Works (30)
Updated: April 3rd, 2024 19:45
2019 article
PeakPass: Automating ChIP-Seq Blacklist Creation
Wimberley, C. E., & Heber, S. (2020, February 1). JOURNAL OF COMPUTATIONAL BIOLOGY, Vol. 27, pp. 259–268.
author keywords: blacklist; ChIP-seq; classification; quality control
open access via www.liebertpub.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 27, 2020
2019 article
PeakPass: Automating ChIP-Seq Blacklist Creation
BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2019, Vol. 11490, pp. 232–243.
author keywords: ChIP-seq; Classification; Quality control; Blacklist
TL;DR:
PeakPass is described, an efficient method to generate blacklists, and it is demonstrated that blacklists can increase ChIP-Seq data quality and be used for upgrading a blacklist to a new reference genome version.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 4, 2019
2019 article
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Perkins, P., Mazzoni-Putman, S., Stepanova, A., Alonso, J., & Heber, S. (2019, June 6). BMC GENOMICS, Vol. 20.
author keywords: Ribo-seq; Next-generation sequencing; Data analysis; Web application
MeSH headings : Computer Graphics; Genomics / methods; High-Throughput Nucleotide Sequencing / methods; Humans; Protein Biosynthesis; Quality Control; RNA, Messenger / genetics; RNA, Messenger / metabolism; Ribosomes / metabolism; Sequence Analysis, RNA; Software; Transcriptome; Web Browser
TL;DR:
RiboStreamR is presented, a comprehensive Ribo-seq quality control (QC) platform in the form of an R Shiny web application that provides visualization and analysis tools for various Ribe-seq QC metrics, including read length distribution, read periodicity, and translational efficiency.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 1, 2019
2017 journal article
Disruption of Trim9 function abrogates macrophage motility in vivo
Journal of Leukocyte Biology, 102(6), 1371–1380.
author keywords: chemotaxis; zebrafish; leukocyte; ubiquitin
MeSH headings : Animals; Cell Movement / genetics; Cell Shape; Chemotaxis; Humans; Macrophages / cytology; Macrophages / metabolism; Nerve Tissue Proteins / genetics; Nerve Tissue Proteins / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism; Tripartite Motif Proteins / genetics; Tripartite Motif Proteins / metabolism; U937 Cells; Ubiquitin-Protein Ligases / genetics; Ubiquitin-Protein Ligases / metabolism; Zebrafish / genetics; Zebrafish / immunology; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism
TL;DR:
It is demonstrated that Trim9 mediates cellular movement and migration in Mϕs as well as neurons, and is implicated in axonal migration, and found that M ϕ chemotaxis and cellular architecture are subsequently impaired in vivo.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: August 6, 2018
2017 conference paper
riboStreamR: A web application for quality control, analysis, and visualization of Ribo-seq data
International conference on computational advances in bio and medical.
TL;DR:
RiboStreamR provides visualization and analysis tools for various Ribo-seq QC metrics, including read length distribution, read periodicity, and translational efficiency, and the platform's environment is centered on providing a user-friendly experience, and includes numerous options for graphical customization and report generation.
(via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2016 journal article
Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana
IEEE Transactions on Nanobioscience, 15(2), 150–159.
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain
PLANT PHYSIOLOGY, 171(1), 42–61.
Contributors: G. Villarino n, Q. Hu n, S. Manrique *, M. Flores-Vergara, B. Sehra n, L. Robles n, J. Brumos n, A. Stepanova n
MeSH headings : Arabidopsis / anatomy & histology; Arabidopsis / genetics; Arabidopsis Proteins / genetics; Arabidopsis Proteins / isolation & purification; Base Sequence; Chloral Hydrate; DNA, Antisense; Flowers / genetics; Gene Expression Regulation, Plant; Genome, Plant; In Situ Hybridization; Indoleacetic Acids / pharmacology; MADS Domain Proteins / genetics; MADS Domain Proteins / isolation & purification; Meristem / genetics; Meristem / growth & development; Meristem / metabolism; Microscopy, Confocal; Ovule / cytology; Ovule / growth & development; Ovule / metabolism; Protein Isoforms; Protoplasts; RNA, Plant / chemistry; RNA, Plant / isolation & purification; Seeds / growth & development; Sequence Alignment; Transcription Factors; Transcriptional Activation; Transcriptome
TL;DR:
A novel approach to analyze the transcriptional signature of the medial domain of the Arabidopsis gynoecium, highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development and identifying additional genes including novel isoforms, cis-natural antisense transcripts, and a previously unrecognized member of the REPRODUCTIVE MERISTEM family of transcriptional regulators that are potential novel regulators of medial domain development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2015 chapter
A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana
In Bioinformatics Research and Applications (Vol. 9096, pp. 138–149).
