Rolf Backofen
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German bioinformatician and author
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Biology
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Bioinformatics
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Biology
Why Is Rolf Backofen Influential?
(Suggest an Edit or Addition)Rolf Backofen's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- An updated evolutionary classification of CRISPR–Cas systems (2015) (1822)
- Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants (2019) (899)
- Autosomal-dominant immune dysregulation syndrome in humans with CTLA4 mutations (2014) (672)
- Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering (2007) (513)
- IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions (2008) (487)
- IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions (2017) (372)
- DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome (2017) (353)
- LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. (2012) (299)
- CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains (2014) (289)
- Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease (2014) (250)
- Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo (2016) (236)
- GraphProt: modeling binding preferences of RNA-binding proteins (2014) (222)
- Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA (2010) (216)
- Comparative genomics boosts target prediction for bacterial small RNAs (2013) (208)
- Pre-mRNA Secondary Structures Influence Exon Recognition (2007) (194)
- Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity (2004) (191)
- The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression (2016) (190)
- MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons (2005) (170)
- Using RNA secondary structures to guide sequence motif finding towards single-stranded regions (2006) (160)
- Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo (2017) (156)
- The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal (2011) (152)
- Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression (2018) (151)
- Excluding Symmetries in Constraint-Based Search (1999) (148)
- Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. (2013) (144)
- Global or local? Predicting secondary structure and accessibility in mRNAs (2012) (136)
- CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein (2013) (134)
- CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems (2013) (132)
- INFO-RNA - a fast approach to inverse RNA folding (2006) (129)
- An Information Extraction Core System for Real World German Text Processing (1997) (129)
- Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization (2018) (124)
- pyGenomeTracks: reproducible plots for multivariate genomic datasets (2020) (123)
- A partition function algorithm for interacting nucleic acid strands (2009) (114)
- Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis (2012) (113)
- Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization (2020) (111)
- Computational prediction of sRNAs and their targets in bacteria (2010) (106)
- Community-driven data analysis training for biology (2017) (105)
- A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models (2006) (100)
- A pan-cancer analysis of synonymous mutations (2019) (97)
- A first-order axiomatization of the theory of finite trees (1995) (97)
- Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments (2008) (91)
- Variations on RNA folding and alignment: lessons from Benasque (2007) (90)
- Practical Computational Reproducibility in the Life Sciences. (2018) (89)
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching (2018) (89)
- RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway (2015) (87)
- MOF-associated complexes ensure stem cell identity and Xist repression (2014) (84)
- Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1 (2009) (83)
- Computational molecular biology - an introduction (2000) (83)
- Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression. (2014) (76)
- GraphClust: alignment-free structural clustering of local RNA secondary structures (2012) (76)
- Sparse RNA folding: Time and space efficient algorithms (2009) (73)
- 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* (2014) (70)
- Deciphering the Epigenetic Code of Cardiac Myocyte Transcription. (2015) (68)
- Fast prediction of RNA-RNA interaction (2009) (68)
- Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets (1999) (66)
- Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B (2013) (66)
- Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families (2018) (65)
- Recent advances in RNA folding. (2017) (61)
- Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. (2006) (60)
- RNAs everywhere: genome-wide annotation of structured RNAs. (2007) (60)
