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List of works by Peter F. Stadler

"Genes".

scientific article published on 5 March 2008

"Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity

scientific article published in December 2011

24 Intron positions and near intron pairs

article

2D meets 4G: G-quadruplexes in RNA secondary structure prediction

scientific article published in July 2013

50 Shades of Rule Composition

article

A STORY OF GROWING CONFUSION: GENES AND THEIR REGULATION

A STORY OF GROWING CONFUSION: GENES AND THEIR REGULATION

A Software Package for Chemically Inspired Graph Transformation

scholarly article by Jakob L. Andersen et al published 2016 in Lecture Notes in Computer Science

A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts

scientific article published on 18 October 2017

A Survey on Hypergraph Products

A Visual Cross-Database Comparison of Metabolic Networks

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.

scientific article published on 16 May 2013

A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus

scientific article published on 12 February 2014

A folding algorithm for extended RNA secondary structures ⬇️

scientific article published on July 2011

A graph-based toy model of chemistry

scientific article published in July 2003

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

scientific article

A note on fundamental, non-fundamental, and robust cycle bases

A novel family of plasmid-transferred anti-sense ncRNAs

scientific article

A prime factor theorem for a generalized direct product

A priori assessment of data quality in molecular phylogenetics

scholarly article by Bernhard Misof et al published January 2014 in Algorithms for Molecular Biology

A simple data-adaptive probabilistic variant calling model ⬇️

scientific article

A stochastic model for the evolution of transcription factor binding site abundance.

scientific article published on 7 March 2007

A survey of nematode SmY RNAs

scientific article

A topological approach to chemical organizations

scientific article published on January 2009

Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards

scientific article published on 3 August 2021

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

scientific article (publication date: October 2009)

Accurate annotation of protein-coding genes in mitochondrial genomes

scientific article

Addendum: topology and prediction of RNA pseudoknots

scientific article published on 20 November 2011

Advances in Bioinformatics and Computational Biology: 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings

5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings

Aggregation of variables and system decomposition: Applications to fitness landscape analysis

scientific article published in June 2004

Aldosterone plasma concentration in horses with heart valve insufficiencies

scientific article

Algebraic Dynamic Programming on Trees

scholarly article by Sarah Berkemer et al published 6 December 2017 in Algorithms

Algebraic Dynamic Programming over general data structures

scientific article

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation

scientific article published on 14 February 2006

Algebraic dynamic programming for multiple context-free grammars

scholarly article by Maik Riechert et al published August 2016 in Theoretical Computer Science

Algebraic theory of recombination spaces

scientific article published in January 1997

Algorithm independent properties of RNA secondary structure predictions

article published in 1996

Alignment of RNA base pairing probability matrices

scientific article

Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny

scientific article published in December 2005

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis

scientific article

Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks

scientific article

Alzheimer-related genes show accelerated evolution

scientific article published on 13 March 2020

Amplitude Spectra of Fitness Landscapes

article published in 1998

An intermediate level of abstraction for computational systems chemistry

scientific article

An updated human snoRNAome

scientific article published on 12 May 2016

Analyses of pig genomes provide insight into porcine demography and evolution

scientific article

Animal snoRNAs and scaRNAs with exceptional structures

scientific article published on November 2011

Anisotropy in fitness landscapes

scientific article published in December 1993

Applicability of a computational design approach for synthetic riboswitches

scientific article published on 19 December 2016

Approximate graph products

Approximate scaling properties of RNA free energy landscapes

scientific article published in August 1996

Are spliced ncRNA host genes distinct classes of lncRNAs?

scientific article published on 21 November 2020

Armless mitochondrial tRNAs in Enoplea (Nematoda)

scientific article

Arthropod 7SK RNA.

scientific article

AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories

scientific article published in 2022

Atom Mapping with Constraint Programming

Atom mapping with constraint programming

scientific article published on 29 November 2014

Atypical RNAs in the coelacanth transcriptome

scientific article published on 30 October 2013

Autocatalytic networks with intermediates. I: Irreversible reactions

scientific article published in February 1997

Autocatalytic networks with translation

article

Autocatalytic replication in a CSTR and constant organization

scientific article

Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum

scientific article

Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns

article

Automatic Curation of Large Comparative Animal MicroRNA Data Sets

scientific article published on 01 November 2019

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions

Automatic detection of conserved base pairing patterns in RNA virus genomes

scientific article published in June 1999

Average Fitness Differences on NK Landscapes

BarMap: RNA folding on dynamic energy landscapes

scientific article

Barrier Trees of Degenerate Landscapes

article

Base pairing probabilities in a complete HIV-1 RNA.

