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J. S. Pedersen · SciRah

Researcher profile · Semantic Scholar

J. S. Pedersen

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J. S. Pedersen — researcher profile on SciRah

h-index: 48
Works: 104
Citations: 18K

Most-cited papers

The UCSC Genome Browser Database: update 2006
A. Hinrichs, D. Karolchik, R. Baertsch, Galt P. Barber +23 more
2005Nucleic Acids Res.2,067 citations Open access
Semantic Scholar
A high-resolution map of human evolutionary constraint using 29 mammals
K. Lindblad-Toh, Manuel Garber, O. Zuk, Michael F. Lin +82 more
2011Nature909 citations Open access
Semantic Scholar
Ancient human genome sequence of an extinct Palaeo-Eskimo
Morten Rasmussen, Ying-Rui Li, S. Lindgreen, J. S. Pedersen +48 more
2010Nature826 citations Open access
Semantic Scholar
Human Accelerated Regions : plus rapide dans l ’ humain mais conservé ailleurs An RNA gene expressed during cortical development evolved rapidly in humans
K. Pollard, Sofie R. Salama, Nelle Lambert, M. Lambot +12 more
2014741 citations
Semantic Scholar
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
A. Stark, Michael F. Lin, P. Kheradpour, J. S. Pedersen +40 more
2007Nature661 citations Open access
Semantic Scholar
The UCSC Genome Browser Database: 2008 update
D. Karolchik, Robert M. Kuhn, R. Baertsch, Galt P. Barber +21 more
2007Nucleic Acids Res.565 citations Open access
Semantic Scholar
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
J. S. Pedersen, G. Bejerano, A. Siepel, K. Rosenbloom +5 more
2006PLoS Comput. Biol.556 citations Open access
Semantic Scholar
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
E. Rheinbay, M. Nielsen, F. Abascal, J. Wala +90 more
2020Nature526 citations Open access
Semantic Scholar
Forces Shaping the Fastest Evolving Regions in the Human Genome
K. Pollard, Sofie R. Salama, B. King, A. Kern +9 more
2006PLoS Genetics525 citations Open access
Semantic Scholar
A dual program for translation regulation in cellular proliferation and differentiation.
Hila Gingold, Disa Tehler, N. R. Christoffersen, M. Nielsen +19 more
2014Cell469 citations Open access
Semantic Scholar
Posttranscriptional Crossregulation between Drosha and DGCR8
Jin-Ju Han, J. S. Pedersen, S. C. Kwon, Cassandra D. Belair +6 more
2009Cell467 citations Open access
Semantic Scholar
Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery
T. Reinert, Lone V. Schøler, Rune Thomsen, Heidi Tobiasen +13 more
2015Gut452 citations Open access
Semantic Scholar
Genomic basis for RNA alterations in cancer
C. Calabrese, Natalie R. Davidson, Deniz C. Demircioglu, Nuno A. Fonseca +70 more
2020Nature357 citations Open access
Semantic Scholar
Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue
J. Hedegaard, K. Thorsen, M. Lund, Anne-Mette K. Hein +12 more
2014PLoS ONE354 citations Open access
Semantic Scholar
Cellular disposal of miR23b by RAB27-dependent exosome release is linked to acquisition of metastatic properties.
M. Ostenfeld, D. K. Jeppesen, J. R. Laurberg, A. Boysen +19 more
2014Cancer Research274 citations Open access
Semantic Scholar
Integrative pathway enrichment analysis of multivariate omics data
M. Paczkowska, J. Barenboim, N. Sintupisut, Natalie S. Fox +129 more
2020Nature Communications212 citations Open access
Semantic Scholar
SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization
N. Damas, Michela Marcatti, C. Côme, L. Christensen +13 more
2016Nature Communications201 citations Open access
Semantic Scholar
Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis
A. Taber, E. Christensen, P. Lamy, I. Nordentoft +10 more
2020Nature Communications197 citations Open access
Semantic Scholar
Structured RNAs in the ENCODE selected regions of the human genome.
Stefan Washietl, J. S. Pedersen, J. Korbel, Claudia Stocsits +20 more
2007Genome Research195 citations Open access
Semantic Scholar
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
J. S. Pedersen, Eivind Valen, A. Velazquez, B. Parker +17 more
2014Genome Research183 citations Open access
Semantic Scholar
Editing modifies the GABAA receptor subunit α3
J. Ohlson, J. S. Pedersen, D. Haussler, Marie Öhman
2007181 citations Open access
Semantic Scholar
SNHG16 is regulated by the Wnt pathway in colorectal cancer and affects genes involved in lipid metabolism
L. Christensen, Kirsten True, M. P. Hamilton, M. Nielsen +14 more
2016Molecular Oncology177 citations Open access
Semantic Scholar
The lncRNA MIR31HG regulates p16INK4A expression to modulate senescence
Marta Montes, M. Nielsen, Giulia Maglieri, A. Jacobsen +7 more
2015Nature Communications174 citations Open access
Semantic Scholar
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Joana Carlevaro-Fita, Andrés Lanzós, L. Feuerbach, Chen Hong +3 more
2020Communications Biology159 citations Open access
Semantic Scholar
Mutational context and diverse clonal development in early and late bladder cancer.
I. Nordentoft, P. Lamy, K. Birkenkamp-Demtröder, K. Shumansky +15 more
2014Cell Reports148 citations Open access
Semantic Scholar
Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences
Sushant Kumar, J. Warrell, Shan-Tao Li, Patrick D. McGillivray +15 more