- DISCO-An HPSG-based NLP System and its Application for Appointment Scheduling Project Note (1994) (56)
- CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci (2014) (56)
- Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers (2017) (55)
- CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies (2008) (55)
- PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences (2010) (54)
- Two CRISPR-Cas systems inMethanosarcina mazeistrain Gö1 display common processing features despite belonging to different types I and III (2013) (53)
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains (2012) (53)
- Characterizing leader sequences of CRISPR loci (2016) (53)
- The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound (2001) (53)
- MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing. (2016) (51)
- Local Sequence-structure Motifs in Rna (2004) (50)
- Photorhabdus‐nematode symbiosis is dependent on hfq‐mediated regulation of secondary metabolites (2017) (50)
- In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors (2018) (50)
- Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants (2019) (50)
- The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts (2018) (50)
- Conserved introns reveal novel transcripts in Drosophila melanogaster. (2009) (49)
- CARNA—alignment of RNA structure ensembles (2012) (48)
- AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments. (2016) (48)
- Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes (2008) (47)
- Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells (2016) (45)
- SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics (2013) (45)
- Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns (2007) (44)
- MechRNA: prediction of lncRNA mechanisms from RNA–RNA and RNA–protein interactions (2018) (43)
- Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding (2010) (42)
- TassDB: a database of alternative tandem splice sites (2006) (41)
- Computational analysis of CLIP-seq data. (2017) (39)
- biRNA: Fast RNA-RNA Binding Sites Prediction (2009) (39)
- The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy (2017) (39)
- The role of Cas8 in type I CRISPR interference (2015) (39)
- DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex (2018) (38)
- AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments (2018) (37)
- Phylogenetically widespread alternative splicing at unusual GYNGYN donors (2006) (37)
- Algorithmic approach to quantifying the hydrophobic force contribution in protein folding (1999) (37)
- A multiple-feature framework for modelling and predicting transcription factor binding sites (2005) (37)
- A Complete and Recursive Feature Theory (1994) (37)
- Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen‐induced retinopathy mouse model (2020) (36)
- Structator: fast index-based search for RNA sequence-structure patterns (2011) (36)
- Mechanism of β-actin mRNA Recognition by ZBP1 (2017) (36)
- Lightweight comparison of RNAs based on exact sequence–structure matches (2009) (35)
- INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints (2007) (35)
- Constraint Techniques for Solving the Protein Structure Prediction Problem (1998) (35)
- GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence (2018) (35)
- Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine (2022) (34)
- antaRNA: ant colony-based RNA sequence design (2015) (34)
- Sparsification of RNA structure prediction including pseudoknots (2010) (33)
- Lifting Prediction to Alignment of RNA Pseudoknots (2009) (32)
- CPSP-web-tools: a server for 3D lattice protein studies (2009) (32)
- CRISPR-Cas Bioinformatics. (2020) (32)
- hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons (2018) (31)
- Accurate prediction of NAGNAG alternative splicing (2009) (31)
- A Complete Axiomatization of a Theory with Feature and Arity Constraints (1995) (30)
- A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods (2003) (30)
- MoDPepInt: an interactive web server for prediction of modular domain–peptide interactions (2014) (30)
- The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences (2011) (30)
- Non-EST based prediction of exon skipping and intron retention events using Pfam information (2005) (30)
- sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1 (2017) (30)
- Creation and disruption of protein features by alternative splicing - a novel mechanism to modulate function (2005) (30)
- Exploring the lower part of discrete polymer model energy landscapes (2006) (29)
- Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs (2016) (29)
- Semi-Supervised Prediction of SH2-Peptide Interactions from Imbalanced High-Throughput Data (2013) (29)
- RNAscClust: clustering RNA sequences using structure conservation and graph based motifs (2017) (28)
- Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains (2012) (28)
- An Active Immune Defense with a Minimal CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) RNA and without the Cas6 Protein* (2014) (28)
- MARNA: A server for multiple alignment of RNAs (2003) (28)
- Methanosarcina Spherical Virus, a Novel Archaeal Lytic Virus Targeting Methanosarcina Strains (2017) (27)
- Accessibility and conservation (2012) (27)
- 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 (2017) (27)
- Atom mapping with constraint programming (2013) (27)
- Computational discovery of human coding and non-coding transcripts with conserved splice sites (2011) (27)
- CRISPRidentify: identification of CRISPR arrays using machine learning approach (2020) (26)
- Structural Local Multiple Alignment of RNA (2008) (24)
- Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots (2012) (24)
- Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More? (2006) (24)
- Comparative analysis of Cas6b processing and CRISPR RNA stability (2013) (24)
- Combinatorial Omics Analysis Reveals Perturbed Lysosomal Homeostasis in Collagen VII-deficient Keratinocytes* (2018) (23)
- Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC (2001) (22)
- RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation. (2017) (22)
- uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins (2018) (22)
- CRISPR-Cas systems in multicellular cyanobacteria (2018) (22)
- EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells (2017) (22)
- SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification (2016) (21)
- CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems (2019) (21)
- BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data (2007) (21)
- Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores (2001) (21)
- Assessing the fraction of short-distance tandem splice sites under purifying selection. (2008) (21)
- Generation of pure monocultures of human microglia-like cells from induced pluripotent stem cells. (2020) (21)
- antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization (2015) (21)
- Bioinformatics and Constraints (2001) (20)
- Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration (2021) (20)
- A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila (2017) (20)
- Fast detection of common sequence structure patterns in RNAs (2004) (20)
- The nuts and bolts of the Haloferax CRISPR-Cas system I-B (2018) (20)
- TassDB2 - A comprehensive database of subtle alternative splicing events (2010) (20)
- Regulatory RNAs in archaea: first target identification in Methanoarchaea. (2013) (20)
- Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots (2008) (19)
- Using constraint programming for lattice protein folding (1997) (19)
- Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity (2014) (18)
- Cluster based prediction of PDZ-peptide interactions (2014) (18)
- A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence (2020) (18)
- RIP-Seq Suggests Translational Regulation by L7Ae in Archaea (2017) (18)
- Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data (2017) (18)
- Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system. (2013) (17)
- A graph kernel approach for alignment-free domain–peptide interaction prediction with an application to human SH3 domains (2013) (17)
- Classifying proteinlike sequences in arbitrary lattice protein models using LatPack (2008) (17)
- A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS (2020) (17)
- The SH2-domain of SHIP1 interacts with the SHIP1 C-terminus: impact on SHIP1/Ig-α interaction. (2012) (17)
- Abstract folding space analysis based on helices. (2012) (16)
- A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources. (2014) (16)
- Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins (2014) (16)
- Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions (2010) (16)
- A Complete and Recursive Feature Theory (1993) (16)
- GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders (2017) (16)
- BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles (2014) (15)
- ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs (2014) (15)
- 5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation (2016) (15)
- LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search (2013) (15)
- Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources (2013) (15)
- SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins (2015) (14)
- The RNA workbench 2.0: next generation RNA data analysis (2019) (14)
- Regular Path Expressions in Feature Logic (1994) (14)
- Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends (1991) (14)
- Bioinformatics of prokaryotic RNAs (2014) (13)
- NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy (2020) (13)
- Towards the Integration of Functions, Relations and Types in an AI Programming Language (1990) (13)
- Structure and Interaction Prediction in Prokaryotic RNA Biology. (2018) (12)
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering (2019) (12)
- Microstructure alignment of wood density profiles: an approach to equalize radial differences in growth rate (2012) (12)
- Locality and Gaps in RNA Comparison (2007) (12)
- A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC) (2004) (12)
- Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI) (2013) (12)
- Selection against tandem splice sites affecting structured protein regions (2008) (12)
- Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens (2010) (12)
- Efficient prediction of alternative splice forms using protein domain homology (2004) (11)
- Excluding Symmetries in Concurrent Constraint Programming (1998) (11)
- FLASH: ultra-fast protocol to identify RNA–protein interactions in cells (2019) (11)
- GraphProt2: A novel deep learning-based method for predicting binding sites of RNA-binding proteins (2019) (11)
- Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition (2021) (11)
- SECISDesign: a server to design SECIS-elements within the coding sequence (2005) (11)
- Integration of accessibility data from structure probing into RNA–RNA interaction prediction (2018) (11)
- CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems (2021) (11)
- Comparative RNA Genomics. (2018) (11)
- State-of-the-art in Bioinformatics (2004) (10)
- Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion. (2002) (10)
- Expressivity and decidability of first-order languages over feature trees (1994) (10)
- An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC) (2000) (10)
- On the Complexity of Protein Similarity Search under mRNA Structure Constraints (2002) (10)
- Tool recommender system in Galaxy using deep learning (2019) (10)
- Plasticity of archaeal C/D box sRNA biogenesis (2017) (10)
- FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus (2018) (9)
- Sequencing errors or SNPs at splice-acceptor guanines in dbSNP? (2006) (9)
- GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge (2018) (9)
- Feature Based Representation and Detection of Transcription Factor Binding Sites (2004) (9)
- Usage of bioinformatics tools and identification of information sources (2005) (9)
- Local Exact Pattern Matching for Non-Fixed RNA Structures (2012) (9)
- Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains (2009) (9)
- uORF-Tools – Workflow for the determination of translation-regulatory upstream open reading frames (2018) (9)
- Exact methods for lattice protein models (2014) (9)
- Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1 (2018) (9)
- Improving CLIP-seq data analysis by incorporating transcript information (2020) (8)
- ShaKer: RNA SHAPE prediction using graph kernel (2019) (8)
- Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching (2018) (8)
- MutaRNA: analysis and visualization of mutation-induced changes in RNA structure (2020) (8)
- Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches (2012) (8)
- Heterogeneous networks integration for disease-gene prioritization with node kernels (2020) (8)
- Constraint Based Protein Structure Prediction Exploiting Secondary Structure Information (2004) (8)
- How to Win a Game with Features (1994) (8)
- Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination (2008) (8)
- MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration (2021) (8)
- CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii (2021) (8)
- Exact Pattern Matching for RNA Structure Ensembles (2012) (7)
- MICA: Multiple interval-based curve alignment (2018) (7)
- The nuts and bolts of the Haloferax CRISPR-Cas system IB (2018) (7)
- Fast RNA Structure Alignment for Crossing Input Structures (2009) (7)
- Local Alignment of RNA Sequences with Arbitrary Scoring Schemes (2006) (7)
- Activation of a GPCR leads to eIF4G phosphorylation at the 5' cap and to IRES-dependent translation. (2014) (7)
- A single-cell RNA-sequencing training and analysis suite using the Galaxy framework (2020) (7)
- RC 3 H 1 post-transcriptionally regulates A 20 mRNA and modulates the activity of the IKK / NFk B pathway (2015) (7)
- crRNA biogenesis and maintenance in Haloferax 1 A complex of Cas proteins 5 , 6 , and 7 is required for the biogenesis and stability of crRNAs in Haloferax volcanii (2014) (7)
- Improved identification of conserved cassette exons using Bayesian networks (2008) (7)
- Methods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA. (2007) (7)
- The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts (2021) (7)
- Introduction to the Special Issue on Bioinformatics (2001) (7)
