Structural profiles of human miRNA families from pairwise clustering (2009)
Kaczkowski, Bogumil, Torarinsson, Elfar, Reiche, Kristin, Havgaard, Jakob Hull, Stadler, Peter F., Gorodkin, Jan
MicroRNAs (miRNAs) are a group of small, ∼21 nt long, riboreg-ulators inhibiting gene expression at a post-transcriptional level. Their most distinctive structural feature is the foldback hairpin...
Principles and Limitations of Computational MicroRNA Gene (2008)
Target Finding, Morten Lindow, Jan Gorodkin
In 2001 there were four PubMed entries matching the word ‘‘microRNA’ ’ (miRNA). Interestingly, this number has now far exceeded 1300 and is still rapidly increasing. This more than anything...
Sequence Analysis Multiple structural alignment and clustering of RNA sequences (2008)
Elfar Torarinsson, Jakob H. Havgaard, Jan Gorodkin
Motivation: An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common...
Ebbe S. Andersen, Allan Lind-thomsen, Bjarne Knudsen, Susie E. Kristensen, Jakob H. Havgaard, Elfar Torarinsson, ...
Running title: Semi-automated RNA sequence editing
Jan Gorodkin, Rune B. Lyngsø, Gary D. Stormo
When a set of coregulated genes share a common structural RNA motif, e.g. a hairpin, most motif search approaches fail to locate the covarying but structurally conserved motif. There do exist methods...
Structural profiles of miRNA families from pairwise clustering (2008)
Kaczkowski, Bogumil, Torarinsson, Elfar, Reiche, Kristin, Havgaard, Jakob Hull, Stadler, Peter F., Gorodkin, Jan
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions (2008)
Torarinsson, Elfar, Yao, Zizhen, Wiklund, Eric D., Bramsen, Jesper B., Hansen, Claus, Kjems, Jørgen, ...
Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA...
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments (2008)
Seemann, Stefan E., Gorodkin, Jan, Backofen, Rolf
Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both....
Bogumił Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin, ...
Structural profiles of human miRNA families from pairwise clustering
Unifying evolutionary and thermodynamic (2008)
Stefan E. Seemann, Jan Gorodkin, Rolf Backofen
information for RNA folding of multiple alignments
Semiautomated improvement of RNA alignments (2007)
Andersen, Ebbe S., Lind-Thomsen, Allan, Knudsen, Bjarne, Kristensen, Susie E., Havgaard, Jakob H., Torarinsson, Elfar, ...
We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its...
Scheibye-Alsing, Karsten, Cirera, Susanna, Gilchrist, Michael J, Fredholm, Merete, Gorodkin, Jan
Abstract Background The mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell. Though the mitochondria have been extensively...
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix (2007)
Jakob H. Havgaard, Elfar Torarinsson, Jan Gorodkin
It has become clear that noncoding RNAs (ncRNA) play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist...
Detection of RNA structures in porcine EST data and related mammals (2007)
Seemann, Stefan E, Gilchrist, Michael J, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan
Abstract Background Non-coding RNAs (ncRNAs) are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and...
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix (2007)
Jakob Hull Havgaard, Elfar Torarinsson, Jan Gorodkin
It has become clear that non-coding RNAs (ncRNA) play important roles in the cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There...
Gorodkin, Jan, Cirera, Susanna, Hedegaard, Jakob, Gilchrist, Michael J, Panitz, Frank, Jørgensen, Claus, ...
Background Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs),...
Elfar Torarinsson, Jakob H. Havgaard, Jan Gorodkin
Motivation: An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common...
2007 Gorodkin et Volume al. 8, Issue 4, Article R45 Open Access (2007)
Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, ...
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Detection of RNA structures in porcine EST data and related mammals. BMC Genomics 8:316 (2007)
Bmc Genomics, Stefan E Seemann, Michael J Gilchrist, Ivo L Hofacker, Peter F Stadler, Jan Gorodkin, ...
Research article
Detection of RNA structures in porcine EST data and related mammals (2007)
Seemann, Stefan E., Gilchrist, Michael J., Hofacker, Ivo L., Stadler, Peter F., Gorodkin, Jan
Multiple structural alignment and clustering of RNA sequences (2007)
Torarinsson, Elfar, Havgaard, Jakob H., Gorodkin, Jan
Motivation: An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common...
Torarinsson, Elfar, Sawera, Milena, Havgaard, Jakob H., Fredholm, Merete, Gorodkin, Jan
Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are...
Torarinsson, Elfar, Sawera, Milena, Havgaard, Jakob H., Fredholm, Merete, Gorodkin, Jan
Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are...
The tmRDB and SRPDB resources (2006)
Andersen, Ebbe Sloth, Rosenblad, Magnus Alm, Larsen, Niels, Westergaard, Jesper Cairo, Burks, Jody, Wower, Iwona K., ...
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located...
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing (2005)
Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Stærfeldt, Hans-Henrik, ...
Abstract Background Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its...
The tmRDB and SRPDB resources (2005)
Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, ...
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing (2005)
Bmc Genomics, Rasmus Wernersson, Mikkel H Schierup, Frank G Jørgensen, Jan Gorodkin, Frank Panitz, ...
Research article
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search (2005)
Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently...
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% (2005)
Havgaard, Jakob Hull, Lyngsø, Rune B., Stormo, Gary D., Gorodkin, Jan
Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in...
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% (2005)
Havgaard, Jakob Hull, Lyngsø, Rune, Stormo, Gary D., Gorodkin, Jan
Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in todays gene finding as these often are conserved in structure rather than in...