scientific article published in January 1996

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes

scientific article published on 19 March 2014

Bcheck: a wrapper tool for detecting RNase P RNA genes

scientific article

Best Match Graphs With Binary Trees

scientific article published on 19 January 2022

Best match graphs

scientific article

Best match graphs and reconciliation of gene trees with species trees

scientific article published on 30 January 2020

Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches

scientific article published on 03 September 2020

Beyond the 3'UTR binding-microRNA-induced protein truncation via DNA binding

Bi-alignments with affine gaps costs

scientific article published in 2022

Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution.

scientific article

Bio-molecular shapes and algebraic structures

scientific article published in March 1996

Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences.

scientific article published on 28 September 2012

Bioinformatics of prokaryotic RNAs

scientific article

Biological evidence for the world's smallest tRNAs

scientific article published on 17 August 2013

CREx: inferring genomic rearrangements based on common intervals

scientific article published on 25 September 2007

Call for proposals

scientific article published on September 1999

Canonical approximation of fitness landscapes

article

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs

scientific article

CelloS: A Multi-level Approach to Evolutionary Dynamics

article

Centers of complex networks

scientific article published on 01 July 2003

Challenges in RNA virus bioinformatics

scientific article published on 03 March 2014

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer

scientific article

ChemInform Abstract: Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry

Chemical Graph Transformation with Stereo-Information

Chemical Transformation Motifs-Modelling Pathways as Integer Hyperflows

scientific article published on 11 December 2017

Chromatin computation: epigenetic inheritance as a pattern reconstruction problem

scientific article published on 20 July 2013

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

scientific article

Circuit bases of strongly connected digraphs

Class-specific prediction of ncRNAs

scientific article published on January 2014

Clustering rfam 10.1: clans, families, and classes

scientific article (publication date: 5 July 2012)

Combinatorial Landscapes

Combinatorial vector fields and the valley structure of fitness landscapes

scientific article published on 22 January 2010

Combinatorics of RNA secondary structures

article

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis

scientific article published on 03 October 2018

Common Features in lncRNA Annotation and Classification: A Survey

scientific article published on 14 December 2021

Comparative RNA Genomics

scientific article published in January 2018

Comparative analysis of eukaryotic U3 snoRNA

scientific article

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions

scientific article

Comparative genomics reveals insights into avian genome evolution and adaptation

scientific article

Comparative promoter region analysis powered by CORG ⬇️

scientific article

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods

scientific article published on 13 September 2019

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

scientific article published on 23 March 2015

Complementary replication ⬇️

scientific article published on November 1, 1991

Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

scientific article published in 2021

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

scientific article (publication date: 23 February 2010)

Computational RNomics of drosophilids

scientific article

Computational RNomics: Genome-wide detection of structured non-coding RNAs and their evolutionary patterns

Computational biology of RNA interactions

scientific article

Computational design of RNAs with complex energy landscapes

scientific article

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

scientific article

Computational prediction of microRNA genes

scientific article published on January 2014

Connectivity Spaces

Conservation and losses of non-coding RNAs in avian genomes

scientific article

Conserved RNA secondary structures in Flaviviridae genomes

scientific article

Conserved RNA secondary structures in Picornaviridae genomes

scientific article published on December 2001

Conserved RNA secondary structures in viral genomes: a survey

scientific article published in July 2004

Conserved introns reveal novel transcripts in Drosophila melanogaster

scientific article published on 20 May 2009

Coordinate systems for supergenomes

scholarly article by Fabian Externbrink published in January 2018

Correlation length, isotropy and meta-stable states

article

Corrigendum to “Best match graphs”

scientific article published in 2021

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

scientific article

Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

scientific article published in May 2016

Counterexamples in chemical ring perception

scientific article published in March 2004

Customized strategies for discovering distant ncRNA homologs

scientific article published on 24 September 2009

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

scientific article published on 27 May 2011

DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial

scientific article published on 16 November 2020

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

scientific article

De novo design of a synthetic riboswitch that regulates transcription termination.

scientific article

Defining genes: a computational framework

scientific article published on 26 June 2009

Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer.

scientific article

Density of states, metastable states, and saddle points exploring the energy landscape of an RNA molecule.

scientific article published in January 1997

Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods

scientific article published on 20 June 2019

Design criteria for synthetic riboswitches acting on transcription.

