Publikationer av Olof Emanuelsson
Refereegranskade
Artiklar
[1]
K. J. Westrin, W. W. Kretzschmar och O. Emanuelsson, "ClusTrast : a short read de novo transcript isoform assembler guided by clustered contigs," BMC Bioinformatics, vol. 25, no. 1, 2024.
[2]
S. Akhter et al., "Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway," New Phytologist, vol. 236, no. 5, s. 1951-1963, 2022.
[3]
J. J. A. Armenteros et al., "Detecting sequence signals in targeting peptides using deep learning," Life Science Alliance, vol. 2, no. 5, 2019.
[4]
S. Akhter et al., "Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies," Frontiers in Plant Science, vol. 9, 2018.
[5]
J. Reimegård et al., "Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana," Nucleic Acids Research, 2017.
[6]
D. Edsgärd et al., "GeneiASE : Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information," Scientific Reports, vol. 6, 2016.
[7]
B. Sigurgeirsson, O. Emanuelsson och J. Lundeberg, "Analysis of stranded information using an automated procedure for strand specific RNA sequencing," BMC Genomics, vol. 15, no. 1, 2014.
[8]
Y. Song et al., "Nuclease-Assisted Suppression of Human DNA Background in Sepsis," PLOS ONE, vol. 9, no. 7, s. e103610, 2014.
[9]
B. Sigurgeirsson, O. Emanuelsson och J. Lundeberg, "Sequencing Degraded RNA Addressed by 3' Tag Counting," PLOS ONE, vol. 9, no. 3, s. e91851, 2014.
[10]
S. Wiegand et al., "The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals," Nucleic Acids Research, vol. 42, no. 5, s. 3330-3345, 2014.
[11]
D. Uddenberg et al., "Early Cone Setting in Picea abies acrocona Is Associated with Increased Transcriptional Activity of a MADS Box Transcription Factor," Plant Physiology, vol. 161, no. 2, s. 813-823, 2013.
[12]
V. Höiom et al., "Hereditary uveal melanoma : A report of a germline mutation in BAP1," Genes, Chromosomes and Cancer, vol. 52, no. 4, s. 378-384, 2013.
[13]
M. J. Iglesias et al., "Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response," PLOS ONE, vol. 7, no. 2, s. e32306, 2012.
[14]
D. Klevebring et al., "Analysis of transcript and protein overlap in a human osteosarcoma cell line," BMC Genomics, vol. 11, no. 1, s. 684, 2010.
[15]
D. Klevebring et al., "In-Depth Transcriptome Analysis Reveals Novel TARs and Prevalent Antisense Transcription in Human Cell Lines," PLOS ONE, vol. 5, no. 3, s. e9762, 2010.
[16]
B. Zybailov et al., "Sorting signals, N-terminal modifications and abundance of the chloroplast proteome," PLOS ONE, vol. 3, no. 4, 2008.
[17]
O. Emanuelsson et al., "Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.," Genome Research, vol. 17, no. 6, s. 886-897, 2007.
[18]
E. Birney et al., "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project," Nature, vol. 447, no. 7146, s. 799-816, 2007.
[19]
O. Emanuelsson et al., "Locating proteins in the cell using TargetP, SignalP and related tools.," Nature Protocols, vol. 2, no. 4, s. 953-971, 2007.
[20]
G. M. Euskirchen et al., "Mapping of transcription factor binding regions in mammalian cells by ChIP : comparison of array- and sequencing-based technologies.," Genome Research, vol. 17, no. 6, s. 898-909, 2007.
[21]
M. B. Gerstein et al., "What is a gene, post-ENCODE? : History and updated definition," Genome Research, vol. 17, no. 6, s. 669-681, 2007.
[22]
P. Bertone et al., "Design optimization methods for genomic DNA tiling arrays.," Genome Research, vol. 16, no. 2, s. 271-281, 2006.
[23]
T. E. Royce et al., "Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies," Methods in Enzymology, vol. 411, s. 282-311, 2006.
[24]
Q. Sun, O. Emanuelsson och K. J. van Wijk, "Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties," Plant Physiology, vol. 135, no. 2, s. 723-734, 2004.
[25]
E. J. White et al., "DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states," Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 51, s. 17771-17776, 2004.
[26]
O. Emanuelsson et al., "In silico prediction of the peroxisomal proteome in fungi, plants and animals.," Journal of Molecular Biology, vol. 330, no. 2, s. 443-456, 2003.
[27]
I. Westerlund, G. Von Heijne och O. Emanuelsson, "LumenP - a neural network predictor for protein localization in the thylakoid lumen," Protein Science, vol. 12, no. 10, s. 2360-2366, 2003.
[28]
J.-B. Peltier et al., "Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction," The Plant Cell, vol. 14, no. 1, s. 211-236, 2002.
[29]
O. Emanuelsson, "Predicting protein subcellular localisation from amino acid sequence information.," Briefings in Bioinformatics, vol. 3, no. 4, s. 361-76, 2002.
[30]
O. Emanuelsson, G. von Heijne och G. Schneider, "Analysis and prediction of mitochondrial targeting peptides.," Methods in Cell Biology, vol. 65, s. 175-187, 2001.
[31]
O. Emanuelsson och G. von Heijne, "Prediction of organellar targeting signals.," Biochimica et Biophysica Acta. Molecular Cell Research, vol. 1541, no. 1-2, s. 114-119, 2001.
[32]
O. Emanuelsson et al., "Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.," Journal of Molecular Biology, vol. 300, no. 4, s. 1005-1016, 2000.
[33]
O. Emanuelsson, H. Nielsen och G. von Heijne, "ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.," Protein Science, vol. 8, no. 5, s. 978-984, 1999.
Konferensbidrag
[34]
O. Emanuelsson, L. Arvestad och L. Käll, "Engagera och aktivera studenter med inspiration från konferenser : examination genom poster-presentation," i Proceedings 2014, 8:e Pedagogiska inspirationskonferensen 17 december 2014, 2014.
Icke refereegranskade
Övriga
[35]
K. J. Westrin, H. Zazzi och O. Emanuelsson, "An experimental application of the meta-heuristic Ant Colony System for low memory intense de novo transcriptome assembly of short reads," (Manuskript).
[36]
K. J. Westrin, W. W. Kretzschmar och O. Emanuelsson, "ClusTrast : a short read de novo transcript isoform assembler guided by clustered contigs," (Manuskript).
[37]
K. J. Westrin et al., "Improving the annotation of three reproductive gene families in Picea abies," (Manuskript).
[38]
D. Klevebring et al., "In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.," (Manuskript).
[39]
[40]
K. J. Westrin, W. W. Kretzschmar och O. Emanuelsson, "Short read de novo transcript isoform assembly guided by clustered contigs," (Manuskript).
Senaste synkning med DiVA:
2024-04-21 00:48:31