   PLoS One

Streptococcus pneumoniae Coinfection Is Correlated with the Severity of H1N1 Pandemic Influenza

(2009) Gustavo Palacios et al.   PLoS One

Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples

(2009) Laura E. MacConaill et al.   PLoS One

Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings

(2009) C. Fraser et al.   SCIENCE

Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans

(2009) R. J. Garten et al.   SCIENCE

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

The Pathology of Influenza Virus Infections

(2008) Jeffery K. Taubenberger et al.   Annual Review of Pathology-Mechanisms of Disease

RNA expression analysis from formalin fixed paraffin embedded tissues

(2008) Susan M. Farragher et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Detection of viral RNA from paraffin-embedded tissues after prolonged formalin fixation

(2008) Michelle D. McKinney et al.   JOURNAL OF CLINICAL VIROLOGY

Predominant Role of Bacterial Pneumonia as a Cause of Death in Pandemic Influenza: Implications for Pandemic Influenza Preparedness

(2008) David M. Morens et al.   JOURNAL OF INFECTIOUS DISEASES

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Pathology of human influenza revisited

(2008) Thijs Kuiken et al.   VACCINE