scientific article published on January 2015

Design of Artificial Riboswitches as Biosensors.

scientific article published on 30 August 2017

Design of multistable RNA molecules

scientific article

Design of transcription regulating riboswitches.

scientific article

Design specifications for cellular regulation

scientific article

Detailed Secondary Structure Models of Invertebrate 7SK RNAs.

scientific article

Detection of Protein Domains in Eukaryotic Genome Sequences

article published in 2010

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

scientific article

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools

scientific article

Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity

scientific article published on 26 March 2020

Developmentally regulated expression and expression strategies of Drosophila snoRNAs

scientific article published on 29 January 2015

Diagonalized Cartesian products of S -prime graphs are S -prime

Dicer-Processed Small RNAs: Rules and Exceptions

article

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

scientific article

Discovering cis-regulatory modules by optimizing barbecues

Discrete nodal domain theorems

Distinct abdominal and gluteal adipose tissue transcriptome signatures are altered by exercise training in African women with obesity

scientific article published on 24 June 2020

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

Disturbance of phylogenetic layer-specific adaptation of human brain gene expression in Alzheimer's disease

scientific article published on 12 October 2021

Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests

article

Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation

Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.

scientific article published on 9 October 2014

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

scientific article

Duplicated RNA genes in teleost fish genomes

scientific article

Dynamics of autocatalytic reaction networks IV: Inhomogeneous replicator networks ⬇️

scientific article published on January 1, 1991

Dynamics of small autocatalytic reaction networks--I. Bifurcations, permanence and exclusion

scientific article published in January 1990

Dynamics of small autocatalytic reaction networks—II. Replication, mutation and catalysis

article

Early Replicons: Origin and Evolution**Dedicated to Manfred Eigen, the pioneer of molecular evolution and intellectual father of quasispecies theory, on the occasion of his 80th birthday

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

scientific article published on 12 October 2017

Effect of autologous adipose tissue-derived mesenchymal stem cells on neovascularization of artificial equine tendon lesions.

scientific article published on January 2014

Effect of head and neck position on pharyngeal diameter in horses

scientific article published on 01 September 2010

Efficient computation of RNA folding dynamics

article

EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics

scientific article published on 12 November 2021

Error Thresholds on Correlated Fitness Landscapes

Error propagation in the hypercycle

scientific article published in March 2000

Evidence for human microRNA-offset RNAs in small RNA sequencing data

scientific article

Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii

article

Evolution and quantitative comparison of genome-wide protein domain distributions

scientific article published on 9 November 2011

Evolution in Systems of Ligation-Based Replicators

scientific article published in 2002

Evolution of 3'UTR-associated RNAs

scientific article

Evolution of 7SK RNA and its protein partners in metazoa

scientific article published on 4 September 2009

Evolution of Fungal U3 snoRNAs: Structural Variation and Introns

scientific article published on 5 January 2017

Evolution of MicroRNAs

Evolution of RNA-Based Networks

scientific article published on 04 September 2015

Evolution of Vault RNAs

Evolution of metabolic networks: a computational frame-work

article

Evolution of microRNAs

scientific article published on January 2006

Evolution of microRNAs located within Hox gene clusters

scientific article

Evolution of mitochondrial gene orders in echinoderms

article

Evolution of spliceosomal snRNA genes in metazoan animals

scientific article

Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε

article published in 2010

Evolution of the let-7 microRNA family

scientific article published on March 2012

Evolution of the unspliced transcriptome

scientific article published on 20 August 2015

Evolution of the vertebrate Y RNA cluster

scientific article

Evolution of the vertebrate parahox clusters

scholarly article by Sonja J. Prohaska & Peter F. Stadler published 2006 in Journal of Experimental Zoology. Part B: Molecular and Developmental Evolution

Evolution of vault RNAs.

scientific article

Evolution. Transitions from nonliving to living matter

scientific article published in February 2004

Evolutionary Genomics of Hox Gene Clusters

article

Evolutionary Genomics of microRNAs and Their Relatives

article published in 2010

Evolutionary clues in lncRNAs

scientific article

Evolving towards the hypercycle: A spatial model of molecular evolution

article

ExceS-A: an exon-centric split aligner

scientific article published on 07 March 2022

Exclusion of repetitive DNA elements from gnathostome Hox clusters

scientific article

Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem

scientific article published on 19 December 2017

Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry

Exploration of the chemical space and its three historical regimes

scientific article published on 11 June 2019

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

scientific article published in 2019

Exploring protein sequence space using knowledge-based potentials.

