Search Results - "ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics"

Multiseed Lossless Filtration

Authors: Kucherov, Gregory Noé, Laurent Roytberg, Mikhail et al.

Contributors: Kucherov, Gregory Noé, Laurent Roytberg, Mikhail et al.

Source: Lecture Notes in Computer Science ISBN: 9783540223412

Subject Terms: string matching, Molecular Sequence Data, 0206 medical engineering, [INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS], 0102 computer and information sciences, 02 engineering and technology, seed family, Quantitative Biology - Quantitative Methods, 01 natural sciences, Sequence Homology, Nucleic Acid, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], filtration, dynamic programming, Expressed Sequence Tags, gapped q-gram, Base Sequence, oligonucleotide selection, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems/F.2.2.3: Pattern matching, local alignment, Sequence Analysis, DNA, ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.3: Applications, sequence similarity, multiple spaced seeds, FOS: Biological sciences, est, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], gapped seed, Sequence Alignment, Algorithms

File Description: application/pdf

Access URL: http://arxiv.org/pdf/0901.3215
https://hal.inria.fr/inria-00354810/file/KucherovNoeRoytberg.pdf
https://pubmed.ncbi.nlm.nih.gov/17044164
http://arxiv.org/abs/0901.3215
https://inria.hal.science/inria-00000718v1
https://doi.org/10.1109/tcbb.2005.12
https://inria.hal.science/inria-00354810v1
https://inria.hal.science/inria-00354810v1/document
https://doi.org/10.1109/tcbb.2005.12
https://rd.springer.com/chapter/10.1007/978-3-540-27801-6_22
https://link.springer.com/chapter/10.1007/978-3-540-27801-6_22
http://ui.adsabs.harvard.edu/abs/2009arXiv0901.3215K/abstract
https://dl.acm.org/doi/10.1109/TCBB.2005.12
http://ieeexplore.ieee.org/document/1416851/
https://ieeexplore.ieee.org/document/1416851/
http://export.arxiv.org/pdf/0901.3215
http://www.ncbi.nlm.nih.gov/pubmed/17044164

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs

Authors: Reinharz, Vladimir Ponty, Yann Waldispühl, Jérôme et al.

Contributors: Reinharz, Vladimir Ponty, Yann Waldispühl, Jérôme et al.

Source: Journal of Computational Biology. 20:905-919

Subject Terms: 0301 basic medicine, RNA, Untranslated, 0206 medical engineering, 02 engineering and technology, Quantitative Biology - Quantitative Methods, Evolution, Molecular, 03 medical and health sciences, RNA, Ribosomal, 16S, Humans, Computer Simulation, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Models, Genetic, Sequence Analysis, RNA, RNA, Ribosomal, 5S, High-Throughput Nucleotide Sequencing, secondary structure, mutations, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], RNA, Bacterial, ROC Curve, FOS: Biological sciences, Next-Generation sequencing, isostericity, RNA, Nucleic Acid Conformation, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithms

File Description: application/pdf

Access URL: https://europepmc.org/articles/pmc3822367?pdf=render
https://pubmed.ncbi.nlm.nih.gov/24134390
http://arxiv.org/abs/1305.7068

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences

Authors: Zhang, Yang Ponty, Yann Blanchette, Mathieu et al.

Contributors: Zhang, Yang Ponty, Yann Blanchette, Mathieu et al.

Source: Nucleic Acids Res

Subject Terms: 0301 basic medicine, Internet, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Saccharomyces cerevisiae Proteins, Sequence Analysis, RNA, Proteins, Articles, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Repressor Proteins, 03 medical and health sciences, Nucleic Acid Conformation, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, RNA, Messenger, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Base Pairing, Algorithms, Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://academic.oup.com/nar/article-pdf/41/W1/W480/16944176/gkt461.pdf
https://pubmed.ncbi.nlm.nih.gov/23748952
https://inria.hal.science/hal-00819017v1
https://inria.hal.science/hal-00819017v1/document
https://doi.org/10.1093/nar/gkt461
https://paperity.org/p/34537783/sparcs-a-web-server-to-analyze-un-structured-regions-in-coding-rna-sequences
https://europepmc.org/articles/PMC3692110
https://dblp.uni-trier.de/db/journals/nar/nar41.html#ZhangPBLW13
https://hal.inria.fr/hal-00819017/document
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692110/
https://hal.inria.fr/hal-00819017

RNA Locally Optimal Secondary Structures

Authors: Saffarian, Azadeh Giraud, Mathieu de Monte, Antoine et al.

