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List of works by Rolf Backofen

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation

scientific article

A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources

scientific article

A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii

scientific article published on 23 January 2014

A dynamic programming approach for finding common patterns in RNAs.

scientific article published in January 2007

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

scientific article published on 27 May 2020

A graph kernel approach for alignment-free domain–peptide interaction prediction with an application to human SH3 domains ⬇️

scientific article published on July 1, 2013

A multiple-feature framework for modelling and predicting transcription factor binding sites.

scientific article published on 19 May 2005

A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

scientific article published on 24 October 2017

A pan-cancer analysis of synonymous mutations

scientific article published on 12 June 2019

A partition function algorithm for interacting nucleic acid strands

scientific article

A phase-field-crystal approach to critical nuclei

scientific article published on 20 August 2010

ABERRANT SPLICING OF A BRAIN-ENRICHED ALTERNATIVE EXON ELIMINATES TUMOR SUPPRESSOR FUNCTION AND PROMOTES ONCOGENE FUNCTION DURING BRAIN TUMORIGENESIS.

scientific article published in July 2014

Abstract folding space analysis based on helices

scientific article published on 25 October 2012

Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?

scientific article published on July 2012

Accurate prediction of NAGNAG alternative splicing

scientific article published on 09 April 2009

Activation of a GPCR leads to eIF4G phosphorylation at the 5' cap and to IRES-dependent translation.

scientific article published on 7 April 2014

Adaptation induced by self-targeting in a type I-B CRISPR-Cas system

scientific article published on 28 July 2020

Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

scientific article

Alternative splicing at NAGNAG acceptors: simply noise or noise and more?

scientific article published in November 2006

An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions.

scientific article published on January 2017

An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein

scientific article published on 15 December 2014

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.

scientific article published on 10 September 2012

An updated evolutionary classification of CRISPR-Cas systems

scientific article

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.

scientific article published on 28 May 2018

Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets.

scientific article published in March 1999

AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments.

scientific article

AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments

scientific article

Assessing the fraction of short-distance tandem splice sites under purifying selection

scientific article published on 11 February 2008

Atom Mapping with Constraint Programming

Atom mapping with constraint programming

scientific article published on 29 November 2014

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

scientific article

BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data

scientific article

Bioinformatics of prokaryotic RNAs

scientific article

Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins.

scientific article published on 13 May 2014

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

scientific article published on June 2014

CARNA--alignment of RNA structure ensembles

scientific article published on 11 June 2012

CMV: visualization for RNA and protein family models and their comparisons

scientific article published on 01 August 2018

CPSP-tools--exact and complete algorithms for high-throughput 3D lattice protein studies

scientific article

CPSP-web-tools: a server for 3D lattice protein studies.

scientific article

CRISPR-Cas bioinformatics

scientific article published on 19 July 2019

CRISPR-Cas systems in multicellular cyanobacteria

scientific article published on 15 August 2018

CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein

scientific article published in 2013

CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems

scientific article published on 01 June 2020

CRISPRidentify: identification of CRISPR arrays using machine learning approach

scientific article published on 08 December 2020

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

scientific article (publication date: September 2013)

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

scientific article published on September 2014

Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity.

scientific article published in January 2015

Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis

scientific article published on 8 August 2012

Characterizing leader sequences of CRISPR loci

scientific article

Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration

scientific article published on 12 July 2021

Classifying proteinlike sequences in arbitrary lattice protein models using LatPack.

scientific article published on 26 November 2008

Cluster based prediction of PDZ-peptide interactions

scientific article

Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data

scientific article published on September 2017

Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes.

scientific article published on 11 January 2018

Community-Driven Data Analysis Training for Biology

scientific article published on 01 June 2018

Comparative RNA Genomics

scientific article published in January 2018

Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens

scientific article

Comparative analysis ofCas6b processing and CRISPR RNA stability.

scientific article published on May 2013

Comparative genomics boosts target prediction for bacterial small RNAs

scientific article

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

article

Computational analysis of CLIP-seq data

scientific article

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

scientific article

Computational prediction of RNA-RNA interactions.

scientific article published on January 2014

Computational prediction of sRNAs and their targets in bacteria.

scientific article published on 13 January 2010

Conserved introns reveal novel transcripts in Drosophila melanogaster

scientific article published on 20 May 2009

CopomuS-Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments

scientific article published on 28 May 2020

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

scientific article (publication date: July 2014)