- The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment (2020) (7)
- Loop detection using Hi-C data with HiCExplorer (2020) (7)
- Evolution as a Computational Engine (1997) (6)
- Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases. (2022) (6)
- Variations on RNA Folding and Alignment (2006) (6)
- Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules (2020) (6)
- Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data (2020) (6)
- A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative (2006) (6)
- CRISPR and Salty: CRISPR-Cas Systems in Haloarchaea (2017) (5)
- Computational prediction of RNA-RNA interactions. (2014) (5)
- Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs (2021) (5)
- Computational Design of New and Recombinant Selenoproteins (2004) (5)
- Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter (2016) (5)
- Casboundary: automated definition of integral Cas cassettes (2020) (5)
- IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction (2019) (5)
- Automated Reasoning on the Web (2004) (5)
- Integration of accessibility data from structure probing into RNA-RNA interaction prediction (2018) (5)
- Shape-based Barrier Estimation for RNAs (2010) (5)
- Normalized Similarity of RNA Sequences (2005) (5)
- RNAProt: an efficient and feature-rich RNA binding protein binding site predictor (2021) (5)
- On the Decidability of Functional Uncertainty (1993) (5)
- Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens. (2016) (5)
- CMV: visualization for RNA and protein family models and their comparisons (2018) (5)
- Conserved accessory proteins encoded with archaeal and bacterial Type III CRISPR-Cas gene cassettes that may specifically modulate, complement or extend interference activity (2018) (4)
- Simultaneous Alignment and Folding of Protein Sequences (2009) (4)
- Structure prediction in an HP-type lattice with an extended alphabet (1998) (4)
- Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures (2013) (4)
- Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains (2009) (4)
- SF CRISPR Comparative analysis of Cas 6 b processing and CRISPR RNA stability (2013) (4)
- Towards a Semantic Web for Bioinformatics (2004) (4)
- Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures (2014) (3)
- Report of the EAGLES Workshop on Implemented Formalisms at DFKI, Saarbrücken (1993) (3)
- Requirements and specification of bioinformatics use cases (2005) (3)
- Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation (2002) (3)
- GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS (2016) (3)
- Dynamic Data for Geospatial Reasoning - A Local Data Stream Management System (L-DSMS) and a Case Study with RDS-TMC (2006) (3)
- A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework (2020) (3)
- Practical computational reproducibility in the life sciences (2017) (3)
- COMPUTATIONAL STUDIES OF NON-CODING RNAS – Session Introduction (2009) (3)
- Poster: Towards a semantic web for bioinformatics (2004) (3)
- Fast Feature Subset Selection in Biological Sequence Analysis (2009) (3)
- ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data (2021) (3)
- Regular Path Expression in Feature Logic (1993) (2)
- AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments (2016) (2)
- uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames (2019) (2)
- uvCLAP: a fast, non-radioactive method to identify in vivo targets of RNA-binding proteins (2017) (2)
- Analysis of the androgen receptor–regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression (2018) (2)
- Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains (2020) (2)
- Structure-aware machine learning identifies microRNAs operating as Toll-like receptor 7/8 ligands (2021) (2)
- RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria (2021) (2)
- Controlling Functional Uncertainty (1996) (2)
- Adaptation induced by self-targeting in a type I-B CRISPR-Cas system (2020) (2)
- Implementation of prototypes (2007) (2)
- CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection (2022) (2)
- Scool: a new data storage format for single-cell Hi-C data (2020) (2)
- Corrigendum: Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity (2005) (2)
- StoatyDive: Evaluation and classification of peak profiles for sequencing data (2019) (2)
- Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis (2020) (2)
- Requirements and specification of use cases (2005) (2)
- Tyrosine kinase inhibitors can activate the NLRP3 inflammasome in myeloid cells through lysosomal damage and cell lysis (2023) (2)
- A Dynamic Programming Approach for Finding Common Patterns in RNAs (2007) (2)
- Sequence analysis antaRNA : ant colony-based RNA sequence design (2015) (1)
- The population genetics of the CRISPR-Cas system in bacteria (2021) (1)