2020Cell130 citations Open access
Semantic Scholar
Widespread DNA hypomethylation and differential gene expression in Turner syndrome
Christian Trolle, M. Nielsen, A. Skakkebæk, P. Lamy +6 more
2016Scientific Reports130 citations Open access
Semantic Scholar
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
T. L. H. Okholm, S. Sathe, Samuel S. Park, A. Kamstrup +11 more
2020Genome Medicine126 citations Open access
Semantic Scholar
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.
B. Parker, I. Moltke, Adam Roth, Stefan Washietl +4 more
2011Genome Research113 citations Open access
Semantic Scholar
Editing modifies the GABA(A) receptor subunit alpha3.
J. Ohlson, J. S. Pedersen, D. Haussler, M. Ohman
2007RNA: A publication of the RNA Society109 citations
Semantic Scholar
Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer
Trine Line Hauge Okholm, M. Nielsen, M. P. Hamilton, L. Christensen +6 more
2017npj Genomic Medicine106 citations Open access
Semantic Scholar
Pathway and network analysis of more than 2500 whole cancer genomes
Matthew A. Reyna, David Haan, M. Paczkowska, L. Verbeke +22 more
2020Nature Communications105 citations Open access
Semantic Scholar
Evolutionarily conserved elements in vertebrate , insect , worm , and yeast genomes
A. Siepel, G. Bejerano, J. S. Pedersen, A. Hinrichs +12 more
2015103 citations
Semantic Scholar
DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
A. Skakkebæk, M. Nielsen, Christian Trolle, S. Vang +9 more
2018Scientific Reports95 citations Open access
Semantic Scholar
The UCSC genome browser database: update 2007
Robert M. Kuhn, D. Karolchik, A. Zweig, Heather Trumbower +21 more
2006Nucleic Acids Res.94 citations Open access
Semantic Scholar
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.
Michael F. Lin, P. Kheradpour, Stefan Washietl, B. Parker +2 more
2011Genome Research92 citations Open access
Semantic Scholar
Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma.
P. Lamy, I. Nordentoft, K. Birkenkamp-Demtröder, Mathilde Borg Houlberg Thomsen +9 more
2016Cancer Research90 citations Open access
Semantic Scholar
Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
M. Jager, F. Blokzijl, E. Kuijk, Johanna Bertl +10 more
2019Genome Research83 citations Open access
Semantic Scholar
miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells
M. Rasmussen, Iben Lyskjær, R. Jersie-Christensen, L. Tarpgaard +9 more
2016Nature Communications81 citations Open access
Semantic Scholar
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis
K. Thorsen, T. Schepeler, Bodil Øster, M. Rasmussen +13 more
2011BMC Genomics77 citations Open access
Semantic Scholar
Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival
H. Hornshøj, M. Nielsen, Nicholas A. Sinnott-Armstrong, Michal P. Switnicki +7 more
2017npj Genomic Medicine61 citations Open access
Semantic Scholar
The whole-genome panorama of cancer drivers
R. Sabarinathan, O. Pich, I. Martincorena, C. Rubio-Perez +23 more
2017bioRxiv59 citations Open access
Semantic Scholar
Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients
E. Christensen, I. Nordentoft, S. Vang, K. Birkenkamp-Demtröder +4 more
2018Scientific Reports56 citations Open access
Semantic Scholar
Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX
Kristian Hanghøj, Andaine Seguin-Orlando, M. Schubert, Tobias Madsen +3 more
2016Molecular biology and evolution54 citations Open access
Semantic Scholar
Identification of expressed and conserved human noncoding RNAs
M. Nielsen, Disa Tehler, S. Vang, F. Sudzina +5 more
2014RNA: A publication of the RNA Society50 citations Open access
Semantic Scholar
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
E. Rheinbay, M. Nielsen, F. Abascal, Grace Tiao +69 more
2017bioRxiv46 citations Open access
Semantic Scholar
The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer
E. B. Hansen, Jacob Fredsøe, Trine Line Hauge Okholm, B. Ulhøi +9 more
2022Genome Medicine45 citations Open access
Semantic Scholar
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
Trine Line Hauge Okholm, S. Sathe, Samuel S. Park, A. Kamstrup +11 more
2020Genome Medicine39 citations Open access
Semantic Scholar
Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate
Malene Juul, Johanna Bertl, Qian-Yun Guo, M. Nielsen +5 more
2017eLife38 citations Open access
Semantic Scholar
miRNA activity inferred from single cell mRNA expression
M. Nielsen, J. S. Pedersen
2020Scientific Reports35 citations Open access
Semantic Scholar

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M. Nielsen×19
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S. Vang×15
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T. Ørntoft×13
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D. Haussler×10
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I. Nordentoft×9

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Manolis Kellis×7

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Malene Juul — researcher profile on SciRah

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K. Rosenbloom×6

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K. Rosenbloom — researcher profile on SciRah