Contributors: Q. Hu n, C. Merchante n, A. Stepanova n , J. Alonso n & n
author keywords: uORF; Translation; Ribosome footprinting; Stacking; Classification; Arabidopsis thaliana
TL;DR:
This paper uses ribosome footprinting together with a stacking-based classification approach to identify translated uORFs in Arabidopsis thaliana, resulting in a set of 5360 potentially translated u ORFs in 2051 genes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
Sources: Crossref, ORCID, NC State University Libraries
Added: December 19, 2019
2015 conference paper
A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana
Bioinformatics research and applications (isbra 2015), 9096, 138–149.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2
CELL, 163(3), 684–697.
Contributors: C. Merchante n, J. Brumos n, J. Yun n, Q. Hu n, K. Spencer n, P. Enríquez n, B. Binder *, n , A. Stepanova n , J. Alonso n
MeSH headings : 3' Untranslated Regions; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; DNA-Binding Proteins; Ethylenes / metabolism; F-Box Proteins / genetics; Gene Expression Regulation, Plant; Nuclear Proteins / metabolism; Protein Biosynthesis; RNA, Messenger / metabolism; Receptors, Cell Surface / metabolism; Ribosomes / metabolism; Signal Transduction; Transcription Factors / metabolism
TL;DR:
Characterization of one of the targets of this translation regulatory machinery, the ethylene signaling component EBF2, indicates that the signaling molecule EIN2 and the nonsense-mediated decay proteins UPFs play a central role in this ethylene-induced translational response.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2015 conference paper
Mining transcript features related to translation in Arabidopsis using LASSO and random forest
International conference on computational advances in bio and medical.
Contributors: Q. Hu n, C. Merchante n, A. Stepanova n , J. Alonso n & n
TL;DR:
It is found that the contribution of features may be different for transcripts belonging to different functional groups, suggesting that transcripts might employ different mechanisms for the regulation of translation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: NC State University Libraries, NC State University Libraries, ORCID
Added: August 6, 2018
2014 journal article
Targeted Combinatorial Alternative Splicing Generates Brain Region-Specific Repertoires of Neurexins
NEURON, 84(2), 386–398.
MeSH headings : Alternative Splicing; Animals; Brain / metabolism; Exons / genetics; Mice; Nerve Tissue Proteins / genetics; Nerve Tissue Proteins / metabolism; Neurons / metabolism; Protein Isoforms / genetics; Protein Isoforms / metabolism; RNA, Messenger / metabolism; Synapses / metabolism
TL;DR:
This analysis defines the molecular diversity of a critical synaptic receptor and provides evidence that neurexin diversity is linked to cellular diversity in the nervous system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2013 journal article
High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants
PLOS ONE, 8(10).
Contributors: B. Howard n, Q. Hu n, A. Babaoglu n, M. Chandra n, M. Borghi n, X. Tan n, L. He n, H. Winter-Sederoff
MeSH headings : Alternative Splicing / genetics; Arabidopsis / microbiology; Exons / genetics; Gene Expression Profiling; Genomics; High-Throughput Nucleotide Sequencing; Introns / genetics; Pseudomonas syringae / genetics; Pseudomonas syringae / physiology; RNA Splice Sites / genetics; Sequence Analysis, RNA; Transcription, Genetic / genetics
TL;DR:
A genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato finds several genes previously known to be alternatively spliced or expressed during the defense response may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for thedefense response against invasive pathogens.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2010 journal article
Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus
Journal of Proteome Research, 9(3), 1209–1217.
author keywords: mass spectrometry; proteomics; alternative splicing; database; Aspergillus flavus
MeSH headings : Alternative Splicing; Aspergillus flavus / genetics; Aspergillus flavus / metabolism; Computer Simulation; Cytochrome-B(5) Reductase / chemistry; Cytochrome-B(5) Reductase / genetics; Databases, Protein; Fungal Proteins / biosynthesis; Fungal Proteins / chemistry; Fungal Proteins / genetics; Isotope Labeling; Mass Spectrometry; Models, Genetic; Protein Isoforms / biosynthesis; Protein Isoforms / chemistry; Protein Isoforms / genetics; Proteomics; Pyruvate Carboxylase / chemistry; Pyruvate Carboxylase / genetics; RNA Splice Sites; Reproducibility of Results
TL;DR:
The introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome, and shows potential to improve genome annotation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: December 27, 2020
2010 article
Towards reliable isoform quantification using RNA-SEQ data
BMC BIOINFORMATICS, Vol. 11.