Contributors: Saffarian, Azadeh Giraud, Mathieu de Monte, Antoine et al.

Source: Journal of Computational Biology. 19:1120-1133

Subject Terms: ACM: I.: Computing Methodologies/I.5: PATTERN RECOGNITION, 0301 basic medicine, Internet, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Sequence Analysis, RNA, ACM: H.: Information Systems/H.3: INFORMATION STORAGE AND RETRIEVAL, 0206 medical engineering, 02 engineering and technology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 03 medical and health sciences, Nucleic Acid Conformation, RNA, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithms, Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://hal.inria.fr/hal-00756249/file/saffarian-2012-locally-optimal.pdf
https://pubmed.ncbi.nlm.nih.gov/23057822
https://inria.hal.science/hal-00756249v1/document
https://doi.org/10.1089/cmb.2010.0178
https://inria.hal.science/hal-00756249v1
https://online.liebertpub.com/doi/abs/10.1089/cmb.2010.0178
https://hal.inria.fr/hal-00756249
http://www.liebertpub.com/doi/10.1089/cmb.2010.0178
https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0178
http://online.liebertpub.com/doi/full/10.1089/cmb.2010.0178
https://hal.inria.fr/hal-00756249/document

CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks

Authors: Mateescu, Radu Monteiro, Pedro T. Dumas, Estelle et al.

Contributors: Mateescu, Radu Monteiro, Pedro T. Dumas, Estelle et al.

Source: Theoretical Computer Science. 412:2854-2883

Subject Terms: 0301 basic medicine, Model checking, [INFO.INFO-SE] Computer Science [cs]/Software Engineering [cs.SE], Temporal logic, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Theoretical Computer Science, 03 medical and health sciences, temporal logic, ACM: D.: Software/D.2: SOFTWARE ENGINEERING/D.2.4: Software/Program Verification/D.2.4.3: Formal methods, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Verification, systems biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], model checking, ACM: D.: Software/D.2: SOFTWARE ENGINEERING/D.2.4: Software/Program Verification/D.2.4.4: Model checking, 3. Good health, genetic regulatory networks, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], verification, Systems biology, Genetic regulatory networks, Computer Science(all)

File Description: application/pdf

Designing Efficient Spaced Seeds for SOLiD Read Mapping

Authors: Noé, Laurent Gîrdea, Marta Kucherov, Gregory et al.

Contributors: Noé, Laurent Gîrdea, Marta Kucherov, Gregory et al.

Source: Adv Bioinformatics

Subject Terms: Spaced seeds, 0301 basic medicine, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Applied Biosystems SOLiD, read mapping, 0206 medical engineering, ACM: E.: Data/E.2: DATA STORAGE REPRESENTATIONS/E.2.2: Hash-table representations, ACM: G.: Mathematics of Computing/G.4: MATHEMATICAL SOFTWARE/G.4.4: Parallel and vector implementations, 02 engineering and technology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.3: Applications, 03 medical and health sciences, seed design, color space alignment, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Research Article

Access URL: http://downloads.hindawi.com/journals/abi/2010/708501.pdf
https://pubmed.ncbi.nlm.nih.gov/20936175
https://www.ncbi.nlm.nih.gov/pubmed/20936175
http://europepmc.org/articles/PMC2945724
https://www.hindawi.com/journals/abi/2010/708501/
https://www.archives-ouvertes.fr/inria-00527029v1
https://pubmed.ncbi.nlm.nih.gov/20936175/
http://downloads.hindawi.com/archive/2010/708501.pdf

A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods

Authors: Eng, Catherine Asthana, Charu Aigle, Bertrand et al.