scientific article

Exploring the lower part of discrete polymer model energy landscapes

article

FORMAN–RICCI CURVATURE FOR HYPERGRAPHS

scientific article published in 2021

FRANz: reconstruction of wild multi-generation pedigrees

scientific article published on 08 February 2009

Fast Fourier Transform for Fitness Landscapes

Fast accessibility-based prediction of RNA-RNA interactions

scientific article published on 18 May 2011

Fast and reliable prediction of noncoding RNAs

scientific article

Fast and sensitive mapping of bisulfite-treated sequencing data

scientific article

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

scientific article published on 18 March 2011

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

scientific article

Finding the K best synthesis plans

scientific article published on 5 April 2018

Fitch Graph Completion

Fitness landscapes

Fitness landscapes arising from the sequence-structure maps of biopolymers

Folding kinetics of large RNAs

scientific article published on 6 March 2008

Fractal geometry of spin-glass models

Fragrep: an efficient search tool for fragmented patterns in genomic sequences

scientific article

From event-labeled gene trees to species trees

From pairs of most similar sequences to phylogenetic best matches

scientific article published on 09 April 2020

From sequences to shapes and back: a case study in RNA secondary structures

scientific article published in March 1994

Full characterization of a strange attractor

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration

scientific article

GC skew and mitochondrial origins of replication

scientific article published on 7 June 2014

GLASSY STATES IN A SHAKEN SANDBOX

Gene phylogenies and protein–protein interactions: possible artifacts resulting from shared protein interaction partners

article

Generalized topological spaces in evolutionary theory and combinatorial chemistry.

scientific article

Generic Context-Aware Group Contributions

scientific article published on 01 June 2020

Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting

Generic Properties of the Sequence-Structure Relations of Biopolymers

Generic properties of combinatory maps: Neutral networks of RNA secondary structures

scientific article published on 01 March 1997

Generic strategies for chemical space exploration

scientific article

Genetic aspects of mitochondrial genome evolution

scientific article

Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits

scientific article published on 26 November 2019

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

scientific article

Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera

Genomic and morphological evidence converge to resolve the enigma of Strepsiptera

scientific article

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

scientific article published on 29 March 2019

Genomic organization of eukaryotic tRNAs

scientific article (publication date: 28 April 2010)

Genotype-Phenotype Maps

article published in 2006

Geometry and Coarse-Grained Representations of Landscapes

article

Glassy States in a Shaken Sandbox

Graph Laplacians, nodal domains, and hyperplane arrangements

article

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

scientific article published on 11 September 2014

HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis

scientific article published on 24 July 2008

HLA-DRB1∗0401 and HLA-DRB1∗0408 Are Strongly Associated with the Development of Antibodies against Interferon-β Therapy in Multiple Sclerosis

scientific article published on 3 October 2008

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data

scientific article

Hamming chromatography

scientific article published in May 1996

Hidden treasures in unspliced EST data

scientific article

High-field (3 Tesla) MRI of the navicular apparatus of sound horses shows good agreement to histopathology

scientific article published on 11 December 2019

Homology Search with Fragmented Nucleic Acid Sequence Patterns

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

scientific article

How to Multiply Dynamic Programming Algorithms

Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)

scientific article (publication date: May 2009)

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny

scholarly article by Jeremy D. Raincrow et al published 17 June 2011 in Journal of Experimental Zoology. Part B: Molecular and Developmental Evolution

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and characterization of novel conserved RNA structures in Drosophila

article published in 2018

Identification and classification of small RNAs in transcriptome sequence data.

scientific article

Identification of RNA 3´ ends and termination sites in Haloferax volcanii

scientific article published on 10 February 2020

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

scientific article published on 9 May 2013

Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach

scientific article published on 12 April 2013

Immune networks modeled by replicator equations

scientific article published in January 1994

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

scientific article published in December 2011

In Silico Evolution of Early Metabolism

article

In silicoSupport for Eschenmoser’s Glyoxylate Scenario

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

scientific article published on 11 April 2018

Independent Hox-cluster duplications in lampreys

article published in 2003

Indications for potential parent-of-origin effects within the FTO gene

scientific article

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

Inferring chemical reaction patterns using rule composition in graph grammars

article

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

scientific article

Inferring phylogenetic trees from the knowledge of rare evolutionary events

scientific article

Influence of subclinical pulmonary findings on cardiac parameters in Icelandic horses

scientific article published in March 2008

Influence of valvular insufficiency and recurrent airway obstruction on haemodynamics and therapy in warmblood horses with atrial fibrillation

scientific article published on 26 December 2007

Innovation in gene regulation: the case of chromatin computation

scientific article published on 18 March 2010

Interactions in Oligonucleotide Hybrid Duplexes on Microarrays

article published in 2004

Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer

scientific article published on 11 May 2007

Invertebrate 7SK snRNAs.