MeSH headings : Algorithms; Alternative Splicing / genetics; Arabidopsis / genetics; Base Sequence; Chi-Square Distribution; Computational Biology / methods; Computer Simulation; Databases, Nucleic Acid; Gene Expression Regulation, Plant; Genes, Plant; Linear Models; Models, Genetic; Molecular Sequence Data; Protein Isoforms / analysis; Protein Isoforms / genetics; Sequence Analysis, RNA / methods; Stress, Physiological
TL;DR:
This research investigates the use of RNA sequencing datasets to address the isoform quantification problem and identifies several alternatively-spliced genes with switch-like, on/off expression properties, as well as a number of other genes that varied more subtly in isoform expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2009 chapter
Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates
In Bioinformatics Research and Applications (pp. 272–283).
TL;DR:
This study provides a dictionary of sequence motifs involved in the regulation of alternative splicing in CNS tissues, and a novel tool to detect such motifs, by applying a two-step approach to identify k-mer seed motifs.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: September 8, 2020
2009 journal article
Common Intervals of Multiple Permutations
ALGORITHMICA, 60(2), 175–206.
author keywords: Common intervals of permutations; Multichromosomal permutations; Circular permutations
TL;DR:
An algorithm is presented that finds in a family of k permutations of n elements all z common intervals in optimal O(kn+z) time and O(n) additional space and how to adapt this algorithm to multichromosomal and circular permutations is shown.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2009 chapter
Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing
In Bioinformatics Research and Applications (pp. 260–271).
TL;DR:
This paper uses distribution-based quantitative association rule mining to find combinatorial cis -regulatory motifs and to investigate the effect of motif pairs, and shows that motifs that occur in motif pairs typically occur in clusters.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: September 8, 2020
2009 chapter
Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression
In Bioinformatics Research and Applications (pp. 18–27).
TL;DR:
A novel quality assessment method is described that is designed to identify chips that should be discarded from an experiment and assesses whether discarding each chip enhances or obscures the recovery of this known set.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: September 8, 2020
2009 journal article
The deep evolution of metazoan microRNAs
EVOLUTION & DEVELOPMENT, 11(1), 50–68.
MeSH headings : Animals; Base Sequence; Blotting, Northern; Chordata / genetics; Computational Biology; Conserved Sequence / genetics; DNA Primers / genetics; Evolution, Molecular; Gene Library; Invertebrates / genetics; MicroRNAs / genetics; Molecular Sequence Data; Phylogeny; Porifera / genetics; Sequence Analysis, DNA; Species Specificity
TL;DR:
The shared complement of miRNAs among 18 animal species is described using a combination of 454 sequencing of small RNA libraries with genomic searches and it is proposed that mi RNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2009 review
Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes
[Review of ]. PLANT AND CELL PHYSIOLOGY, 51(1), 144–163.
author keywords: Lignin systems biology; Monolignol biosynthesis; Populus trichocarpa; Promoter motifs; Transcript abundance; Xylem-specific expression
MeSH headings : Amino Acid Motifs / genetics; Biosynthetic Pathways / genetics; Enzymes / biosynthesis; Enzymes / genetics; Gene Expression Regulation, Enzymologic / physiology; Gene Expression Regulation, Plant / physiology; Genome, Plant / genetics; Lignin / biosynthesis; Lignin / genetics; Phloem / enzymology; Phloem / genetics; Plant Shoots / enzymology; Plant Shoots / genetics; Populus / genetics; Populus / metabolism; Promoter Regions, Genetic / genetics; RNA, Messenger / analysis; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Plant / analysis; RNA, Plant / genetics; RNA, Plant / metabolism; Transcription, Genetic / physiology; Xylem / enzymology; Xylem / genetics
TL;DR:
The identified 23 genes that most probably encode monolignol biosynthesis enzymes during wood formation are identified and evidence suggesting functional redundancy at the transcript level for phenylalanine ammonia-lyase and cinnamate 4-hydroxylase is found.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2009 journal article
Unsupervised assessment of microarray data quality using a Gaussian mixture model
BMC BIOINFORMATICS, 10.
