Suchergebnisse - "sequence"

Coevolutionary signals in multiple sequence alignments improve virulence factor prediction with an MSA Transformer.

Autoren: Kim T Cho C Lee D et al.

Quelle: Scientific reports [Sci Rep] 2025 Nov 19; Vol. 15 (1), pp. 40688. Date of Electronic Publication: 2025 Nov 19.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH-Schlagworte: Virulence Factors*/genetics , Virulence Factors*/chemistry , Sequence Alignment*/methods , Evolution, Molecular* , Computational Biology*/methods , Bacterial Proteins*/genetics , Bacterial Proteins*/chemistry, Algorithms ; Amino Acid Sequence ; Deep Learning ; Sequence Analysis, Protein/methods

Evaluating the significance of embedding-based protein sequence alignment with clustering and double dynamic programming for remote homology.

Autoren: Spicer R Raychawdhary N Danwada S et al.

Quelle: Scientific reports [Sci Rep] 2025 Nov 12; Vol. 15 (1), pp. 39601. Date of Electronic Publication: 2025 Nov 12.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH-Schlagworte: Proteins*/chemistry , Proteins*/genetics , Sequence Alignment*/methods , Sequence Homology, Amino Acid* , Sequence Analysis, Protein*/methods, Cluster Analysis ; Algorithms ; Computational Biology/methods ; Amino Acid Sequence ; Dynamic Programming

Enhancing the Feature Representation of Protein Sequence Descriptors in Protein-Protein Interaction Prediction.

Autoren: Tran HN Quynh NP Zhao H et al.

Quelle: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2025 Dec; Vol. 17 (4), pp. 1018-1037. Date of Electronic Publication: 2025 Jun 02.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1867-1462 (Electronic) Linking ISSN: 18671462 NLM ISO Abbreviation: Interdiscip Sci Subsets: MEDLINE

MeSH-Schlagworte: Proteins*/chemistry , Proteins*/metabolism , Computational Biology*/methods , Protein Interaction Mapping*/methods , Sequence Analysis, Protein*/methods, Databases, Protein ; Amino Acid Sequence ; Software ; Machine Learning ; Algorithms

Conservation of human NMDA receptor subunits and disease variants in zebrafish.

Autoren: Nebet ER Aprea C Zoodsma JD et al.

Quelle: BMC genomics [BMC Genomics] 2025 Nov 13; Vol. 26 (1), pp. 1042. Date of Electronic Publication: 2025 Nov 13.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH-Schlagworte: Zebrafish*/genetics , Receptors, N-Methyl-D-Aspartate*/genetics , Receptors, N-Methyl-D-Aspartate*/chemistry , Receptors, N-Methyl-D-Aspartate*/metabolism , Conserved Sequence*, Animals ; Humans ; Protein Subunits/genetics ; Protein Subunits/chemistry ; Amino Acid Sequence ; Models, Molecular

BridgeNet: a high-efficiency framework integrating sequence and structure for protein and enzyme function prediction.

Autoren: Ye Y Duan H Mu Y et al.

Quelle: Briefings in bioinformatics [Brief Bioinform] 2025 Nov 01; Vol. 26 (6).

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH-Schlagworte: Proteins*/chemistry , Proteins*/metabolism , Enzymes*/chemistry , Enzymes*/metabolism , Computational Biology*/methods , Deep Learning* , Sequence Analysis, Protein*/methods , Software*, Protein Conformation ; Amino Acid Sequence ; Databases, Protein ; Algorithms

Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors.

Autoren: Bogaerts B Maex M Commans F et al.

Quelle: Journal of clinical microbiology [J Clin Microbiol] 2025 Oct 08; Vol. 63 (10), pp. e0041025. Date of Electronic Publication: 2025 Aug 22.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 7505564 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-660X (Electronic) Linking ISSN: 00951137 NLM ISO Abbreviation: J Clin Microbiol Subsets: MEDLINE

MeSH-Schlagworte: Multilocus Sequence Typing*/methods , Neisseria meningitidis*/genetics , Neisseria meningitidis*/classification , Neisseria meningitidis*/isolation & purification , Salmonella enterica*/genetics , Salmonella enterica*/classification , Salmonella enterica*/isolation & purification , Disease Outbreaks* , Nanopore Sequencing*/methods , Meningococcal Infections*/epidemiology , Meningococcal Infections*/microbiology , Salmonella Infections*/epidemiology , Salmonella Infections*/microbiology, Humans ; Genome, Bacterial ; DNA Methylation ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods

MFF-HPO: Protein-Phenotype Associations Prediction Based on Sequence Using Multi-Feature Fusion.

Autoren: Bi X Ji Z Zhang L et al.