Contributors: Eng, Catherine Asthana, Charu Aigle, Bertrand et al.

Source: Journal of Computational Biology 9 (16), 1211-1225. (2009)

Subject Terms: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], 0301 basic medicine, 0303 health sciences, Binding Sites, Models, Genetic, second-order hidden markov models, transcription factor binding site, Streptomyces coelicolor, STOCHASTIC MODEL, COMBINATORIAL METHODS, SECOND-ORDER HIDDEN MARKOV MODELS, BACTERIAL PROMOTERS, TRANSCRIPTION FACTOR BINDING SITE, STREPTOMYCES COELICOLOR, Streptomyces, Markov Chains, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], fouille de données, modèle stochastique, 03 medical and health sciences, modèle mathématique, modèle de markov caché, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, Promoter Regions, Genetic, stochastic model, bacterial promoters, Genome, Bacterial, combinatorial methods

File Description: application/pdf

Access URL: https://hal.inria.fr/inria-00419969/file/jcb-eng.pdf
https://pubmed.ncbi.nlm.nih.gov/19772433
https://inria.hal.science/inria-00419969v1/document
https://doi.org/10.1089/cmb.2008.0122
https://inria.hal.science/inria-00419969v1
http://prodinra.inra.fr/record/48251

On Subset Seeds for Protein Alignment

Authors: Roytberg, Mikhail Gambin, Anna Noé, Laurent et al.

Contributors: Roytberg, Mikhail Gambin, Anna Noé, Laurent et al.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6:483-494

Subject Terms: 0301 basic medicine, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 0206 medical engineering, Computational Biology, Proteins, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems/F.2.2.3: Pattern matching, 02 engineering and technology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Quantitative Biology - Quantitative Methods, Models, Biological, ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.3: Applications, 03 medical and health sciences, ROC Curve, Terminology as Topic, FOS: Biological sciences, Cluster Analysis, ACM: H.: Information Systems/H.2: DATABASE MANAGEMENT/H.2.8: Database Applications, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, Amino Acid Sequence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Amino Acids, Sequence Alignment, Algorithms, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: http://arxiv.org/pdf/0901.3198
https://pubmed.ncbi.nlm.nih.gov/19644175
http://arxiv.org/abs/0901.3198
https://inria.hal.science/inria-00354773v1/document
https://doi.org/10.1109/tcbb.2009.4
https://inria.hal.science/inria-00354773v1
http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.ieee-000004752807
https://hal.inria.fr/inria-00354773
https://dl.acm.org/doi/10.1109/TCBB.2009.4
https://www.computer.org/csdl/journal/tb/2009/03/ttb2009030483/13rRUxZRbmA
https://www.ncbi.nlm.nih.gov/pubmed/19644175
https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_1584087

Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana

Authors: Tempel, Sébastien Nicolas, Jacques El Amrani, Abdelhak et al.

Contributors: Tempel, Sébastien Nicolas, Jacques El Amrani, Abdelhak et al.

Source: Gene. 403:18-28

Subject Terms: 0301 basic medicine, Combinatorial optimization, DNA, Plant, Bioinformatics, Molecular Sequence Data, Arabidopsis, Chromosomes, Plant, 03 medical and health sciences, Terminology as Topic, Genome dynamics, Cluster Analysis, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Plant Proteins, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Base Sequence, Models, Genetic, Chimera, Helitron, Transposable Elements, Sequence analysis, Computational Biology, Sequence Analysis, DNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], DNA Transposable Elements, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Syntactical Modelling, Genome, Plant

File Description: application/pdf

Access URL: https://hal.inria.fr/inria-00180376/file/GENE.pdf
https://pubmed.ncbi.nlm.nih.gov/17889452
https://hal.inria.fr/inria-00180376/document
https://europepmc.org/abstract/MED/17889452
https://www.sciencedirect.com/science/article/pii/S0378111907003654
https://www.ncbi.nlm.nih.gov/pubmed/17889452
https://hal.inria.fr/inria-00180376

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks

Authors: Siegel, Anne Radulescu, Ovidiu Le Borgne, Michel et al.

