Ernst Stefan Seemann

Publikation

Publikationer pr. år 2007 2015 2017 2018 2019 2019

• 26 Tidsskriftartikel
• 6 Konferenceabstrakt til konference
• 1 Ph.d.-afhandling
• 1 Paper

Publikationer pr. år

Publikationer pr. år

Søgeresultater

• 2019

  Production of stellate cells from induced pluripotent stem cells to study Alzheimer's disease pathology

  Mogus, L., Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Handfield, L.-F., Asenjo Martinez, A., Seemann, E. S., Witter, M., Khodosevich, K., Gorodkin, J., Hemberg, M., Pers, T. H. & Hall, V. J., 2019. 1 s.

  Publikation: Konferencebidrag › Konferenceabstrakt til konference › Formidling

• Proteomic profiling of the thrombin-activated canine platelet secretome (CAPS)

  Cremer, S. E., Catalfamo, J. L., Goggs, R., Seemann, S. E., Kristensen, A. T. & Brooks, M. B., 1 nov. 2019, I: PLoS ONE. 14, 11, e0224891.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Thrombin 100%
  • Secretome 100%
  • Proteomics 100%
  • Platelet 100%
  • Canine 100%
  2 Citationer (Scopus)

  3 Downloads (Pure)

• RNAcentral: a hub of information for non-coding RNA sequences

  Gorodkin, J., Seemann, E. S. & The RNAcentral Constortium , 2019, I: Nucleic Acids Research. 47, D1, s. D221–D229

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Non-coding RNA (ncRNA) 100%
  • RNA Sequence 100%
  • Non-Coding RNA 100%
  • Genomics 50%
  • Gene Ontology 25%
  50 Citationer (Scopus)

  44 Downloads (Pure)

• Sandwich cortial lamination and single-cell analysis decodes the developing spatial processing system

  Liu, Y., Bergmann, T. B., Lee, J., Pfisterer, U. G., Handfield, L.-F., Mori, Y., Asenjo Martinez, A., Lisa Vargas, I., Seemann, E. S., Lee, J. T. H., Patikis, N., Peralvo Vidal, J. M., Pihl, M., Kornum, B. R., Thomsen, P. D., Hyttel, P., Witter, M., Khodosevich, K., Gorodkin, J. & Hemberg, M. & 2 flere, Pers, T. H. & Hall, V. J., 2019. 45 s.

  Publikation: Konferencebidrag › Paper › Formidling

• The developing Entorhinal Cortex – a cellular map

  Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Asenjo Martinez, A., Seemann, E. S., Pihl, M., Thomsen, P. D., Hyttel, P., witter, M., Khodosevich, K., Gorodkin, J., Pers, T. H. & Hall, V. J., 2019.

  Publikation: Konferencebidrag › Konferenceabstrakt til konference › Forskning

• The developing Entorhinal cortex - a cellular map

  Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Handfield, L.-F., Asenjo Martinez, A., Seemann, E. S., Witter, M., Khodosevich, K., Gorodkin, J., Hemberg, M., Pers, T. H. & Hall, V. J., 25 nov. 2019. 1 s.

  Publikation: Konferencebidrag › Konferenceabstrakt til konference › Formidling

• Uncovering the anatomical and molecular landscape of the starting point of Alzheimer’s disease in the brain

  Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Asenjo Martinez, A., Seemann, E. S., Pihl, M., Thomsen, P. D., Hyttel, P., witter, M., Khodosevich, K., Gorodkin, J., Pers, T. H. & Hall, V. J., 2019.

  Publikation: Konferencebidrag › Konferenceabstrakt til konference › Forskning
• 2018

  Identification and characterization of novel conserved RNA structures in Drosophila

  Kirsch, R., Seemann, S. E., Ruzzo, W. L., Cohen, S. M., Stadler, P. F. & Gorodkin, J., 2018, I: BMC Genomics. 19, 20 s., 899.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Drosophilidae 100%
  • Conserved RNA Structure 100%
  • RNA Structure 100%
  • Non-coding RNA (ncRNA) 41%
  • RNA 33%
  3 Citationer (Scopus)

  45 Downloads (Pure)

• Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures

  Sabarinathan, R., Anthon, C., Gorodkin, J. & Seemann, S. E., 4 dec. 2018, I: Genes. 9, 12, 17 s., 604.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Sequence Alignment 100%
  • RNA Structure 100%
  • Boundary Definition 100%
  • RNA 80%
  • Non-Coding RNA 60%
  1 Citationer (Scopus)

  35 Downloads (Pure)

• The developmental neurogenic niche of the Entorhinal cortex revealed by single-cell transcriptomics.

