FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1

(2021) Antony V E Chapman et al.   GENETICS

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

(2021) Valeria Velásquez-Zapata et al.   PLoS Computational Biology

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

(2020) Michael W. Gray et al.   BMC BIOLOGY

The genome of Shaw’s sea snake (Hydrophis curtus) reveals secondary adaptation to its marine environment

(2020) Changjun Peng et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection

(2020) Manjula G. Elmore et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode

(2020) Shuangyang Wu et al.   Genes

Fault isolation for a complex decentralized waste water treatment facility

(2020) Molly C. Klanderman et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

Machine learning in plant–pathogen interactions: empowering biological predictions from field scale to genome scale

(2019) Jana Sperschneider   NEW PHYTOLOGIST

phylostratr: A framework for phylostratigraphy

(2019) Zebulun Arendsee et al.   BIOINFORMATICS

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

(2019) Antonio Torres-Méndez et al.   Nature Ecology & Evolution

Spaceflight-induced alternative splicing during seedling development in Arabidopsis thaliana

(2019) Nicole S. Beisel et al.   NPJ Microgravity

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

Identification and Analysis of Micro-Exon Genes in the Rice Genome

(2019) Qi Song et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Atypical Splicing Accompanied by Skipping Conserved Micro-exons Produces Unique WRINKLED1, An AP2 Domain Transcription Factor in Rice Plants

(2019) Mano et al.   Plants-Basel

Small RNA discovery in the interaction between barley and the powdery mildew pathogen

(2019) Matt Hunt et al.   BMC GENOMICS

Genome-wide identification and characterization of long intergenic noncoding RNAs in the regenerative flatworm Macrostomum lignano

(2019) Azali Azlan et al.   GENOMICS

A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae

(2019) Kevin Weitemier et al.   PeerJ

Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era

(2019) Xuchu Wang   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A multi-sample approach increases the accuracy of transcript assembly

(2019) Li Song et al.   Nature Communications

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

(2019) Paulo Rapazote-Flores et al.   BMC GENOMICS

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

(2018) Fuyi Li et al.   BIOINFORMATICS

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

(2018) Xian Adiconis et al.   NATURE METHODS

Raising orphans from a metadata morass: A researcher's guide to re-use of public ’omics data

(2018) Priyanka Bhandary et al.   PLANT SCIENCE

Full disclosure: Genome assembly is still hard

(2018) Stephen Richards   PLOS BIOLOGY

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing

(2018) Alberto Parras et al.   NATURE

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

(2018) Luca Venturini et al.   GigaScience

DeepPhos: prediction of protein phosphorylation sites with deep learning

(2018) Fenglin Luo et al.   BIOINFORMATICS

Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer’s disease patients

(2018) Shunian Xiang et al.   BMC Medical Genomics

Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life

(2018) Stefania Morganti et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Long noncoding RNA expression profiling in cancer: Challenges and opportunities

(2018) Lucía Lorenzi et al.   GENES CHROMOSOMES & CANCER

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

(2018) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

(2017) Bernardo J. Clavijo et al.   GENOME RESEARCH

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Accurate assembly of transcripts through phase-preserving graph decomposition

(2017) Mingfu Shao et al.   NATURE BIOTECHNOLOGY

Cancer transcriptome profiling at the juncture of clinical translation

(2017) Marcin Cieślik et al.   NATURE REVIEWS GENETICS

Gramene 2018: unifying comparative genomics and pathway resources for plant research

(2017) Marcela K Tello-Ruiz et al.   NUCLEIC ACIDS RESEARCH

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Uncovering hidden variation in polyploid wheat

(2017) Ksenia V. Krasileva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq

(2017) Ruolin Liu et al.   PLoS Computational Biology

Microexons: discovery, regulation, and function

(2017) Dmytro Ustianenko et al.   Wiley Interdisciplinary Reviews-RNA

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo

(2016) Erik Holmqvist et al.   EMBO JOURNAL

Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

(2016) A. Marchant et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

(2015) Jorge Duitama et al.   PLoS One

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

A single-nucleotide exon found in Arabidopsis

(2015) Lei Guo et al.   Scientific Reports

Insights into the Evolution of Longevity from the Bowhead Whale Genome

(2015) Michael Keane et al.   Cell Reports

changepoint: AnRPackage for Changepoint Analysis

(2015) Rebecca Killick et al.   Journal of Statistical Software

ALDB: A Domestic-Animal Long Noncoding RNA Database

(2015) Aimin Li et al.   PLoS One

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Coming of age: orphan genes in plants

(2014) Zebulun W. Arendsee et al.   TRENDS IN PLANT SCIENCE

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

(2013) Jie Wu et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

(2013) Xin Qi et al.   PLANT MOLECULAR BIOLOGY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human genome project: big science transforms biology and medicine

(2013) Leroy Hood et al.   Genome Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Ruffus: a lightweight Python library for computational pipelines

(2010) Leo Goodstadt   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region

(2010) S Wu et al.   ONCOGENE

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

(2010) Keyan Zhao et al.   PLoS One

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

mGene: Accurate SVM-based gene finding with an application to nematode genomes

(2009) G. Schweikert et al.   GENOME RESEARCH

Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs

(2009) Shuo Gu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

A SNP in a let-7 microRNA Complementary Site in the KRAS 3' Untranslated Region Increases Non-Small Cell Lung Cancer Risk

(2008) L. J. Chin et al.   CANCER RESEARCH

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region

(2008) Andrea B Eberle et al.   PLOS BIOLOGY