Contributors: Siegel, Anne Radulescu, Ovidiu Le Borgne, Michel et al.

Source: Biosystems. 84:153-174

Subject Terms: 0301 basic medicine, GENE EXPRESSION, REGULATION NETWORK, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV]Life Sciences [q-bio], BIOINFORMATICS, Fatty Acids, 0206 medical engineering, 02 engineering and technology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], EXPRESSION DE GENES, Models, Biological, [SDV] Life Sciences [q-bio], 03 medical and health sciences, RESEAU DE REGULATION, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Oligonucleotide Array Sequence Analysis

File Description: application/pdf

Access URL: https://hal.inria.fr/inria-00178809/file/BiosystemsSRLVOL.pdf
https://pubmed.ncbi.nlm.nih.gov/16556482
https://hal.inrae.fr/hal-02656133v1
https://inria.hal.science/inria-00178809v1
https://hal.inria.fr/inria-00178809/document
https://hal.inria.fr/inria-00178809
https://www.sciencedirect.com/science/article/pii/S0303264705001723
http://www.sciencedirect.com/science/article/pii/S0303264705001723
https://www.ncbi.nlm.nih.gov/pubmed/16556482

Topology and static response of interaction networks in molecular biology

Authors: Radulescu, Ovidiu Lagarrigue, Sandrine Siegel, Anne et al.

Contributors: Radulescu, Ovidiu Lagarrigue, Sandrine Siegel, Anne et al.

Source: Journal of The Royal Society Interface. 3:185-196

Subject Terms: 0301 basic medicine, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Models, Statistical, [SDV]Life Sciences [q-bio], BIOINFORMATICS, 0206 medical engineering, Gene Expression, 02 engineering and technology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Models, Biological, Cell Physiological Phenomena, [SDV] Life Sciences [q-bio], MOLECULAR NETWORK, 03 medical and health sciences, Protein Interaction Mapping, Animals, Humans, TRANSCRIPTOMICS, Computer Simulation, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Molecular Biology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Signal Transduction

File Description: application/pdf

Access URL: https://europepmc.org/articles/pmc1618492?pdf=render
https://pubmed.ncbi.nlm.nih.gov/16849230
https://hal.inrae.fr/hal-02654772v1
https://inria.hal.science/inria-00178842v1
https://doi.org/10.1098/rsif.2005.0092
https://inria.hal.science/inria-00178842v1/document
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618492/
https://rsif.royalsocietypublishing.org/content/3/6/185
https://www.royalsocietypublishing.org/doi/10.1098/rsif.2005.0092
https://hal.inria.fr/inria-00178842/document
https://europepmc.org/article/MED/16849230
https://hal.inria.fr/inria-00178842

Complex Qualitative Models in Biology: A New Approach

Authors: Veber, Philippe Le Borgne, Michel Siegel, Anne et al.

Contributors: Veber, Philippe Le Borgne, Michel Siegel, Anne et al.

Source: Complexus. 2:140-151

Subject Terms: 0301 basic medicine, 03 medical and health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Molecular Networks (q-bio.MN), FOS: Biological sciences, 0206 medical engineering, Quantitative Biology - Molecular Networks, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, 02 engineering and technology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

Access URL: https://www.karger.com/Article/Pdf/93686
http://arxiv.org/abs/q-bio/0604017
https://inria.hal.science/inria-00178819v1
https://hal.archives-ouvertes.fr/inria-00178819
https://hal.inria.fr/inria-00178819
https://www.irisa.fr/symbiose/people/asiegel/Articles/eccs.pdf

Computational Protein Design: trying an Answer Set Programming approach to solve the problem

Authors: Bazille, Hugo Nicolas, Jacques École normale supérieure - Rennes (ENS Rennes) et al.

