Interpreting Microbial Species–Area Relationships: Effects of Sequence Data Processing Algorithms and Fitting Models.

Authors: Qi, Fu-Liang, Deng, Wei, Cheng, Yi-Ting, Yang, Xiao-Yan, Li, Na, Xiao, Wen

Source: Microorganisms; Mar2025, Vol. 13 Issue 3, p635, 12p

Subject Terms: Nucleotide sequencing, Data structures, Microbial diversity, Electronic data processing, Algorithms

Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data

Authors: Jun Teng, Dan Wang, Changheng Zhao, Xinyi Zhang, Zhi Chen, Jianfeng Liu, Dongxiao Sun, Hui Tang, Wenwen Wang, Jianbin Li, Cheng Mei, Zhangping Yang, Chao Ning, Qin Zhang

Source: Journal of Dairy Science, Vol 106, Iss 4, Pp 2535-2550 (2023)

Subject Terms: 2. Zero hunger, 0301 basic medicine, 0303 health sciences, Genotype, Quantitative Trait Loci, milk production traits, imputation, SF250.5-275, Polymorphism, Single Nucleotide, Dairying, 03 medical and health sciences, SF221-250, Milk, Phenotype, Animals, Cattle, Female, Longitudinal Studies, whole-genome sequence data, Holstein cattle, longitudinal GWAS, Dairy processing. Dairy products, Genome-Wide Association Study

Access URL: https://pubmed.ncbi.nlm.nih.gov/36797187
https://doaj.org/article/a7c0e3cf7d684cd79fcc162685102cea

Single nucleotide polymorphism associated with nonsyndromic cleft palate influences the processing of miR‐140

Authors: Ling, Li, Tian, Meng, Zhonglin, Jia, Guiquan, Zhu, Bing, Shi

Source: American Journal of Medical Genetics Part A. :856-862

Subject Terms: Male, 0301 basic medicine, Base Sequence, Genetic Vectors, Molecular Sequence Data, Transfection, Polymorphism, Single Nucleotide, Cell Line, Cleft Palate, MicroRNAs, 03 medical and health sciences, Case-Control Studies, RNA Precursors, Humans, Female, Genetic Predisposition to Disease, RNA Processing, Post-Transcriptional, Alleles

Access URL: https://pubmed.ncbi.nlm.nih.gov/20358594

Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA

Authors: Ranhui, Duan, Changhui, Pak, Peng, Jin

Source: Human Molecular Genetics. 16:1124-1131

Subject Terms: 0301 basic medicine, 0303 health sciences, Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, Molecular Sequence Data, Blotting, Northern, Polymorphism, Single Nucleotide, Cell Line, MicroRNAs, 03 medical and health sciences, Protein Biosynthesis, RNA Precursors, Humans, Nucleic Acid Conformation, RNA Processing, Post-Transcriptional

Access URL: https://academic.oup.com/hmg/article-pdf/16/9/1124/17244198/ddm062.pdf
https://pubmed.ncbi.nlm.nih.gov/17400653

TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

Authors: Wacker EM; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany., Rühlemann MC; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.; Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany., Franke A; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany., Ellinghaus D; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. d.ellinghaus@ikmb.uni-kiel.de.

Source: Nature communications [Nat Commun] 2026 Jun 11; Vol. 17 (1). Date of Electronic Publication: 2026 Jun 11.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Metagenome*/genetics , Metagenomics*/methods , Software*, Sequence Analysis, DNA/methods ; Humans ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Shotgun Sequencing ; Workflow

Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing

Authors: Michael P, Heaton, James E, Keen, Michael L, Clawson, Gregory P, Harhay, Nathan, Bauer, Craig, Shultz, Benedict T, Green, Lisa, Durso, Carol G, Chitko-McKown, William W, Laegreid

Source: Journal of the American Veterinary Medical Association. 226:1311-1314

Subject Terms: Genetic Markers, Male, 2. Zero hunger, 0301 basic medicine, 0303 health sciences, Meat, Base Sequence, Genotype, Molecular Sequence Data, Animal Identification Systems, DNA, Sequence Analysis, DNA, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, 03 medical and health sciences, Gene Frequency, Liver, Animals, Cattle, Female, Food-Processing Industry, Prospective Studies

Access URL: https://pubmed.ncbi.nlm.nih.gov/15844419

A Common Single Nucleotide Polymorphism in Endoplasmic Reticulum Aminopeptidase 2 Induces a Specificity Switch That Leads to Altered Antigen Processing

Authors: Irini Evnouchidou, James Birtley, Sergey Seregin, Athanasios Papakyriakou, Efthalia Zervoudi, Martina Samiotaki, George Panayotou, Petros Giastas, Olivia Petrakis, Dimitris Georgiadis, Andrea Amalfitano, Emmanuel Saridakis, Irene M. Mavridis, Efstratios Stratikos

