Works (30)

Updated: April 3rd, 2024 19:45

2020 article

PeakPass: Automating ChIP-Seq Blacklist Creation

Wimberley, C. E., & Heber, S. (2020, February 1). JOURNAL OF COMPUTATIONAL BIOLOGY, Vol. 27, pp. 259–268.

By: C. Wimberley n & S. Heber n

author keywords: blacklist; ChIP-seq; classification; quality control
Sources: Web Of Science, ORCID
Added: February 27, 2020

2019 article

PeakPass: Automating ChIP-Seq Blacklist Creation

BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2019, Vol. 11490, pp. 232–243.

By: C. Wimberley n & S. Heber n

author keywords: ChIP-seq; Classification; Quality control; Blacklist
Sources: Web Of Science, ORCID
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.

By: P. Perkins n, S. Mazzoni-Putman n, A. Stepanova n, J. Alonso n & S. Heber n

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
Sources: Web Of Science, ORCID
Added: July 1, 2019

2017 journal article

Disruption of Trim9 function abrogates macrophage motility in vivo

Journal of Leukocyte Biology, 102(6), 1371–1380.

By: D. Tokarz n, A. Heffelfinger n, D. Jima n, J. Gerlach n, R. Shah n, I. Rodriguez-Nunez n, A. Kortum n, A. Fletcher n ...

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
Sources: Web Of Science, 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.

By: P. Perkins n & S. Heber n

Sources: NC State University Libraries, ORCID
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.

By: Q. Hu, C. Merchante, A. Stepanova, J. Alonso & S. Heber

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.

By: G. Villarino n, Q. Hu n, S. Manrique*, M. Flores-Vergara n, B. Sehra n, L. Robles n, J. Brumos n, A. Stepanova n ...

co-author countries: Italy 🇮🇹 Sweden 🇸🇪

Contributors: G. Villarino n, Q. Hu n, S. Manrique*, M. Flores-Vergara n, 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
Sources: Web Of Science, 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 & S. Heber n

author keywords: uORF; Translation; Ribosome footprinting; Stacking; Classification; Arabidopsis thaliana
Sources: Crossref, ORCID
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.

By: Q. Hu, C. Merchante, A. Stepanova, J. Alonso & S. Heber

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.

co-author countries: Spain 🇪🇸

Contributors: C. Merchante n, J. Brumos n, J. Yun n, Q. Hu n, K. Spencer n, P. Enríquez n, B. Binder*, S. Heber 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
Sources: Web Of Science, 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.

By: Q. Hu n, C. Merchante n, A. Stepanova n, J. Alonso n & S. Heber n

Contributors: Q. Hu n, C. Merchante n, A. Stepanova n, J. Alonso n & S. Heber n

Sources: 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.

By: D. Schreiner*, T. Nguyen*, G. Russo*, S. Heber n, A. Patrignani*, E. Ahrne*, P. Scheiffele*

co-author countries: Switzerland 🇨🇭
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
Sources: Web Of Science, ORCID
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).

By: B. Howard n, Q. Hu n, A. Babaoglu n, M. Chandra n, M. Borghi n, X. Tan n, L. He n, H. Winter-Sederoff ...

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
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Common Intervals of Multiple Permutations

ALGORITHMICA, 60(2), 175–206.

By: S. Heber n, R. Mayr* & J. Stoye*

co-author countries: Germany 🇩🇪 United Kingdom of Great Britain and Northern Ireland 🇬🇧
author keywords: Common intervals of permutations; Multichromosomal permutations; Circular permutations
Sources: Web Of Science, 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.

By: K. Chang n, D. Georgianna n, S. Heber n, G. Payne n & D. Muddiman n

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
Sources: Crossref, ORCID
Added: December 27, 2020

2010 journal article

Developmental surface and phonological dysgraphia in German 3rd graders

Reading and Writing, 23(1), 97–127.

By: J. Cholewa*, S. Mantey*, S. Heber* & W. Hollweg*

co-author countries: Germany 🇩🇪
author keywords: Developmental dysgraphia; Spelling disorders; Developmental cognitive neuropsychology
Sources: Crossref, ORCID
Added: December 27, 2020

2010 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.

By: R. Shi n, Y. Sun n, Q. Li n, S. Heber n, R. Sederoff n & V. Chiang n

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
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 article

Towards reliable isoform quantification using RNA-SEQ data

BMC BIOINFORMATICS, Vol. 11.

By: B. Howard n & S. Heber n

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
Sources: Web Of Science, ORCID
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).

By: S. Zhao n, J. Kim n & S. Heber n

Sources: Crossref, ORCID
Added: September 8, 2020

2009 chapter

Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing

In Bioinformatics Research and Applications (pp. 260–271).

By: J. Kim n, S. Zhao n, B. Howard n & S. Heber n

Sources: Crossref, ORCID
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).

By: B. Howard n, B. Sick* & S. Heber n

co-author countries: Switzerland 🇨🇭
Sources: Crossref, ORCID
Added: September 8, 2020

2009 journal article

The deep evolution of metazoan microRNAs

EVOLUTION & DEVELOPMENT, 11(1), 50–68.

By: B. Wheeler n, A. Heimberg*, V. Moy*, E. Sperling*, T. Holstein*, S. Heber n, K. Peterson*

co-author countries: Germany 🇩🇪
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
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 journal article

Unsupervised assessment of microarray data quality using a Gaussian mixture model

BMC BIOINFORMATICS, 10.

By: B. Howard n, B. Sick* & S. Heber n

co-author countries: Switzerland 🇨🇭
MeSH headings : Algorithms; Computational Biology / methods; Gene Expression Profiling / methods; Normal Distribution; Oligonucleotide Array Sequence Analysis / methods
Sources: Web Of Science, ORCID
Added: August 6, 2018

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
Sources: Web Of Science, ORCID
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.

By: L. Li*, M. Andersen, S. Heber* & Q. Zhang

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
Sources: Web Of Science, ORCID
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.

By: J. Frahm n, B. Howard n, S. Heber n & D. Muddiman n

MeSH headings : Biotechnology / instrumentation; Biotechnology / methods; Electrophoresis, Gel, Two-Dimensional; Fourier Analysis; Mass Spectrometry; Peptides / analysis; Proteomics / instrumentation; Proteomics / methods
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Common intervals of trees

INFORMATION PROCESSING LETTERS, 93(2), 69–74.

By: S. Heber* & C. Savage*

author keywords: combinatorial problems; algorithms; labeled trees
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

RACE: Remote Analysis Computation for gene Expression data

NUCLEIC ACIDS RESEARCH, 33, W638–W643.

By: M. Psarros*, S. Heber*, M. Sick, G. Thoppae, K. Harshman & B. Sick

co-author countries: Switzerland 🇨🇭
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
Sources: Web Of Science, ORCID
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.

By: J. Leipzig, P. Pevzner & S. Heber

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2001 chapter

Finding All Common Intervals of k Permutations

In Combinatorial Pattern Matching (pp. 207–218).

By: S. Heber* & J. Stoye*

co-author countries: Germany 🇩🇪
Sources: Crossref, ORCID
Added: September 8, 2020

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