Contributors: Bazille, Hugo Nicolas, Jacques École normale supérieure - Rennes (ENS Rennes) et al.

Source: 10th Workshop on Constraint-Based Methods for Bioinformatics (WCB'14)
https://inria.hal.science/hal-01063030
10th Workshop on Constraint-Based Methods for Bioinformatics (WCB'14), Nicos Angelopoulos (Imperial College, UK) Simon de Givry (MIAT-INRA, France), Sep 2014, Lyon, France

Subject Terms: Computational Protein Design, Answer Set Programming, Bioinformatics, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, ACM: I.: Computing Methodologies/I.2: ARTIFICIAL INTELLIGENCE/I.2.1: Applications and Expert Systems/I.2.1.4: Medicine and science, ACM: I.: Computing Methodologies/I.2: ARTIFICIAL INTELLIGENCE/I.2.3: Deduction and Theorem Proving/I.2.3.3: Logic programming, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]

Subject Geographic: Lyon, France

Availability: https://inria.hal.science/hal-01063030
https://inria.hal.science/hal-01063030v1/document
https://inria.hal.science/hal-01063030v1/file/main.pdf

Modeling parsimonious putative regulatory networks: complexity and heuristic approach

Authors: Acuña, Vicente Aravena, Andrés Maass, Alejandro et al.

Contributors: Acuña, Vicente Aravena, Andrés Maass, Alejandro et al.

Source: 15th conference in Verification, Model Checking, and Abstract Interpretation
https://inria.hal.science/hal-00926477
15th conference in Verification, Model Checking, and Abstract Interpretation, 2014, San Diego, United States. pp.322-336, ⟨10.1007/978-3-642-54013-4_18⟩

Subject Terms: ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]

Subject Geographic: San Diego, United States

Availability: https://inria.hal.science/hal-00926477
https://inria.hal.science/hal-00926477v1/document
https://inria.hal.science/hal-00926477v1/file/complex.pdf
https://doi.org/10.1007/978-3-642-54013-4_18

Flexible RNA design under structure and sequence constraints using formal languages

Authors: Zhou, Yu Ponty, Yann Vialette, Stéphane et al.

Contributors: Zhou, Yu Ponty, Yann Vialette, Stéphane et al.

Source: ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013 ; https://inria.hal.science/hal-00823279 ; ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States

Subject Terms: RNA design, Context-free languages, Random generation, ACM: F.: Theory of Computation/F.4: MATHEMATICAL LOGIC AND FORMAL LANGUAGES/F.4.3: Formal Languages/F.4.3.1: Classes defined by grammars or automata (e.g., regular sets, recursive sets), ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.1: Combinatorics/G.2.1.0: Combinatorial algorithms, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]

Subject Geographic: Bethesda, Washigton DC, United States

Relation: info:eu-repo/semantics/altIdentifier/arxiv/1305.3830; ARXIV: 1305.3830

Availability: https://inria.hal.science/hal-00823279
https://inria.hal.science/hal-00823279v2/document
https://inria.hal.science/hal-00823279v2/file/design.pdf

A spectral clustering approach of vegetation components for describing plant topology and geometry from terrestrial waveform LiDAR data

Authors: Boltcheva, Dobrina Casella, Eric Cumont, Rémy et al.

Contributors: Boltcheva, Dobrina Casella, Eric Cumont, Rémy et al.

Source: FSPM2013 - 7th International Conference on Functional-Structural Plant Models ; https://inria.hal.science/hal-00817508 ; FSPM2013 - 7th International Conference on Functional-Structural Plant Models, Jun 2013, Saariselkä, Finland

Subject Terms: ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR]

Subject Geographic: Saariselkä, Finland

Availability: https://inria.hal.science/hal-00817508
https://inria.hal.science/hal-00817508v1/document
https://inria.hal.science/hal-00817508v1/file/742-3717-1-PB.pdf

Compareads: comparing huge metagenomic experiments

Authors: Maillet, Nicolas Lemaitre, Claire Chikhi, Rayan et al.

