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List of works by Jan Gorodkin

454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

scientific article

A QUANTITATIVE STUDY OF PRUNING BY OPTIMAL BRAIN DAMAGE

scientific article (publication date: June 1993)

A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints

A mini-greedy algorithm for faster structural RNA stem-loop search.

scientific article published in January 2001

A splice-site variant in the lncRNA gene cosegregates in the large Volkmann cataract family

article

A study of alternative splicing in the pig

scientific article

Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

scientific article published on 2 December 2017

Analyses of pig genomes provide insight into porcine demography and evolution

scientific article

Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia

scientific article published on 16 March 2017

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

scientific article published on 18 July 2017

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

scientific article published on 4 September 2013

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

article published in 2018

CRISPRi screen for enhancing heterologous α-amylase yield in<i>Bacillus subtilis</i>

scientific article published on 23 December 2022

CRISPRroots: on- and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells

scientific article published on 01 February 2022

Comparative RNA Genomics

scientific article published in January 2018

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

scientific article

Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM.

scientific article published in September 2012

Comparing two K-category assignments by a K-category correlation coefficient

scientific article

Computational applications of DNA structural scales

scientific article published in January 1998

Concepts and introduction to RNA bioinformatics

scientific article published on January 2014

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

scientific article

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

scientific article published on 19 November 2018

De novo discovery of structured ncRNA motifs in genomic sequences

scientific article published on January 2014

De novo prediction of structured RNAs from genomic sequences

scientific article

Detection of RNA structures in porcine EST data and related mammals.

scientific article

Development of the Entorhinal Cortex Occurs via Parallel Lamination During Neurogenesis

scholarly article

Differential and coherent processing patterns from small RNAs

scientific article

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

scientific article

Discovering common stem-loop motifs in unaligned RNA sequences

scientific article published on May 2001

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

scientific article

Displaying the information contents of structural RNA alignments: the structure logos.

scientific article

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

scientific article

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

scientific article

Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism

scientific article published on 17 December 2019

Evolutionary rate variation and RNA secondary structure prediction.

scientific article published in July 2004

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

scientific article published on 18 March 2011

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

scientific article

Finding common sequence and structure motifs in a set of RNA sequences.

scientific article published in January 1997

Finding the most significant common sequence and structure motifs in a set of RNA sequences

scientific article

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

scientific article

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

scientific article published on August 4, 2011

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

scientific article

Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs

scientific article (publication date: 2015)

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

scientific article published in PLoS ONE

Global microRNA analysis of the NCI-60 cancer cell panel

scientific article published on 20 January 2011

Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a

scientific article published on 01 April 2020

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

scientific article published on 21 May 2010

IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs

scientific article published on 20 April 2018

Identification and characterization of novel conserved RNA structures in Drosophila

article published in 2018

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

scientific article published on 09 June 2007

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles

article

Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model.

scientific article

Linkage mapping of gene-associated SNPs to pig chromosome 11.

scientific article

Mapping and expression studies of the mir17-92 cluster on pig chromosome 11

scientific article

MatrixPlot: visualizing sequence constraints

scientific article published in September 1999

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

scientific article (publication date: 2013)

MicroRNA sequence motifs reveal asymmetry between the stem arms

scientific article published on 22 June 2006

Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures

article

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

scientific article (publication date: 23 July 2012)

Multiple structural alignment and clustering of RNA sequences

scientific article

Neural Networks and Cellular Automata Complexity ⬇️

scientific article (publication date: 1993)

Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation

scientific article published on 11 January 2021

Optimizing RNA structures by sequence extensions using RNAcop

scientific article

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

scientific article published on 18 November 2010

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

scientific article

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing

scientific article

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

scientific article

Principles and limitations of computational microRNA gene and target finding

scientific article published on May 2007

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

scientific article

Profiling of ribose methylations in RNA by high-throughput sequencing

scientific article

Protein distance constraints predicted by neural networks and probability density functions

scientific article published in November 1997

Protein-driven inference of miRNA-disease associations

scientific article (publication date: 21 November 2013)

Quality Assessment of Domesticated Animal Genome Assemblies

scientific article

RAIN: RNA-protein Association and Interaction Networks

scientific article published on 10 January 2017

RILogo: visualizing RNA-RNA interactions.

scientific article

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets

scientific article published on 20 January 2017

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

scientific article published on 24 August 2012

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

scientific article published on 28 October 2015

RNA interactions in the 5' region of the HIV-1 genome

scientific article (publication date: 13 February 2004)

RNA structural alignments, part I: Sankoff-based approaches for structural alignments

scientific article published in January 2014

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

scientific article published on 5 November 2018

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

scholarly article published in Nucleic Acids Research

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs

scientific article published on 27 February 2017

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced bySNPs.

scientific article published on 15 March 2013

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

scientific article

Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks

scientific article published in May 2001

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.

scientific article

SNP-finding in pig mitochondrial ESTs

SRPDB (Signal Recognition Particle Database).

scientific article

SRPDB: Signal Recognition Particle Database

scientific article published on January 2003

Semi-automated update and cleanup of structural RNA alignment databases.

scientific article published in July 2001

Semiautomated improvement of RNA alignments

scientific article

Sequence and expression analysis of gaps in human chromosome 20

scientific article (publication date: August 2012)

Sequence assembly.

scientific article published on 06 December 2008

Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers

scientific article published on 30 June 2015

Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.

scientific article

Special Issue: Computational Analysis of RNA Structure and Function

article

Structural profiles of human miRNA families from pairwise clustering

scientific article published on 4 December 2008

Structured RNAs and synteny regions in the pig genome

scientific article

TISSUES 2.0: an integrative web resource on mammalian tissue expression

scientific article published on 12 February 2018

TISSUES 2.0: an integrative web resource on mammalian tissue expression.

scientific article published on 16 March 2018

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

scientific article

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

scientific article published on 23 May 2011

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

scientific article published on 29 April 2013

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

scientific article published on 9 May 2017

The tedious task of finding homologous noncoding RNA genes

scientific article (publication date: December 2009)

The tmRDB and SRPDB resources

scientific article

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

scientific article

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

scientific article published on 8 January 2014

Transcriptomic landscape of lncRNAs in inflammatory bowel disease

scientific article published on 13 May 2015

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

scientific article

Translational co-regulation of a ligand and inhibitor by a conserved RNA element.

scientific article

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

scientific article

Universal distribution of saliencies for pruning in layered neural networks

scientific article published in October 1997

Using sequence motifs for enhanced neural network prediction of protein distance constraints

scientific article published in January 1999

Warburg Effect Metabolism Drives Neoplasia in a Drosophila Genetic Model of Epithelial Cancer

scientific article published on 04 October 2018

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA

scientific article published on 6 November 2018

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

scientific article

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences ⬇️

scientific article published on February 1, 2011

tmRDB (tmRNA database)

scientific article published on 01 January 2003

tmRDB (tmRNA database).

scientific article

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