Source: The Journal of Immunology. 189:2383-2392

Subject Terms: 0301 basic medicine, Antigen Presentation, 0303 health sciences, Molecular Sequence Data, Genetic Variation, Crystallography, X-Ray, Endoplasmic Reticulum, Aminopeptidases, Immunoglobulin Class Switching, Polymorphism, Single Nucleotide, Substrate Specificity, 3. Good health, Enzyme Activation, 03 medical and health sciences, Health Sciences, Humans, Επιστήμες Υγείας, Amino Acid Sequence, HeLa Cells

Access URL: https://www.jimmunol.org/content/jimmunol/189/5/2383.full.pdf
https://pubmed.ncbi.nlm.nih.gov/22837489
https://pergamos.lib.uoa.gr/uoa/dl/object/2955566

BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus

Authors: Vázquez, Noé^{Aff1, Aff2}, López-Fernández, Hugo^{Aff1, Aff2, Aff3, Aff4, Aff5, cor2}, Vieira, Cristina P.^{Aff4, Aff5}, Fdez-Riverola, Florentino^{Aff1, Aff2, Aff3}, Vieira, Jorge^{Aff4, Aff5}, Reboiro-Jato, Miguel^{Aff1, Aff2, Aff3}

Source: Interdisciplinary Sciences: Computational Life Sciences. 11(1):57-67

The W232R Suppressor Mutation Promotes Maturation of a Truncation Mutant Lacking both Nucleotide-Binding Domains and Restores Interdomain Assembly and Activity of P-glycoprotein Processing Mutants

Authors: Tip W, Loo, M Claire, Bartlett, David M, Clarke

Source: Biochemistry. 50:672-685

Subject Terms: 0301 basic medicine, Protein Folding, 0303 health sciences, Binding Sites, Nucleotides, Molecular Sequence Data, Molecular Conformation, Cell Line, 03 medical and health sciences, Suppression, Genetic, Amino Acid Substitution, Cricetinae, Animals, Humans, ATP Binding Cassette Transporter, Subfamily B, Member 1, Amino Acid Sequence, Protein Binding

Access URL: https://pubmed.ncbi.nlm.nih.gov/21182301

Evidences for Adenine Nucleotide Binding in the Subunits ofNeurosporaMitochondrial Processing Peptidase

Authors: R, Botweva, B, Fillippi, B, Salvato

Source: Archives of Biochemistry and Biophysics. 332:329-334

Subject Terms: 0301 basic medicine, 0303 health sciences, Neurospora crassa, Adenine Nucleotides, Protein Conformation, Circular Dichroism, Molecular Sequence Data, Metalloendopeptidases, Mitochondria, Mitochondrial Processing Peptidase, 3. Good health, Adenosine Diphosphate, Kinetics, 03 medical and health sciences, Adenosine Triphosphate, Spectrometry, Fluorescence, Amino Acid Sequence, Chromatography, Thin Layer, Chromatography, High Pressure Liquid

Access URL: https://pubmed.ncbi.nlm.nih.gov/8806742

FMDVSerPred: A Novel Computational Solution for Foot-and-mouth Disease Virus Classification and Serotype Prediction Prevalent in Asia Using VP1 Nucleotide Sequence Data

Authors: Samarendra Das, Soumen Pal, Samyak Mahapatra, Jitendra K. Biswal, Sukanta K. Pradhan, Aditya P. Sahoo, Rabindra Prasad Singh

Source: Current Bioinformatics. 19:794-809

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, 3. Good health

Pretraining model for biological sequence data

Authors: Bosheng, Song, Zimeng, Li, Xuan, Lin, Jianmin, Wang, Tian, Wang, Xiangzheng, Fu

Source: Briefings in Functional Genomics. 20:181-195

Subject Terms: 0301 basic medicine, 0206 medical engineering, Computational Biology, Datasets as Topic, High-Throughput Nucleotide Sequencing, 02 engineering and technology, Models, Theoretical, 3. Good health, 03 medical and health sciences, Deep Learning, Data Mining, Humans, Algorithms, Software, Natural Language Processing

Access URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194843
https://pubmed.ncbi.nlm.nih.gov/34050350

Regulation of RNA processing and transport by a nuclear guanine nucleotide release protein and members of the Ras superfamily

Authors: T, Kadowaki, D, Goldfarb, L M, Spitz, A M, Tartakoff, M, Ohno

Source: The EMBO Journal. 12:2929-2937

Subject Terms: 0301 basic medicine, Base Sequence, Cell Cycle, Molecular Sequence Data, DNA, Single-Stranded, Nuclear Proteins, Proteins, Biological Transport, GTP Phosphohydrolases, DNA-Binding Proteins, Enzyme Activation, Fungal Proteins, 03 medical and health sciences, Cricetinae, CDC2 Protein Kinase, Animals, Guanine Nucleotide Exchange Factors, Point Mutation, RNA, Amino Acid Sequence, RNA Processing, Post-Transcriptional, Poly A

Access URL: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/j.1460-2075.1993.tb05955.x
https://pubmed.ncbi.nlm.nih.gov/7687541

In Silico Separation of in Vitro Transcription-Derived Duplicates From PCR Duplicates to Enhance Sequence Data Utilization.