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

scientific article

Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function

scientific article

Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1

scientific article published on 13 September 2018

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome.

scientific article

DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex

scientific article published on 01 January 2019

Deciphering the Epigenetic Code of Cardiac Myocyte Transcription.

scientific article

Derivation of the phase-field-crystal model for colloidal solidification.

scientific article published on 27 May 2009

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

scientific article

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

scientific article

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo.

scientific article

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

scientific article

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells.

scientific article published on 2 October 2017

Efficient prediction of alternative splice forms using protein domain homology

scientific article published in January 2004

Engineered Coalescence by Annealing 3D Ge Microstructures into High-Quality Suspended Layers on Si.

scientific article published on 7 August 2015

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B.

scientific article published on 17 April 2013

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources

scientific article

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)

scientific article (publication date: 2013)

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

scientific article published on 19 December 2019

ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs

scientific article

Exploring the lower part of discrete polymer model energy landscapes

article

FLASH: ultra-fast protocol to identify RNA-protein interactions in cells

scientific article published on 01 February 2020

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus

scientific article published on 11 December 2018

Fast RNA structure alignment for crossing input structures

Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains

scientific article published on 13 November 2020

Fast prediction of RNA-RNA interaction

scientific article

Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

scientific article

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

scientific article published in July 2018

GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.

scientific article published on 17 April 2018

GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders.

scientific article published on 30 January 2017

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

scientific article published on 17 April 2020

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

scientific article published in July 2018

GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS.

scientific article

Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

scientific article

Global or local? Predicting secondary structure and accessibility in mRNAs

scientific article (publication date: July 2012)

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

scientific article published on 11 September 2014

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

scientific article published on 01 December 2019

GraphClust: alignment-free structural clustering of local RNA secondary structures

scientific article

GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge

scientific article published in Nature Communications

GraphProt: modeling binding preferences of RNA-binding proteins.

scientific article

HRIBO - High-throughput analysis of bacterial ribosome profiling data

scientific article published on 29 April 2020

Heterogeneous Networks Integration for Disease Gene Prioritization with Node Kernels

scientific article published on 28 January 2020

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

scientific article published on 21 May 2010

INFO-RNA--a fast approach to inverse RNA folding.

scientific article

INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints

scientific article

Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens

scientific article

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots

Improved identification of conserved cassette exons using Bayesian networks.

scientific article

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors

scientific article published on 11 April 2018

Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

scientific article

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions

scientific article

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

scientific article

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction

scientific article published on 01 October 2019

Integration of accessibility data from structure probing into RNA-RNA interaction prediction

scientific article published on 01 August 2019

Interactive implementations of thermodynamics-based RNA structure and RNA-RNA interaction prediction approaches for example-driven teaching

scientific article published on 30 August 2018

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

scientific article

Lifting prediction to alignment of RNA pseudoknots.

scientific article published in March 2010

Lightweight comparison of RNAs based on exact sequence-structure matches

scientific article published on 2 February 2009

Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression

scientific article

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs

scientific article published on 26 March 2012

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

scientific article (publication date: 2013)

Local Exact Pattern Matching for Non-Fixed RNA Structures.

scientific article published in January 2014

Local sequence-structure motifs in RNA.

scientific article published in December 2004

Locality and gaps in RNA comparison.

scientific article published in October 2007

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.

scientific article published on 21 June 2005

MOF-associated complexes ensure stem cell identity and Xist repression.

scientific article

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions

scientific article published on 3 April 2018

Mechanism of β-actin mRNA Recognition by ZBP1

scientific article published on January 2017

Methanosarcina Spherical Virus, a Novel Archaeal Lytic Virus Targeting Methanosarcina Strains.

scientific article published on 6 September 2017

Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA

scientific article published on 01 January 2007

MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing.

