MicroRNA discovery by similarity search to a database of RNA-seq profiles

by Pundhir, Sachin, Gorodkin, Jan
Published 2013

Differential and coherent processing patterns from small RNAs

by Pundhir, Sachin, Gorodkin, Jan
Published 2015

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

by Gorodkin, Jan, Hofacker, Ivo L.
Published 2011

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

by Havgaard, Jakob H, Torarinsson, Elfar, Gorodkin, Jan
Published 2007

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

by Wenzel, Anne, Akbaşli, Erdinç, Gorodkin, Jan
Published 2012

Emerging applications of read profiles towards the functional annotation of the genome

by Pundhir, Sachin, Poirazi, Panayiota, Gorodkin, Jan
Published 2015

The foldalign web server for pairwise structural RNA alignment and mutual motif search

by Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Published 2005

Fast local fragment chaining using sum-of-pair gap costs

by Otto, Christian, Hoffmann, Steve, Gorodkin, Jan, Stadler, Peter F
Published 2011

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

by Seemann, Stefan E., Menzel, Peter, Backofen, Rolf, Gorodkin, Jan
Published 2011

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

by Croft, Larry, Szklarczyk, Damian, Jensen, Lars Juhl, Gorodkin, Jan
Published 2012

Quality Assessment of Domesticated Animal Genome Assemblies

by Seemann, Stefan E., Anthon, Christian, Palasca, Oana, Gorodkin, Jan
Published 2016

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns

by Langenberger, David, Pundhir, Sachin, Ekstrøm, Claus T., Stadler, Peter F., Hoffmann, Steve, Gorodkin, Jan
Published 2012

EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues

by Scheibye-Alsing, Karsten, Cirera, Susanna, Gilchrist, Michael J, Fredholm, Merete, Gorodkin, Jan
Published 2007

Detection of RNA structures in porcine EST data and related mammals

by Seemann, Stefan E, Gilchrist, Michael J, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan
Published 2007

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

by Seemann, Stefan E, Sunkin, Susan M, Hawrylycz, Michael J, Ruzzo, Walter L, Gorodkin, Jan
Published 2012

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

by Sabarinathan, Radhakrishnan, Tafer, Hakim, Seemann, Stefan E., Hofacker, Ivo L., Stadler, Peter F., Gorodkin, Jan
Published 2013

Protein-driven inference of miRNA–disease associations

by Mørk, Søren, Pletscher-Frankild, Sune, Palleja Caro, Albert, Gorodkin, Jan, Jensen, Lars Juhl
Published 2014

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

by Theis, Corinna, Höner zu Siederdissen, Christian, Hofacker, Ivo L., Gorodkin, Jan
Published 2013

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites

by Sabarinathan, Radhakrishnan, Wenzel, Anne, Novotny, Peter, Tang, Xiaojia, Kalari, Krishna R., Gorodkin, Jan
Published 2014

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

by Sabarinathan, Radhakrishnan, Tafer, Hakim, Seemann, Stefan E, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan
Published 2013