MeSH headings : Algorithms; Computational Biology / methods; Gene Expression Profiling / methods; Normal Distribution; Oligonucleotide Array Sequence Analysis / methods
TL;DR:
This research illustrates the efficacy of an unsupervised classification approach for the purpose of automated microarray data quality assessment, which requires only unannotated training data and is easy to customize and to keep up-to-date as technology evolves.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2008 journal article
Developmental surface and phonological dysgraphia in German 3rd graders
Reading and Writing, 23(1), 97–127.
author keywords: Developmental dysgraphia; Spelling disorders; Developmental cognitive neuropsychology
UN Sustainable Development Goal Categories
4. Quality Education
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: December 27, 2020
2007 journal article
Correcting base-assignment errors in repeat regions of shotgun assembly
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 4(1), 54–64.
author keywords: fragment assembly; finishing; expectation maximization
MeSH headings : Algorithms; Campylobacter jejuni / genetics; Cluster Analysis; Computational Biology / methods; Genome, Bacterial; Lactococcus lactis / genetics; Models, Statistical; Repetitive Sequences, Nucleic Acid / genetics; Sequence Alignment; Sequence Analysis, DNA / methods; Sequence Analysis, DNA / statistics & numerical data; Software; Staphylococcus epidermidis / genetics; Wolbachia / genetics
TL;DR:
An iterative algorithm, EULER-AIR, is developed that is able to correct base-assignment errors in finished genome sequences in public databases and is demonstrated to be a software tool that can be used to find and correctbase-assigned errors in a genome assembly project.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2007 journal article
Non-monotonic dose-response relationship in steroid hormone receptor-mediated gene expression
JOURNAL OF MOLECULAR ENDOCRINOLOGY, 38(5-6), 569–585.
MeSH headings : Animals; Dimerization; Dose-Response Relationship, Drug; Gene Expression Regulation / drug effects; Hormones / pharmacology; Humans; Ligands; Models, Biological; Models, Theoretical; Receptors, Steroid / agonists; Receptors, Steroid / antagonists & inhibitors; Receptors, Steroid / genetics; Receptors, Steroid / metabolism; Repressor Proteins / metabolism; Repressor Proteins / pharmacology; Trans-Activators / metabolism; Trans-Activators / pharmacology
TL;DR:
This work provides a novel mechanism for non-monotonic, particularly U-shaped, dose-response behaviors observed with certain steroid mimics, and may help not only understand how selective steroid receptor modulators work but also improve risk assessment for EACs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2006 journal article
Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry
JOURNAL OF MASS SPECTROMETRY, 41(3), 281–288.
MeSH headings : Biotechnology / instrumentation; Biotechnology / methods; Electrophoresis, Gel, Two-Dimensional; Fourier Analysis; Mass Spectrometry; Peptides / analysis; Proteomics / instrumentation; Proteomics / methods
TL;DR:
The results indicate that reverse-phase-nanoHPLC (RP-nHPLC) separation coupled with FT-ICR MS offers an order of magnitude improvement in peak capacity over RP- nHPLC separation coupling with TOF MS, and the addition of an orthogonal separation method, strong cation exchange (SCX), for 2D LC-MS demonstrates an additional 10-fold improvement inpeak capacity over 1D LC -MS methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2005 journal article
Common intervals of trees
INFORMATION PROCESSING LETTERS, 93(2), 69–74.
author keywords: combinatorial problems; algorithms; labeled trees
TL;DR:
This paper considers the problem of finding common intervals of trees, a generalization of the concept of common intervals in permutations, and proposes some genetic algorithms using subtour exchange crossover based on common intervals.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2005 journal article
RACE: Remote Analysis Computation for gene Expression data
NUCLEIC ACIDS RESEARCH, 33, W638–W643.
MeSH headings : Computational Biology; Computer Graphics; Gene Expression Profiling / methods; Gene Expression Profiling / standards; Internet; Oligonucleotide Array Sequence Analysis / methods; Oligonucleotide Array Sequence Analysis / standards; Quality Control; Software; User-Computer Interface
TL;DR:
The Remote Analysis Computation for gene Expression data (RACE) suite is a collection of bioinformatics web tools designed for the analysis of DNA microarray data that estimates the false discovery rates of lists of potentially regulated genes and provides a Gene Ontology-term analysis tool for GeneChip data to support the biological interpretation and annotation of results.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2004 journal article
The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome
Nucleic Acids Research, 32(13), 3977–3983.
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2001 chapter
Finding All Common Intervals of k Permutations
In Combinatorial Pattern Matching (pp. 207–218).
TL;DR:
The set of irreducible intervals is introduced, a generating subset of the set of all common intervals of k permutations that finds in a family of kpermutations of n elements all K common intervals in optimal O(nk+K) time and O( n) additional space.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: September 8, 2020
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