Genomics: the state of the art in RNA-seq analysis

Abstract In the past decade, over 3000 samples of soybean transcriptomic data have accumulated in public repositories. Here, we review the state of the art in soybean transcriptomics, highlighting the major microarray and RNA-seq studies that investigated soybean transcriptional programs in different tissues and conditions. Further, we propose approaches for integrating such big data using gene coexpression network and outline important web resources that may facilitate soybean data acquisition and analysis, contributing to the acceleration of soybean breeding and functional genomics research.

Graphmap2 - splice-aware RNA-seq mapper for long reads

10.1101/720458 ◽

2019 ◽

Cited By ~ 1

Author(s):

Josip Marić ◽

Ivan Sović ◽

Krešimir Križanović ◽

Niranjan Nagarajan ◽

Mile Šikić

Keyword(s):

State Of The Art ◽

The State ◽

Rna Seq ◽

Link Type ◽

Pacific Biosciences ◽

Long Reads ◽

Oxford Nanopore

AbstractIn this paper we present Graphmap2, a splice-aware mapper built on our previously developed DNA mapper Graphmap. Graphmap2 is tailored for long reads produced by Pacific Biosciences and Oxford Nanopore devices. It uses several newly developed algorithms which enable higher precision and recall of correctly detected transcripts and exon boundaries. We compared its performance with the state-of-the-art tools Minimap2 and Gmap. On both simulated and real datasets Graphmap2 achieves higher mappability and more correctly recognized exons and their ends. In addition we present an analysis of potential of splice aware mappers and long reads for the identification of previously unknown isoforms and even genes. The Graphmap2 tool is publicly available at https://github.com/lbcb-sci/graphmap2.

HLA-MA: Simple yet powerful matching of samples using HLA typing results

10.1101/066548 ◽

2016 ◽

Author(s):

Clemens Messerschmidt ◽

Manuel Holtgrewe ◽

Dieter Beule

Keyword(s):

Microsatellite Instability ◽

State Of The Art ◽

The State ◽

Hla Typing ◽

Whole Genome ◽

Consistency Checking ◽

Rna Seq ◽

Simple Method ◽

Link Type ◽

Typing Result

AbstractSummaryWe propose the simple method HLA-MA for consistency checking in pipelines operating on human HTS data. The method is based on the HLA typing result of the state-of-the-art method Opti-Type. Provided that there is sufficient coverage of the HLA loci, comparing HLA types allows for simple, fast, and robust matching of samples from whole genome, exome, and RNA-seq data. This approach is reliable for sample re-identification even for samples with high mutational loads, e.g., caused by microsatellite instability or POLE1 defects.Availability and ImplementationThe software is implemented In Python 3 and freely available under the MIT license at https://github.com/bihealth/hlama and via [email protected]

Curse: building expression atlases and co-expression networks from public RNA-Seq data

Bioinformatics ◽

10.1093/bioinformatics/bty1052 ◽

2018 ◽

Vol 35 (16) ◽

pp. 2880-2881 ◽

Cited By ~ 6

Author(s):

Dries Vaneechoutte ◽

Klaas Vandepoele

Keyword(s):

Rna Sequencing ◽

State Of The Art ◽

The State ◽

Supplementary Information ◽

Supplementary Data ◽

Rna Seq ◽

Valuable Resource ◽

Sequencing Data ◽

Imperfect Quality ◽

Sequence Read Archive

Abstract Summary Public RNA-Sequencing (RNA-Seq) datasets are a valuable resource for transcriptome analyses, but their accessibility is hindered by the imperfect quality and presentation of their metadata and by the complexity of processing raw sequencing data. The Curse suite was created to alleviate these problems. It consists of an online curation tool named Curse to efficiently build compendia of experiments hosted on the Sequence Read Archive, and a lightweight pipeline named Prose to download and process the RNA-Seq data into expression atlases and co-expression networks. Curse networks showed improved linking of functionally related genes compared to the state-of-the-art. Availability and implementation Curse, Prose and their manuals are available at http://bioinformatics.psb.ugent.be/webtools/Curse/. Prose was implemented in Java. Supplementary information Supplementary data are available at Bioinformatics online.

Practical Picture Processing

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051700 ◽

1974 ◽

Vol 32 ◽

pp. 338-339

Author(s):

T. A. Welton

Keyword(s):

Radiation Damage ◽

Coherence Length ◽

Spatial Information ◽

State Of The Art ◽

Coherent Radiation ◽

The State ◽

Energy Spread ◽

Electron Micrograph ◽

Picture Processing ◽

Molecular Skeleton

Various authors have emphasized the spatial information resident in an electron micrograph taken with adequately coherent radiation. In view of the completion of at least one such instrument, this opportunity is taken to summarize the state of the art of processing such micrographs. We use the usual symbols for the aberration coefficients, and supplement these with £ and 6 for the transverse coherence length and the fractional energy spread respectively. He also assume a weak, biologically interesting sample, with principal interest lying in the molecular skeleton remaining after obvious hydrogen loss and other radiation damage has occurred.

Hypothesis-Evidence Coordination: The State of the Art

Contemporary Psychology ◽

10.1037/000988 ◽

2003 ◽

Vol 48 (6) ◽

pp. 826-829 ◽

Cited By ~ 1

Author(s):

Eric Amsel

Keyword(s):

State Of The Art ◽

The State

The State of the Art

Contemporary Psychology ◽

10.1037/009537 ◽

1968 ◽

Vol 13 (9) ◽

pp. 479-480

Author(s):

LEWIS PETRINOVICH

Keyword(s):

State Of The Art ◽

The State

Needs Assessment: The State of the Art

Contemporary Psychology ◽

10.1037/022896 ◽

1984 ◽

Vol 29 (5) ◽

pp. 426-428

Author(s):

Anthony R. D'Augelli

Keyword(s):

Needs Assessment ◽

State Of The Art ◽

The State

Biofeedback: The State of the Art

Contemporary Psychology ◽

10.1037/029422 ◽

1991 ◽

Vol 36 (2) ◽

pp. 140-140

Author(s):

John A. Corson

Keyword(s):

State Of The Art ◽

The State

Adult development meets social sciences—Reviewing the state of the art.

Behavioral Development ◽

10.1037/bdb0000051 ◽

2016 ◽

Vol 21 (2) ◽

pp. 136-153 ◽

Cited By ~ 1

Author(s):

Elke Fein ◽

Thomas Jordan

Keyword(s):

Social Sciences ◽

Adult Development ◽

State Of The Art ◽

The State