Authors: Suzuki, Ryoga¹ (AUTHOR), Horisawa, Kenichi¹ (AUTHOR) horisawa@bioreg.kyushu-u.ac.jp, Maehara, Kazumitsu^2,3 (AUTHOR), Ohkawa, Yasuyuki² (AUTHOR), Suzuki, Atsushi¹ (AUTHOR)

Source: Bioinformatics & Biology Insights. 8/26/2025, Vol. 19, p1-7. 7p.

Subject Terms: *Nucleic acid amplification techniques, *Nucleotide sequencing, *Gene amplification, *Data management, *Transcription factors, *Computer simulation, *Chromatin

GenoM7GNet: An Efficient N7-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model

Authors: Li, C., Wang, H., Wen, Y., Yin, R., Zeng, X., Li, K.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 21(6):2258-2268 Jan, 2024

Pentatricopeptide repeat motifs in the processing enzyme PRORP1 in Arabidopsis thaliana play a crucial role in recognition of nucleotide bases at TψC loop in precursor tRNAs

Authors: Takayoshi, Imai, Takahiro, Nakamura, Taku, Maeda, Kaoru, Nakayama, Xuzhu, Gao, Takashi, Nakashima, Yoshimitsu, Kakuta, Makoto, Kimura

Source: Biochemical and Biophysical Research Communications. 450:1541-1546

Subject Terms: Repetitive Sequences, Amino Acid, 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, DNA, Complementary, RNA, Transfer, Arabidopsis Proteins, Molecular Sequence Data, Arabidopsis, Amino Acid Sequence, Ribonuclease P, 3. Good health

Access URL: https://pubmed.ncbi.nlm.nih.gov/25034328

Nucleotide sequence of vitellogenin mRNA in the bean bug, Riptortus clavatus: analysis of processing in the fat body and ovary

Authors: M, Hirai, D, Watanabe, A, Kiyota, Y, Chinzei

Source: Insect Biochemistry and Molecular Biology. 28:537-547

Subject Terms: 0301 basic medicine, 0303 health sciences, DNA, Complementary, Base Sequence, Transcription, Genetic, Fat Body, Molecular Sequence Data, Ovary, Genes, Insect, Hemiptera, Juvenile Hormones, Vitellogenins, 03 medical and health sciences, Animals, Insect Proteins, Female, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Protein Processing, Post-Translational

Access URL: https://pubmed.ncbi.nlm.nih.gov/9753765

Distribution of both lengths and 5' terminal nucleotides of mammalian pre-tRNA 3' trailers reflects properties of 3' processing endoribonuclease

Authors: M, Nashimoto

Source: Nucleic Acids Research. 25:1148-1154

Subject Terms: Mammals, 0301 basic medicine, 0303 health sciences, Base Sequence, Swine, RNA Splicing, Molecular Sequence Data, Genetic Variation, RNA, Transfer, Arg, Cell Line, Substrate Specificity, Kinetics, Mice, 03 medical and health sciences, Liver, Endoribonucleases, RNA Precursors, Animals, Humans, RNA Processing, Post-Transcriptional

Access URL: https://academic.oup.com/nar/article-pdf/25/6/1148/4027669/25-6-1148.pdf
https://pubmed.ncbi.nlm.nih.gov/9092623

BINSEQ: A family of high-performance binary formats for nucleotide sequences.

Authors: Teyssier, Noam, Dobin, Alexander

Source: PLoS Computational Biology; 5/28/2026, Vol. 22 Issue 5, p1-19, 19p

Subject Terms: Parallel processing, Data compression, Storage, Nucleotide sequence, Sequence alignment, Real-time computing, Bioinformatics software

Nearest Neighbor CCP-Based Molecular Sequence Analysis

Authors: Ali, S., Chourasia, P., Koirala, B., Patterson, M.

Source: IEEE Transactions on Computational Biology and Bioinformatics IEEE Trans. Comput. Biol. Bioinform. Computational Biology and Bioinformatics, IEEE Transactions on. 23(1):1-13 Jan, 2026