SRPDB: Signal Recognition Particle Database (2003)
Rosenblad, Magnus Alm, Gorodkin, Jan, Knudsen, Bjarne, Zwieb, Christian, Samuelsson, Tore
The Signal Recognition Particle Database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html assists in the better understanding of the...
Zwieb, Christian, Gorodkin, Jan, Knudsen, Bjarne, Burks, Jody, Wower, Jacek
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located...
The Signal Recognition Particle Database (SRPDB) (2002)
Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson
html assists in the better understanding of the structure and function of the signal recognition particle (SRP), a ribonucleoprotein complex that recognizes signal sequences as they emerge from the...
SRPDB (Signal Recognition Particle Database) (2001)
Gorodkin, Jan, Knudsen, Bjarne, Zwieb, Christian, Samuelsson, Tore
Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB)...
Knudsen, Bjarne, Wower, Jacek, Zwieb, Christian, Gorodkin, Jan
The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL...
Discovering common stem-loop motifs in unaligned RNA sequences (2001)
Gorodkin, Jan, Stricklin, Shawn L., Stormo, Gary D.
Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are...
Using sequence motifs for enhanced neural network prediction of protein distance constraints (1999)
Jan Gorodkin, Ole Lund, Claus A. Andersen, Søren Brunak
Correlations between sequence separation (in residues) and distance (in Angstrom) of any pair of amino acids in polypeptide chains are investigated. For each sequence separation we define a distance...
Computational applications of DNA structural scales (1998)
Pierre Baldi, Yves Chauvin, Søren Brunak, Jan Gorodkin, Anders Gorm Pedersen
We study from a computational standpoint several different physical scales associated with structural features of DNA sequences, including dinucleotide scales such as base stacking energy and...
Jan Gorodkin, Bodil Søgaard, Hanne Bay, Hans Doll, Per Kølster, Søren Brunak
High performance liquid chromatography (HPLC) spectra were analyzed by computer in order to find correlations between secondary metabolites and growth conditions of six varieties of barley. Five of...
Knudsen, Bjarne, Wower, Jacek, Zwieb, Christian, Gorodkin, Jan
The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL...
SRPDB (Signal Recognition Particle Database)
Gorodkin, Jan, Knudsen, Bjarne, Zwieb, Christian, Samuelsson, Tore
Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB)...
Discovering common stem–loop motifs in unaligned RNA sequences
Gorodkin, Jan, Stricklin, Shawn L., Stormo, Gary D.
Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are...
Zwieb, Christian, Gorodkin, Jan, Knudsen, Bjarne, Burks, Jody, Wower, Jacek
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located...
SRPDB: Signal Recognition Particle Database
Rosenblad, Magnus Alm, Gorodkin, Jan, Knudsen, Bjarne, Zwieb, Christian, Samuelsson, Tore
The Signal Recognition Particle Database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html assists in the better understanding of the...
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Stærfeldt, Hans-Henrik, ...
The foldalign web server for pairwise structural RNA alignment and mutual motif search
Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently...
Andersen, Ebbe Sloth, Rosenblad, Magnus Alm, Larsen, Niels, Westergaard, Jesper Cairo, Burks, Jody, Wower, Iwona K., ...
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL with mirror sites located at Auburn University, Auburn, Alabama () and...
Knudsen, Bjarne, Wower, Jacek, Zwieb, Christian, Gorodkin, Jan
The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL...
SRPDB (Signal Recognition Particle Database)
Gorodkin, Jan, Knudsen, Bjarne, Zwieb, Christian, Samuelsson, Tore
Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB)...
Discovering common stem–loop motifs in unaligned RNA sequences
Gorodkin, Jan, Stricklin, Shawn L., Stormo, Gary D.
Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are...
Zwieb, Christian, Gorodkin, Jan, Knudsen, Bjarne, Burks, Jody, Wower, Jacek
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located...
SRPDB: Signal Recognition Particle Database
Rosenblad, Magnus Alm, Gorodkin, Jan, Knudsen, Bjarne, Zwieb, Christian, Samuelsson, Tore
The Signal Recognition Particle Database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html assists in the better understanding of the...
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson, Rasmus, Schierup, Mikkel H, Jørgensen, Frank G, Gorodkin, Jan, Panitz, Frank, Stærfeldt, Hans-Henrik, ...
The foldalign web server for pairwise structural RNA alignment and mutual motif search
Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently...
Andersen, Ebbe Sloth, Rosenblad, Magnus Alm, Larsen, Niels, Westergaard, Jesper Cairo, Burks, Jody, Wower, Iwona K., ...
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL with mirror sites located at Auburn University, Auburn, Alabama () and...
Torarinsson, Elfar, Sawera, Milena, Havgaard, Jakob H., Fredholm, Merete, Gorodkin, Jan
Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are...
Gorodkin, Jan, Cirera, Susanna, Hedegaard, Jakob, Gilchrist, Michael J, Panitz, Frank, Jørgensen, Claus, ...
A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine...
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
Havgaard, Jakob H, Torarinsson, Elfar, Gorodkin, Jan
It has become clear that noncoding RNAs (ncRNA) play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist...
Detection of RNA structures in porcine EST data and related mammals
Seemann, Stefan E, Gilchrist, Michael J, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan
Semiautomated improvement of RNA alignments
Andersen, Ebbe S., Lind-Thomsen, Allan, Knudsen, Bjarne, Kristensen, Susie E., Havgaard, Jakob H., Torarinsson, Elfar, ...
We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its...
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
Torarinsson, Elfar, Yao, Zizhen, Wiklund, Eric D., Bramsen, Jesper B., Hansen, Claus, Kjems, Jørgen, ...
Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA...
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
Seemann, Stefan E., Gorodkin, Jan, Backofen, Rolf
Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both....