  Bergmann, T. B., Liu, Y., Lee, J., Peralvo Vidal, J. M., Mori, Y., Seemann, E. S., Pihl, M., Thomsen, P. D., Hyttel, P., witter, M., Gorodkin, J., Hall, V. J. & Pers, T. H., 2018.

  Publikation: Konferencebidrag › Konferenceabstrakt til konference › Forskning

• Uncovering the anatomical and molecular landscape of the developing entorhinal cortex.

  Liu, Y., Bergmann, T. B., Peralvo Vidal, J. M., Lee, J., Mori, Y., Seemann, E. S., Pihl, M., Thomsen, P. D., Gorodkin, J., Hyttel, P., Pers, T. H., witter, M. & Hall, V. J., 2018.

  Publikation: Konferencebidrag › Konferenceabstrakt til konference › Forskning
• 2017

  Associating transcription factors and conserved RNA structures with gene regulation in the human brain

  Hecker, N., Seemann, S. E., Silahtaroglu, A., Ruzzo, W. L. & Gorodkin, J., 2017, I: Scientific Reports. 7, 1, 16 s., 5776.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Transcription Factor 100%
  • Gene Control 100%
  • RNA Structure 100%
  • Gene Expression 100%
  • Protein Secondary Structure 75%
  6 Citationer (Scopus)

  76 Downloads (Pure)

• DotAligner: Identification and clustering of RNA structure motifs

  Smith, M. A., Seemann, S. E., Quek, X. C. & Mattick, J. S., dec. 2017, I: Genome Biology. 18, 1, 12 s., 244.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA Motif 100%
  • RNA Structure 100%
  • RNA-binding Protein 50%
  • Co-immunoprecipitation (co-IP) 50%
  • Structure Motifs 50%
  8 Citationer (Scopus)

  48 Downloads (Pure)

• RNAscClust: Clustering RNA sequences using structure conservation and graph based motifs

  Miladi, M., Junge, A., Costa, F., Seemann, S. E., Havgaard, J. H., Gorodkin, J. & Backofen, R., 2017, I: Bioinformatics. 33, 14, s. 2089-2096 8 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA Sequencing (RNA-seq) 100%
  • Structure Diagram 100%
  • Structured RNA 100%
  • Structure Conservation 100%
  • Graph-based 100%
  20 Citationer (Scopus)

  56 Downloads (Pure)

• The identification and functional annotation of RNA structures conserved in vertebrates

  Seemann, E. S., Mirza, A. H., Hansen, C., Bang-Berthelsen, C. H., Garde, C., Christensen-Dalsgaard, M., Torarinsson, E., Yao, Z., Workman, C. T., Pociot, F., Nielsen, H., Tommerup, N., Ruzzo, W. L. & Gorodkin, J., aug. 2017, I: Genome Research. 27, s. 1371-1383 14 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA Structure 100%
  • RNA 33%
  • RNA Stabilization 14%
  • Identity Content 14%
  • Shared Structure 14%
  37 Citationer (Scopus)

  69 Downloads (Pure)
• 2016

  Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells: [Plus] Corrigendum

  Hölzer, M., Krähling, V., Amman, F., Barth, E., Bernhart, S. H., Carmelo, V. A. O., Collatz, M., Doose, G., Eggenhofer, F., Ewald, J., Fallmann, J., Feldhahn, L. M., Fricke, M., Gebauer, J., Gruber, A. J., Hufsky, F., Indrischek, H., Kanton, S., Linde, J. & Mostajo, N. & 19 flere, Ochsenreiter, R., Riege, K., Rivarola-Duarte, L., Sahyoun, A. H., Saunders, S. J., Seemann, E. S., Tanzer, A., Vogel, B., Wehner, S., Wolfinger, M. T., Backofen, R., Gorodkin, J., Grosse, I., Hofacker, I., Hoffmann, S., Kaleta, C., Stadler, P. F., Becker, S. & Marz, M., 7 okt. 2016, I: Scientific Reports. 6, 16 s., 34589.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  26 Citationer (Scopus)