Quelle: Journal of computational biology : a journal of computational molecular cell biology [J Comput Biol] 2025 Oct; Vol. 32 (10), pp. 913-922. Date of Electronic Publication: 2025 Jun 30.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Mary Ann Liebert, Inc Country of Publication: United States NLM ID: 9433358 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1557-8666 (Electronic) Linking ISSN: 10665277 NLM ISO Abbreviation: J Comput Biol Subsets: MEDLINE

MeSH-Schlagworte: Computational Biology*/methods , Proteins*/chemistry , Proteins*/genetics , Sequence Analysis, Protein*/methods, Phenotype ; Humans ; Neural Networks, Computer ; Algorithms ; Amino Acid Sequence

Conserved Sequence Identification Within Large Genomic Datasets Using 'Unikseq2': Application in Environmental DNA Assay Development.

Autoren: Lopez MLD Warren RL Allison MJ et al.

Quelle: Molecular ecology resources [Mol Ecol Resour] 2025 Oct; Vol. 25 (7), pp. e70014. Date of Electronic Publication: 2025 Jul 11.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE

MeSH-Schlagworte: DNA, Environmental*/genetics , Conserved Sequence* , Computational Biology*/methods , Genomics*/methods, Animals ; Fishes/genetics ; Fishes/classification ; Sequence Analysis, DNA/methods

Enzyme sequence optimisation via Gromov-Wasserstein Autoencoders integrating MSA techniques.

Autoren: Wang X Li Y Hou X et al.

Quelle: Journal of enzyme inhibition and medicinal chemistry [J Enzyme Inhib Med Chem] 2025 Dec; Vol. 40 (1), pp. 2524742. Date of Electronic Publication: 2025 Jul 03.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Taylor & Francis Country of Publication: England NLM ID: 101150203 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1475-6374 (Electronic) Linking ISSN: 14756366 NLM ISO Abbreviation: J Enzyme Inhib Med Chem Subsets: MEDLINE

MeSH-Schlagworte: Sequence Alignment* , Enzymes*/chemistry , Enzymes*/metabolism, Hydrophobic and Hydrophilic Interactions ; Amino Acid Sequence ; Autoencoder

Target-enriched multilocus assay on poriferan museum collections unsettles tethyid classification.

Autoren: Erpenbeck D Deister F Ekins M et al.

Quelle: Molecular phylogenetics and evolution [Mol Phylogenet Evol] 2025 Dec; Vol. 213, pp. 108436. Date of Electronic Publication: 2025 Aug 13.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Academic Press Country of Publication: United States NLM ID: 9304400 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9513 (Electronic) Linking ISSN: 10557903 NLM ISO Abbreviation: Mol Phylogenet Evol Subsets: MEDLINE

MeSH-Schlagworte: Phylogeny* , Multilocus Sequence Typing*/methods , Porifera*/genetics , Porifera*/classification, Animals ; Museums ; Queensland ; Sequence Analysis, DNA ; Genome, Mitochondrial ; Biodiversity ; Bayes Theorem

Detection of hemizygous deletions in the genome of Fleckvieh cattle using SNP chip data and the concept of Mendelian mismatches in parent-offspring pairs.

Autoren: Dekar T Gebre KT Mészáros G et al.

Quelle: Animal genetics [Anim Genet] 2025 Dec; Vol. 56 (6), pp. e70057.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Wiley-Blackwell Country of Publication: England NLM ID: 8605704 Publication Model: Print Cited Medium: Internet ISSN: 1365-2052 (Electronic) Linking ISSN: 02689146 NLM ISO Abbreviation: Anim Genet Subsets: MEDLINE

MeSH-Schlagworte: Polymorphism, Single Nucleotide* , Genome* , Sequence Deletion*, Animals ; Cattle/genetics ; Germany ; Oligonucleotide Array Sequence Analysis/veterinary ; Male ; Genotype ; Female ; Austria

OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders.

Autoren: Flöge K Udayakumar S Sommer J et al.

Quelle: PLoS computational biology [PLoS Comput Biol] 2025 Nov 13; Vol. 21 (11), pp. e1013679. Date of Electronic Publication: 2025 Nov 13 (Print Publication: 2025).

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH-Schlagworte: Proteins*/chemistry , Proteins*/metabolism , Sequence Alignment*/methods, Binding Sites ; Computational Biology/methods ; Deep Learning ; Neural Networks, Computer ; Sequence Analysis, Protein/methods ; Databases, Protein

Motif caller for sequence reconstruction in motif-based DNA storage.