Contributors: Maillet, Nicolas Lemaitre, Claire Chikhi, Rayan et al.

Source: RECOMB Comparative Genomics 2012 ; https://inria.hal.science/hal-00720951 ; RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil

Subject Terms: ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, ACM: E.: Data/E.1: DATA STRUCTURES, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]

Subject Geographic: Niterói, Brazil

Availability: https://inria.hal.science/hal-00720951
https://inria.hal.science/hal-00720951v1/document
https://inria.hal.science/hal-00720951v1/file/compareads_recomb_cg.pdf

Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots

Authors: Sheikh, Saad Backofen, Rolf Ponty, Yann et al.

Contributors: Sheikh, Saad Backofen, Rolf Ponty, Yann et al.

Source: CPM - 23rd Annual Symposium on Combinatorial Pattern Matching - 2012 ; https://inria.hal.science/hal-00670232 ; CPM - 23rd Annual Symposium on Combinatorial Pattern Matching - 2012, Juha Kärkkäinen, Jul 2012, Helsinki, Finland. pp.321--333, ⟨10.1007/978-3-642-31265-6_26⟩

Subject Terms: RNA folding, General pseudoknots, Hardness, Inapproximability, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.2: Graph Theory/G.2.2.0: Graph algorithms, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems/F.2.2.1: Computations on discrete structures, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems/F.2.2.3: Pattern matching, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]

Subject Geographic: Helsinki, Finland

Availability: https://inria.hal.science/hal-00670232
https://inria.hal.science/hal-00670232v3/document
https://inria.hal.science/hal-00670232v3/file/NPCompleteness-Stacking.pdf
https://doi.org/10.1007/978-3-642-31265-6_26

Small-sample brain mapping: sparse recovery on spatially correlated designs with randomization and clustering

Authors: Varoquaux, Gaël Gramfort, Alexandre Thirion, Bertrand et al.

Contributors: Varoquaux, Gaël Gramfort, Alexandre Thirion, Bertrand et al.

Source: International Conference on Machine Learning ; https://inria.hal.science/hal-00705192 ; International Conference on Machine Learning, Andrew McCallum, Jun 2012, Edimbourg, United Kingdom

Subject Terms: brain imaging, fMRI, Sparse recovery, correlated design, clustering, randomization, ACM: G.: Mathematics of Computing/G.3: PROBABILITY AND STATISTICS/G.3.5: Multivariate statistics, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, ACM: I.: Computing Methodologies/I.5: PATTERN RECOGNITION/I.5.1: Models/I.5.1.4: Statistical, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH]

Subject Geographic: Edimbourg, United Kingdom

Availability: https://inria.hal.science/hal-00705192
https://inria.hal.science/hal-00705192v1/document
https://inria.hal.science/hal-00705192v1/file/paper.pdf

Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models

Authors: Gardy, Danièle Ponty, Yann Parallélisme, Réseaux, Systèmes, Modélisation (PRISM) et al.

Contributors: Gardy, Danièle Ponty, Yann Parallélisme, Réseaux, Systèmes, Modélisation (PRISM) et al.

Source: Proceedings of GASCOM'10 ; GASCOM - 8th conference on random generation of combinatorial structures - 2010 ; https://inria.hal.science/inria-00543150 ; GASCOM - 8th conference on random generation of combinatorial structures - 2010, LACIM, UQAM, Sep 2010, Montréal, Canada. 14pp

Subject Terms: Coupon collector, Birthday paradox, Random generation, Context-free languages, ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.1: Combinatorics/G.2.1.2: Generating functions, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems/F.2.2.1: Computations on discrete structures, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]

Subject Geographic: Montréal

Time: Montréal, Canada

Relation: info:eu-repo/semantics/altIdentifier/arxiv/1012.1129; ARXIV: 1012.1129

Availability: https://inria.hal.science/inria-00543150
https://inria.hal.science/inria-00543150v1/document
https://inria.hal.science/inria-00543150v1/file/GASCOM-2010-Allocations.pdf