scientific article

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions

scientific article published on 28 May 2014

MutaRNA: analysis and visualization of mutation-induced changes in RNA structure

scientific article published on 11 May 2020

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

scientific article published on 10 October 2012

Non-EST based prediction of exon skipping and intron retention events using Pfam information

scientific article

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

scientific article published on 18 November 2010

Phase-field simulation of stripe arrays on metal bcc(110) surfaces

scientific article published on 22 May 2008

Photorhabdus-nematode symbiosis is dependent on hfq-mediated regulation of secondary metabolites

scientific article

Phylogenetically widespread alternative splicing at unusual GYNGYN donors

scientific article published on January 2006

Plasticity of archaeal C/D box sRNA biogenesis

scientific article published on 14 October 2016

Practical Computational Reproducibility in the Life Sciences

scientific article published on 01 June 2018

Practical computational reproducibility in the life sciences

scientific article published on 10 October 2017

Pre-mRNA secondary structures influence exon recognition.

scientific article

Producing high-accuracy lattice models from protein atomic coordinates including side chains

scientific article

Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion

scientific article published on 01 January 2002

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway

scientific article published on 14 July 2015

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea

scientific article published on August 2017

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

scientific article

RNAs everywhere: genome-wide annotation of structured RNAs

scientific article

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

scientific article published on 27 February 2017

Recent advances in RNA folding

scientific article

Regulatory RNAs in archaea: first target identification in Methanoarchaea.

scientific article published on February 2013

Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system.

scientific article published on December 2013

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

scientific article published on 9 June 2021

SECISDesign: a server to design SECIS-elements within the coding sequence.

scientific article published on 26 May 2005

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

scientific article published on 2 April 2015

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

scientific article

Selection against tandem splice sites affecting structured protein regions

scientific article

Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data.

scientific article

Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?

article published in 2006

ShaKer: RNA SHAPE prediction using graph kernel

scientific article published on 01 July 2019

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

scientific article

Simultaneous alignment and folding of protein sequences

scientific article

Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing

scientific article

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.

scientific article

Solid–liquid interfacial energies and equilibrium shapes of nanocrystals ⬇️

scientific article published on October 27, 2009

Sparsification of RNA structure prediction including pseudoknots

scientific article

Stress Induced Branching of Growing Crystals on Curved Surfaces

scientific article published on 01 April 2016

Structator: fast index-based search for RNA sequence-structure patterns

scientific article

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs

scientific article published on 5 September 2016

Structure and Interaction Prediction in Prokaryotic RNA Biology

scientific article published in April 2018

Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands

scientific article published on 09 July 2021

Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila

scientific article published on July 2013

TassDB2 - A comprehensive database of subtle alternative splicing events

scientific article

TassDB: a database of alternative tandem splice sites

scientific article

Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen-induced retinopathy mouse model

scientific article published on 09 March 2020

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

scientific article published on 23 May 2011

The RNA workbench 2.0: next generation RNA data analysis

scientific article published on 01 July 2019

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

scientific article published on 05 June 2017

The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts

scientific article published on 26 March 2018

The SH2-domain of SHIP1 interacts with the SHIP1 C-terminus: impact on SHIP1/Ig-α interaction.

scientific article

The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment

scientific article published on 13 January 2020

The influence of membrane bound proteins on phase separation and coarsening in cell membranes.

scientific article published on 17 July 2012

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

scientific article published on 26 September 2016

The locality dilemma of Sankoff-like RNA alignments

scientific article published on 01 July 2020

The nuts and bolts of the Haloferax CRISPR-Cas system I-B.

scientific article published on 13 April 2018

The role of Cas8 in type I CRISPR interference.

scientific article

The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal

scientific article

The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts

scientific article published on 09 September 2021

Two CRISPR-Cas systems in Methanosarcina mazei strain Gö1 display common processing features despite belonging to different types I and III.

scientific article published on 25 April 2013

Two-dimensional liquid crystalline growth within a phase-field-crystal model

scientific article published on 10 July 2015

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

scientific article

Unraveling the small proteome of the plant symbiont by ribosome profiling and proteogenomics

scientific article published in 2023

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

scientific article

Using constraint programming for lattice protein folding ⬇️

scientific article published on January 1, 1998

Variations on RNA folding and alignment: lessons from Benasque.

scientific article

Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns

scientific article

Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity

scientific article

antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization

scientific article

antaRNA: ant colony-based RNA sequence design

scientific article

hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons

scientific article published on 5 March 2018

pyGenomeTracks: reproducible plots for multivariate genomic data sets

scientific article published on 03 August 2020

sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1

scientific article (publication date: 15 March 2017)

uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames

scientific article published on 12 September 2019

uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins.

scientific article published on 20 March 2018

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