Autoren: Agarwal P Pinnamaneni N Heinis T

Quelle: Scientific reports [Sci Rep] 2025 Nov 10; Vol. 15 (1), pp. 39236. Date of Electronic Publication: 2025 Nov 10.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH-Schlagworte: Nucleotide Motifs* , DNA*/genetics , DNA*/chemistry , Sequence Analysis, DNA*/methods , Information Storage and Retrieval*/methods, Machine Learning ; Base Sequence ; Nanopore Sequencing/methods ; Algorithms

miRScore: A rapid and precise microRNA validation tool.

Autoren: Vanek A Griffiths-Jones S Meyers BC et al.

Quelle: PLoS computational biology [PLoS Comput Biol] 2025 Nov 03; Vol. 21 (11), pp. e1013663. Date of Electronic Publication: 2025 Nov 03 (Print Publication: 2025).

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH-Schlagworte: MicroRNAs*/genetics , MicroRNAs*/chemistry , Molecular Sequence Annotation*/methods , Computational Biology*/methods , Software*, Humans ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA/methods ; Databases, Nucleic Acid ; Databases, Genetic

Identification of conserved residues essential for the ciliogenic functions of WDPCP.

Autoren: Choi YJ Hwang S Lee C et al.

Quelle: Disease models & mechanisms [Dis Model Mech] 2025 Nov 01; Vol. 18 (11). Date of Electronic Publication: 2025 Nov 21.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Company of Biologists Ltd Country of Publication: England NLM ID: 101483332 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1754-8411 (Electronic) Linking ISSN: 17548403 NLM ISO Abbreviation: Dis Model Mech Subsets: MEDLINE

MeSH-Schlagworte: Cilia*/metabolism , Conserved Sequence* , Carrier Proteins*/chemistry , Carrier Proteins*/metabolism , Carrier Proteins*/genetics, Animals ; Humans ; Hedgehog Proteins/metabolism ; Mice ; Amino Acid Sequence ; Signal Transduction ; Phenotype ; Mutation/genetics ; Models, Molecular

scDIFF: automatic cell type annotation using scATAC-seq data by incorporating bulk-level genomic and epigenomic information in a deep diffusive transformer.

Autoren: Wang HY Dong H Du PF

Quelle: Briefings in bioinformatics [Brief Bioinform] 2025 Nov 01; Vol. 26 (6).

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH-Schlagworte: Epigenomics*/methods , Software* , Genomics*/methods , Single-Cell Analysis*/methods , Molecular Sequence Annotation* , Chromatin*/genetics, Humans ; Transposases/metabolism ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA

gReLU: a comprehensive framework for DNA sequence modeling and design.

Autoren: Lal A Gunsalus L Nair S et al.

Quelle: Nature methods [Nat Methods] 2025 Nov; Vol. 22 (11), pp. 2253-2257. Date of Electronic Publication: 2025 Oct 15.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH-Schlagworte: Software* , Sequence Analysis, DNA*/methods , DNA*/genetics , DNA*/chemistry , Computational Biology*/methods, Deep Learning ; Humans ; Base Sequence ; Algorithms

DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models.

Autoren: Kim M Bae H Jo G et al.

Quelle: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Nov 01; Vol. 41 (11).

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH-Schlagworte: Proteins*/chemistry , Software* , Sequence Alignment*/methods , Computational Biology*/methods, Protein Conformation ; Databases, Protein ; Models, Molecular ; Sequence Analysis, Protein/methods ; Algorithms

An effective statistical moment-based feature extraction technique to identify the phosphoglycerylation sites from protein sequences.

Autoren: Sohrawordi M Hossain MA Al Mehedi Hasan M

Quelle: Journal of molecular graphics & modelling [J Mol Graph Model] 2025 Nov; Vol. 140, pp. 109108. Date of Electronic Publication: 2025 Jun 16.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Elsevier Science, Inc Country of Publication: United States NLM ID: 9716237 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4243 (Electronic) Linking ISSN: 10933263 NLM ISO Abbreviation: J Mol Graph Model Subsets: MEDLINE

MeSH-Schlagworte: Protein Processing, Post-Translational* , Proteins*/chemistry , Proteins*/metabolism , Sequence Analysis, Protein*, Support Vector Machine ; Algorithms ; Amino Acid Sequence ; Computational Biology/methods ; Humans

wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes.

Autoren: Elliott L Boyer F Lemane T et al.

Körperschaften: Elliott L Boyer F Lemane T et al.

Quelle: Molecular ecology resources [Mol Ecol Resour] 2025 Nov; Vol. 25 (8), pp. e70001. Date of Electronic Publication: 2025 Jul 21.

Publikationsart: Journal Article

Info zur Zeitschrift: Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE

MeSH-Schlagworte: Metagenome* , Software* , DNA, Ancient*/analysis , Computational Biology*/methods , Metagenomics*/methods , Molecular Sequence Annotation*/methods, Sequence Analysis, DNA/methods