  106 Downloads (Pure)

• SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization

  Damas, N. D., Marcatti, M., Côme, C., Christensen, L.-L., Nielsen, M. M., Baumgartner, R., Gylling, H. M., Maglieri, G., Rundsten, C. F., Seemann, E. S., Rapin, N., Thézenas, S., Vang, S., Ørntoft, T., Andersen, C. L., Pedersen, J. S. & Lund, A. H., 22 dec. 2016, I: Nature Communications. 7, 14 s., 13875.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Cancer Cell 100%
  • Programmed Cell Death 100%
  • Messenger RNA 100%
  • Long Non-Coding RNA 100%
  • Cell Survival 100%
  122 Citationer (Scopus)

  169 Downloads (Pure)
• 2015

  Emerging tools for RNA structure analysis in polymorphic data

  Radhakrishnan, S., Seemann, E. S. & Gorodkin, J., 2015, I: Biozoom. 2, s. 10-13 4 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Formidling

• Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

  Sükösd, Z., Andersen, E. S., Seemann, E. S., Jensen, M. K., Hansen, M., Gorodkin, J. & Kjems, J., 2 dec. 2015, I: Nucleic Acids Research. 43, 21, s. 10168-79 12 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • HIV-1 Genome 100%
  • RNA Structure Prediction 100%
  • Human Immunodeficiency Virus 1 100%
  • Structure Prediction 100%
  • RNA Structure 100%
  13 Citationer (Scopus)

  66 Downloads (Pure)

• Optimizing RNA structures by sequence extensions using RNAcop

  Hecker, N., Christensen-Dalsgaard, M., Seemann, E. S., Havgaard, J. H., Stadler, P. F., Hofacker, I. L., Nielsen, H. & Gorodkin, J., 30 sep. 2015, I: Nucleic Acids Research. 43, 17, s. 8135-8145 11 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA 100%
  • DNA Flanking Region 100%
  • RNA Structure 100%
  • Computational Analysis 100%
  • Structure Prediction 100%
  3 Citationer (Scopus)

  327 Downloads (Pure)

• Quality Assessment of Domesticated Animal Genome Assemblies

  Seemann, S. E., Anthon, C., Palasca, O. & Gorodkin, J., 1 jan. 2015, I: Bioinformatics and Biology Insights. 9, Suppl 4, s. 49-58 10 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Domestic Animal 100%
  • Genomics 66%
  • Genotyping 33%
  • High Throughput Sequencing 33%
  • Transcriptome 33%
  8 Citationer (Scopus)

  56 Downloads (Pure)

• Transcriptomic landscape of lncRNAs in inflammatory bowel disease

  Mirza, A. H., Bang-Berthelsen, C. H., Seemann, E. S., Pan, X., Frederiksen, K. S., Vilien, M., Gorodkin, J. & Pociot, F., 14 dec. 2015, I: Genome Medicine. 7, 22 s., 39.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Inflammatory Bowel Disease 100%
  • Transcriptomics 100%
  • Long Non-Coding RNA 100%
  • Transcriptomic Landscape 100%
  • Ulcerative Colitis 85%
  100 Citationer (Scopus)

  774 Downloads (Pure)
• 2014

  Structured RNAs and synteny regions in the pig genome

  Anthon, C., Tafer, H., Havgaard, J. H., Thomsen, B., Hedegaard, J., Seemann, E. S., Pundhir, S., Kehr, S., Bartschat, S., Nielsen, M., Nielsen, R. O., Fredholm, M., Stadler, P. F. & Gorodkin, J., 10 jun. 2014, I: BMC Genomics. 15, 27 s., 459.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Structured RNA 100%
  • Non-coding RNA (ncRNA) 100%
  • Synteny 100%
  • Pig Genome 100%
  • RNA 100%
  16 Citationer (Scopus)

  913 Downloads (Pure)
• 2013

  RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs: efficient detection of local RNA secondary structure changes induced by SNPs

  Radhakrishnan, S., Tafer, H., Seemann, E. S., Hofacker, I. L., Stadler, P. F. & Gorodkin, J., 2013, I: Human Mutation. 34, 4, s. 546-556 11 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA 100%
  • Single Nucleotide Polymorphism 100%
  • Protein Secondary Structure 100%
  • Efficient Detection 100%
  • Secondary Structure Changes 100%
  72 Citationer (Scopus)