scientific article published on 12 January 2008

Keeping it complicated: Mitochondrial genome plasticity across diplonemids

scientific article published on 26 October 2017

Kiwi genome provides insights into evolution of a nocturnal lifestyle

scientific article

Knowledge-based reasoning to annotate noncoding RNA using multi-agent system

scientific article published on 24 June 2015

LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing

scientific article published on 16 September 2019

Lacking alignments? The next-generation sequencing mapper segemehl revisited

scientific article published on 13 March 2014

Landscape encodings enhance optimization

scientific article

Landscape statistics of the low-autocorrelation binary string problem

article published in 2000

Landscapes and Effective Fitness

Landscapes and their correlation functions

Landscapes on spaces of trees

Landscapes: complex optimization problems and biopolymer structures

scientific article published on September 1994

Laplacian Eigenvectors of Graphs

article

Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch

scientific article published on 01 February 2021

Linear operators on correlated landscapes

article published in 1994

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 Algorithms for the Prime Factorization of Strong Product Graphs

Local RNA base pairing probabilities in large sequences

scientific article published on 20 December 2005

MCPIP1 ribonuclease can bind and cleave AURKA mRNA in MYCN-amplified neuroblastoma cells

scientific article published on 06 August 2020

MITOS: improved de novo metazoan mitochondrial genome annotation

scientific article published on 7 September 2012

MOLECULAR REPLICATOR DYNAMICS

article

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

article published in 2005

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.

scientific article

Matching of Soulmates: coevolution of snoRNAs and their targets

scientific article published on 24 October 2013

Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete

article

Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies

scientific article

Memory efficient folding algorithms for circular RNA secondary structures

scientific article

Metastable states in short-rangedp-spin glasses

MicroRNA or Not MicroRNA?

Minimum cycle bases of Halin graphs

Minimum path bases and relevant paths

Mitochondrial Genome Evolution

Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata

scientific article published on 10 February 2010

Mitochondrial genomes in <i>Perkinsus</i> decode conserved frameshifts in all genes

Mitogenomics and metazoan evolution

scientific article published in November 2013

Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example

Modeling RNA Folding

article

Modeling amino acid substitution patterns in orthologous and paralogous genes.

scientific article published on 26 July 2006

Molecular Phylogenetics 2014

scientific article published on 2 June 2015

Molecular Phylogenetics 2016.

scientific article

Molecular evolution of a microRNA cluster

scientific article

Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.

scientific article published on May 2005

Molecular evolution of the non-coding eosinophil granule ontogeny transcript

scientific article published in 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Multiple sequence alignment with user-defined anchor points

scientific article published on 19 April 2006

Multiple sequence alignment with user-defined constraints at GOBICS.

scientific article published on 16 November 2004

Multiple sequence alignments of partially coding nucleic acid sequences

scientific article

Mutate now, die later. Evolutionary dynamics with delayed selection

Mutation in autocatalytic reaction networks

article

Mutation in autocatalytic reaction networks. An analysis based on perturbation theory

scientific article published in January 1992

NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES

Nature and evolution of early replicons

article

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

article by Jakob L. Andersen et al published 25 September 2013 in Entropy

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences

scientific article published on 3 June 2008

Near intron pairs and the metazoan tree

scientific article published on 28 November 2012

Near intron positions are reliable phylogenetic markers: an application to holometabolous insects

scientific article published on 21 February 2008

Nematode sbRNAs: homologs of vertebrate Y RNAs

scientific article

Networks in molecular evolution

article

Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force

scientific article

Neutrality in fitness landscapes

scholarly article by Christian Reidys & Peter F. Stadler published January 2001 in Applied Mathematics and Computation

Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell

article published in 2016

New journal: Algorithms for Molecular Biology

scientific article published on 28 February 2006

Noisy: identification of problematic columns in multiple sequence alignments

scientific article published on 24 June 2008

Non-coding RNA annotation of the genome of Trichoplax adhaerens

scientific article published on 16 January 2009

Non-coding RNAs in Ciona intestinalis

scientific article published in September 2005

Noncoding RNA

article from 2010

On the Complexity of Reconstructing Chemical Reaction Networks

On the evolution of primitive genetic codes

article

Optimization of parameters for coverage of low molecular weight proteins

scientific article published on 28 August 2010

Optimizing RNA structures by sequence extensions using RNAcop

scientific article

Oriented components and their separations

Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies

scientific article

Orthology detection combining clustering and synteny for very large datasets

scientific article

Orthology relations, symbolic ultrametrics, and cographs

scientific article published on 29 March 2012

PCR survey of hox genes in the goldfish Carassius auratus auratus

scientific article published in May 2007

PCR survey ofXenoturbella bockiHox genes

article

PLEXY: efficient target prediction for box C/D snoRNAs

scientific article

PROCESS FLOW FOR CLASSIFICATION AND CLUSTERING OF FRUIT FLY GENE EXPRESSION PATTERNS.

scientific article published on December 2008

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements

scientific article published on 23 August 2017

Partition function and base pairing probabilities for RNA-RNA interaction prediction

scientific article published on 11 August 2009

Partition function and base pairing probabilities of RNA heterodimers

scientific article

Patterning the insect eye: From stochastic to deterministic mechanisms

scientific article published on 15 November 2018

Permanence of sparse catalytic networks

scientific article published in January 1996

Phase transition and landscape statistics of the number partitioning problem

scientific article

Phylogenetic Footprinting and Consistent Sets of Local Aligments

scholarly article by Wolfgang Otto et al published 2011 in Lecture Notes in Computer Science

Phylogenetic distribution of plant snoRNA families

scientific article

Phylogenetics beyond biology

scholarly article by Nancy Retzlaff & Peter F. Stadler published 21 June 2018 in Theory in Biosciences

Phylogenomics with paralogs

scientific article

Plasma atrial natriuretic peptide concentration in warmblood horses with heart valve regurgitations

scientific article published on 26 November 2007

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

scientific article published on 2 June 2010

Population Dependent Fourier Decomposition of Fitness Landscapes over Recombination Spaces: Evolvability of Complex Characters

scientific article published on 01 May 2000

Prediction of RNA base pairing probabilities on massively parallel computers

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Prediction of consensus RNA secondary structures including pseudoknots

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Prediction of locally stable RNA secondary structures for genome-wide surveys

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scholarly article by Kristin Missal et al published 15 July 2006 in Journal of Experimental Zoology. Part B: Molecular and Developmental Evolution

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Prevalent and distinct spliceosomal 3'-end processing mechanisms for fungal telomerase RNA.

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Processed Small RNAs in Archaea and BHB Elements

Product Grammars for Alignment and Folding

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Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.

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Pseudoknots in RNA folding landscapes.

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Pulmonary artery wedge pressure during treadmill exercise in warmblood horses with atrial fibrillation

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Quasi-independence, homology and the unity of type: a topological theory of characters.

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RELEVANT CYCLES IN CHEMICAL REACTION NETWORKS

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RNAalifold: improved consensus structure prediction for RNA alignments

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The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

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The primary transcriptome of the major human pathogen Helicobacter pylori

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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

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Three different premature stop codons lead to skipping of exon 7 in neurofibromatosis type I patients

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Time-consistent reconciliation maps and forbidden time travel

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Topology and prediction of RNA pseudoknots

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Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution

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Tractable RNA-ligand interaction kinetics

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Translation in Mammalian Mitochondria: Order and Disorder Linked to tRNAs and Aminoacyl-tRNA Synthetases

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction

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U6 snRNA intron insertion occurred multiple times during fungi evolution

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U7 snRNAs: a computational survey

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Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

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Unique square property, equitable partitions, and product-like graphs

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate

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Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster.

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Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum

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Variations on RNA folding and alignment: lessons from Benasque.

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ViennaRNA Package 2.0

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Viral RNA and evolved mutational robustness

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Visual Network Analysis of Dynamic Metabolic Pathways

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Why Some Fitness Landscapes are Fractal

Widespread purifying selection on RNA structure in mammals

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ceRNAs in plants: computational approaches and associated challenges for target mimic research

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

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

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metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

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miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes

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ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation

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plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants

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snoStrip: a snoRNA annotation pipeline

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tRNAdb 2009: compilation of tRNA sequences and tRNA genes

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