- Distributed Disjunctions for LIFE (1991) (1)
- De Novo Molecular Design Using Graph Kernels (2011) (1)
- The importance of incorporating transcript information in CLIP-seq data analysis (2020) (1)
- An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria (2021) (1)
- Sparsification of RNA structure prediction including pseudoknots Citation (2011) (1)
- Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease (2021) (1)
- High detection rate for disease-causing variants in a cohort of 30 Iranian pediatric steroid resistant nephrotic syndrome cases (2022) (1)
- Tyrosine kinase inhibitors trigger lysosomal damage-associated cell lysis to activate the NLRP3 inflammasome (2022) (1)
- A new distance measure of RNA ensembles and its application to phylogenetic tree construction (2005) (1)
- Bioinformatics of Bacterial sRNAs and Their Targets (2012) (1)
- Scool: a new data storage format for single-cell Hi-C data (2021) (1)
- DatabaseTassDB 2-A comprehensive database of subtle alternative splicing events (2011) (1)
- Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia (2023) (1)
- CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments (2020) (1)
- Approximate k-nearest neighbors graph for single-cell Hi-C dimensional reduction with MinHash (2020) (1)
- Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs (2019) (1)
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni (2022) (1)
- Fast prediction of RNA-RNA interaction Algorithms (2010) (1)
- Spectrum of Genetic Variants in a Cohort of 37 Laterality Defect Cases (2022) (1)
- Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimised mass spectrometry (2023) (1)
- The potential of intra-annual density information for crossdating of short tree-ring series (2020) (1)
- A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive (2021) (1)
- Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA (2022) (1)
- structural RNAs LocARNA-P : Accurate boundary prediction and improved detection of Material Supplemental (2012) (1)
- Atom mapping with constraint programming (2014) (1)
- The role of the 5’ sensing function of ribonuclease E in cyanobacteria (2023) (1)
- Cluster based prediction of PDZ-peptide interactions (2014) (1)
- Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction (2019) (1)
- Accuracy-based identification of local RNA elements (2010) (1)
- Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein 1 (LRP1) as crucial cellular receptor (2022) (1)
- Author response: MOF-associated complexes ensure stem cell identity and Xist repression (2014) (1)
- COMPUTATIONAL STUDIES OF NON-CODING RNAS (2009) (1)
- MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions (2018) (0)
- Fast and accurate structure probability estimation 1 for simultaneous alignment and folding of RNAs 2 (2019) (0)
- Mechanism of b-actin mRN A Recognition by ZBP 1 Graphical Abstract Highlights (0)
- Graph kernel based aromaticity prediction thesis submitted in fulfilment of the requirements for the degree of Bachelor of Science in the Chair for Bioinformatics Department of Computer Science Done (0)
- How to make Sense out of CLIP-seq data (2015) (0)
- New Approach to Combat Glioblastoma Shows Promise in Preclinical Studies (2005) (0)
- A 2-D 3 Requirements and specification of bioinformatics use cases (2005) (0)
- 1 uvCLAP : a fast , non-radioactive method to identify in vivo targets of RNA-binding proteins (2017) (0)
- MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction (2018) (0)
- The locality dilemma of Sankoff-like RNA alignments (2020) (0)
- Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells (2017) (0)
- RNA Consensus Interaction Prediction - Cameron Smith (2011) (0)
- 2010 TCBB Reviewers List (2011) (0)
- RNA-Sequence-Structure Properties and Selenocysteine Insertion (2001) (0)
- GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge (2018) (0)
- 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 (2017) (0)
- PSB 2010 Tutorial : Computational Studies of Non-coding RNAs (2009) (0)
- ISMB 2010 Organization (2010) (0)
- Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains (2020) (0)
- DEWSeq addresses the pervasive disparity of crosslink site distributions in the discovery of RNA-binding protein binding sites in eCLIP data (2022) (0)
- Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics (2023) (0)
- Scalable and accessible clustering of ncRNAs based on sequence and secondarystructures (2017) (0)
- The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment (2020) (0)
- Structure probing data enhances RNA-RNA interaction prediction (2018) (0)
- 2011 Reviewers List (2012) (0)
- Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252) (2017) (0)
- The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity (2022) (0)
- Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings (2019) (0)
- A methodical analysis of target structure characteristics in RNA-RNA interactions (2010) (0)
- Structure and Interaction Prediction in Prokaryotic RNA Biology (2018) (0)
- Prokaryotic immune defence with an icrRNA and without Cas 6 1 An Active Immune Defence with a Minimal CRISPR ( clustered regularly interspaced short palindromic repeats ) RNA and Without the Cas 6 Protein (2014) (0)
- 2009 Reviewer's List (2010) (0)
- Palindromic Repeats ( CRISPR )-derived Clustered Regularly Interspaced (2014) (0)
- SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification (2016) (0)
- Peakhood: individual site context extraction for CLIP-seq peak regions (2021) (0)
- The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts (2018) (0)
- Faculty Opinions recommendation of Piercing the fog of the RNA structure-ome. (2021) (0)
- A pan-cancer analysis of synonymous mutations (2019) (0)
- AptaTRACE Elucidates RNA Sequence-StructureMotifs from Selection Trends in HT-SELEX Experiments Graphical Abstract Highlights (2016) (0)
- Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo (2018) (0)
- Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342) (2019) (0)
- Effect of spacer sequence on efficiency of Type I-E CRISPR-Cas systems (2017) (0)
- An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions. (2017) (0)
- 2018 - TRANSPOSABLE ELEMENTS ENHANCE HEMATOPOIETIC REGENERATION VIA ACTIVATION OF INNATE IMMUNE SIGNALLING (2019) (0)
- Exploration of biopolymer energy landscapes via random sampling (2007) (0)
- Exclusion of Symmetries in Search - A Spin-off from Bioinformatics Research (2000) (0)
- ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs (2014) (0)
- Publications of Sebastian Will Journal Articles (2015) (0)
- purifying selection Assessing the fraction of short-distance tandem splice sites under Material Supplemental (2011) (0)
- MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration (2021) (0)
- ABERRANT SPLICING OF A BRAIN-ENRICHED ALTERNATIVE EXON ELIMINATES TUMOR SUPPRESSOR FUNCTION AND PROMOTES ONCOGENE FUNCTION DURING BRAIN TUMORIGENESIS (2014) (0)
- Identifying Key Regulators in Gene Regulatory Networks (2007) (0)
- An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy (2022) (0)
- Transformer-based tool recommendation system in Galaxy (2022) (0)
- Improving CLIP-seq data analysis by incorporating transcript information (2020) (0)
- Biological and bioinformatical approaches to study crosstalk of long-non-coding RNAs and chromatin-modifying proteins (2014) (0)
- Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures (2014) (0)
- 3D-Structure-Motifs Aware Sequence Structure Alignment of RNAs (2007) (0)
- uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins (2018) (0)
- TREK-1 knock-down in human atrial fibroblasts leads to a myofibroblastic phenotype: a role in phenoconversion and over-view of mechano-sensitive channel mRNA expression in cardiac diseases (2022) (0)
- Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq (2022) (0)
- antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization (2015) (0)
- Decomposition Techniques for Subgraph Matching (2008) (0)
- Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (2015) (0)
- Scalable structural clustering of local RNA secondary structures (2014) (0)
- FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus (2018) (0)
- HRIBO: high-throughput analysis of bacterial ribosome profiling data (2020) (0)
- Publisher Correction: Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration (2021) (0)
- Microstructure alignment of wood density profiles: an approach to equalize radial differences in growth rate (2012) (0)
- Biochemistry 11-16-2007 Pre-mRNA Secondary Structures Influence Exon Recognition (2017) (0)
- LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search (2013) (0)
- Session Introduction (2003) (0)
- Faculty Opinions recommendation of An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. (2021) (0)
- ECCB 2010 Organization (2010) (0)
- A 2-D 1 State-ofthe-art in Bioinformatics (2004) (0)
- GraphProt: modeling binding preferences of RNA-binding proteins (2014) (0)
- Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources (2013) (0)
- Repetitive Elements Enhance Hematopoietic Regeneration Via Activation of the Innate Immune Receptor MDA5 (2019) (0)
- Introduction to Bioinformatics (2001) (0)
- Atom Mapping of Chemical Reactions via Constraint Programming (2013) (0)
- Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti (2022) (0)
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What Schools Are Affiliated With Rolf Backofen?
Rolf Backofen is affiliated with the following schools:
