Jens Reeder

发表

Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.

R. Knight, I. Majerfeld, J. Chocholousová, 2010, RNA.

QIIME allows analysis of high-throughput community sequencing data

William A. Walters, Jesse R. Zaneveld, F. Bushman, 2010, Nature Methods.

Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

R. Knight, Jens Reeder, R. Knight, 2010, Nature Methods.

Human gut microbiome viewed across age and geography

J. Clemente, R. Knight, R. Baldassano, 2012, Nature.

Algorithms for RNA secondary structure analysis : prediction of pseudoknots and the consensus shapes approach

Jens Reeder, 2007 .

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.

R. Guigó, C. Manichanh, F. Guarner, 2010, Genome research.

A comprehensive transcriptional portrait of human cancer cell lines

Thomas D. Wu, Gregory J. Zynda, Jeremiah D. Degenhardt, 2014, Nature Biotechnology.

Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

R. Knight, Jens Reeder, R. Knight, 2010, Nature Methods.

PhyloSift: phylogenetic analysis of genomes and metagenomes

Henry C. M. Leung, Brian C. Thomas, Ocn, 2014, PeerJ.

Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration

Matthew J. Brauer, Steve Lianoglou, M. Brauer, 2018, Proceedings of the National Academy of Sciences.

Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer

Thomas D. Wu, M. Yaylaoglu, R. Neve, 2014, Nature Communications.

Defining seasonal marine microbial community dynamics

R. Knight, J. Gilbert, J. Caporaso, 2011, The ISME Journal.

Analysis of protein-altering variants in telomerase genes and their association with MUC5B common variant status in patients with idiopathic pulmonary fibrosis: a candidate gene sequencing study.

Christopher R. Cabanski, Matthew J. Brauer, B. Yaspan, 2018, The Lancet. Respiratory medicine.

Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes

Lisa N Kinch, Nick V Grishin, Na Zhang, 2014, Nature Genetics.

Previously reported placebo-response-associated variants do not predict patient outcomes in inflammatory disease Phase III trial placebo arms

B. Yaspan, J. Vogel, M. Brauer, 2018, Genes & Immunity.

Changes in the taxonomic / phylogenetic composition of fecal communities as a function of age and population

J. Clemente, R. Knight, J. Caporaso, 2016 .

Defining seasonal marine microbial community dynamics

Susan M. Huse, R. Knight, J. Gilbert, 2011, The ISME Journal.

Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers.

Leonard D. Goldstein, R. Gentleman, F. Gnad, 2016, Cell reports.

Identifying and mitigating batch effects in whole genome sequencing data

Jens Reeder, T. Behrens, R. Graham, 2017, BMC Bioinformatics.

GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality

Thomas D. Wu, Michael Lawrence, Matthew J. Brauer, 2016, Statistical Genomics.

Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype

Allyson L. Byrd, Z. Modrušan, Jens Reeder, 2023, Cell reports. Medicine.

KnotInFrame: prediction of −1 ribosomal frameshift events

Robert Giegerich, Corinna Theis, Jens Reeder, 2008, Nucleic acids research.

A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk

Matthew J. Brauer, M. McCarthy, B. Yaspan, 2022, Scientific Reports.

The 'rare biosphere': a reality check

Rob Knight, Jens Reeder, R. Knight, 2009, Nature Methods.

RNAshapes: an integrated RNA analysis package based on abstract shapes.

Robert Giegerich, Peter Steffen, Björn Voß, 2006, Bioinformatics.

RNA Secondary Structure Analysis Using The RNAshapes Package

Robert Giegerich, Jens Reeder, R. Giegerich, 2009, Current protocols in bioinformatics.

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

Robert Giegerich, Jens Reeder, R. Giegerich, 2005, Bioinform..

Shape based indexing for faster search of RNA family databases

Robert Giegerich, Stefan Janssen, Jens Reeder, 2008, BMC Bioinformatics.

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

Robert Giegerich, Jens Reeder, R. Giegerich, 2004, BMC Bioinformatics.

Locomotif: from graphical motif description to RNA motif search

Robert Giegerich, Jens Reeder, Janina Reeder, 2007, ISMB/ECCB.

Beyond Mfold: Recent advances in RNA bioinformatics

Robert Giegerich, Matthias Höchsmann, Marc Rehmsmeier, 2006, Journal of Biotechnology.

Cognitive Deficits, Changes in Synaptic Function, and Brain Pathology in a Mouse Model of Normal Aging

Benjamin E. L. Lauffer, K. Scearce-Levie, G. Prusky, 2015, eNeuro.

pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows

Robert Giegerich, Jens Reeder, Peter Steffen, 2007, Nucleic Acids Res..

Enabling genome-wide association testing with multiple diseases and no healthy controls.

Matthew J. Brauer, B. Yaspan, J. Vogel, 2019, Gene.

Extrapolation of Urn Models via Poissonization: Accurate Measurements of the Microbial Unknown

Manuel E. Lladser, Jens Reeder, Raúl Gouet, 2011, PloS one.

Identifying and mitigating batch effects in whole genome sequencing data

Jennifer A. Tom, Jens Reeder, William F. Forrest, 2017, BMC Bioinformatics.

Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

Jens Reeder, R. Knight, 2010, Nature Methods.

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

R. Giegerich, Jens Reeder, 2004, BMC Bioinformatics.