• The RNAsnp web server: predicting SNP effects on local RNA secondary structure

  Radhakrishnan, S., Tafer, H., Seemann, E. S., Hofacker, I. L., Stadler, P. F. & Gorodkin, J., jul. 2013, I: Nucleic Acids Research. 41, s. W475-W479 5 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA Secondary Structure 100%
  • Web Server 100%
  • RNA 100%
  • Single-Nucleotide Polymorphism 100%
  • Protein Secondary Structure 100%
  76 Citationer (Scopus)
• 2012

  RILogo: visualising RNA-RNA interactions

  Menzel, K. P., Seemann, E. S. & Gorodkin, J., okt. 2012, I: Bioinformatics. 28, 19, s. 2523-2526 4 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Mutual Information 100%
  • RNA Molecules 100%
  • RNA-RNA Interaction 100%
  • RNA 100%
  • Information-based Measures 50%
  10 Citationer (Scopus)

• Sequence and expression analysis of gaps in human chromosome 20

  Minocherhomji, S., Seemann, S., Mang, Y., Elschich, Z., Bak, M., Hansen, C., Papadopoulos, N., Josefsen, K., Nielsen, H., Gorodkin, J., Tommerup, N. & Silahtaroglu, A., aug. 2012, I: Nucleic Acids Research. 40, 14, s. 6660-6672 13 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Chromosome 20 100%
  • Sequence Analysis 100%
  • Human Chromosomes 100%
  • Expression Analysis 100%
  • Chromosome 20 (Human) 100%
  4 Citationer (Scopus)

  46 Downloads (Pure)

• Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

  Seemann, E. S., Sunkin, S. M., Hawrylycz, M. J., Ruzzo, W. L. & Gorodkin, J., 31 maj 2012, I: BMC Genomics. 13, 1, s. 214-227 14 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Mouse Brain 100%
  • In Silico 100%
  • RNA Structure 100%
  • 3′-untranslated Region (3′-UTR) 60%
  • RNA 60%
  9 Citationer (Scopus)
• 2011

  PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

  Seemann, E. S., Richter, A. S., Gesell, T., Backofen, R. & Gorodkin, J., jan. 2011, I: Bioinformatics. 27, 2, s. 211-219 9 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Conserved Interactions 100%
  • Covariance 100%
  • Bacterial RNA 50%
  • Non-Coding RNA 33%
  • Curated Database 25%
  43 Citationer (Scopus)

• The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

  Seemann, E. S., Menzel, K. P., Backofen, R. & Gorodkin, J., 1 jul. 2011, I: Nucleic Acids Research. 39, Suppl. 2, s. W107-W111 5 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  20 Citationer (Scopus)
• 2010

  Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

  Seemann, E. S., Richter, A. S., Gorodkin, J. & Backofen, R., 21 maj 2010, I: Algorithms for Molecular Biology. 5, 22, 13 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  14 Citationer (Scopus)

• Prediction of structured non-coding RNAs, RNA-RNA interactions and their (co)-expression in the brain

  Seemann, E. S., 2010, Department of Basic Animal and Veterinary Sciences, University of Copenhagen. 195 s.

  Publikation: Bog/antologi/afhandling/rapport › Ph.d.-afhandling
• 2008

  Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

  Seemann, E. S., Gorodkin, J. & Backofen, R., 2008, I: Nucleic Acids Research. 36, 20, s. 6355-6362 8 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • RNA Folding 100%
  • Evolution 100%
  • RNA Sequence 100%
  • RNA 50%
  • Rfam 50%
  59 Citationer (Scopus)

  551 Downloads (Pure)
• 2007

  Detection of RNA structures in porcine EST data and related mammals

  Seemann, E. S., Gilchrist, M. J., Hofacker, I. L., Stadler, P. F. & Gorodkin, J., 2007, I: BMC Genomics. 8, 316, 17 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Trans-Acting Factor 100%
  • Existing Knowledge 49%
  • Ravenna 49%
  • Developmental Brain 49%
  • Structure Similarity 49%
  13 Citationer (Scopus)

  1051 Downloads (Pure)