Identification of stable reference genes in Edwardsiella ictaluri for accurate gene expression analysis.

Authors: Lu J; Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, United States of America., Abdelhamed H; Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, United States of America., Al-Janabi N; Department of Medical Biotechnology, College of Biotechnology, Al-Qasim Green University, Babylon, Iraq., Eissa N; Department of Immunology, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada., Lawrence M; Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, United States of America., Karsi A; Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, United States of America.

Source: PloS one [PLoS One] 2025 May 02; Vol. 20 (5), pp. e0309585. Date of Electronic Publication: 2025 May 02 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Edwardsiella ictaluri*/genetics , Edwardsiella ictaluri*/growth & development , Gene Expression Profiling*/standards , Gene Expression Profiling*/methods , Genes, Bacterial* , Gene Expression Regulation, Bacterial*, Animals ; Reference Standards ; Genes, Essential ; Catfishes/microbiology

Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning.

Authors: Tu W; School of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, China., Zhang L; School of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, China.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 03; Vol. 21 (4), pp. e1012948. Date of Electronic Publication: 2025 Apr 03 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: 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 Terms: Computational Biology*/methods , Gene Expression Profiling*/methods , Gene Expression Profiling*/statistics & numerical data , Transcriptome*/genetics , Machine Learning*, Humans ; Algorithms ; Databases, Genetic

Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes.

Authors: Degen PM; Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.; Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland., Medo M; Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.; Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.

Source: PLoS computational biology [PLoS Comput Biol] 2025 May 05; Vol. 21 (5), pp. e1011630. Date of Electronic Publication: 2025 May 05 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: 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 Terms: RNA-Seq*/methods , RNA-Seq*/statistics & numerical data , Gene Expression Profiling*/methods , Sequence Analysis, RNA*/methods, Humans ; Reproducibility of Results ; Computational Biology/methods ; Transcriptome/genetics ; Cohort Studies

Transcriptomic comparison analysis across seven developmental stages of the Triatoma rubrofasciata, a vector of Chagas disease.

Authors: Duan L; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China.; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China., Tian Y; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China.; Chongqing Jiangjin District Center for Disease Control and Prevention, Chongqing, 402260, People's Republic of China., Wang Z; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Yang L; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Guo Y; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Li Y; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Zhou Z; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Shen Y; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Zhang Y; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China., Liu Q; NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China. liuqin@nipd.chinacdc.cn.

Source: BMC genomics [BMC Genomics] 2025 May 05; Vol. 26 (1), pp. 444. Date of Electronic Publication: 2025 May 05.

Publication Type: Journal Article; Comparative Study

Journal Info: 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 Terms: Triatoma*/genetics , Triatoma*/growth & development , Insect Vectors*/genetics , Insect Vectors*/growth & development , Gene Expression Profiling* , Transcriptome*, Animals ; Chagas Disease/transmission ; Chagas Disease/parasitology ; Insect Proteins/genetics ; Female ; Male ; Gene Expression Regulation, Developmental

lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression.

Authors: Maden SK; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA., Huuki-Myers LA; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.; Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, Cambridge, UK.; UK Dementia Research Institute at The University of Cambridge, Cambridge, UK., Kwon SH; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA., Collado-Torres L; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA., Maynard KR; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA., Hicks SC; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. shicks19@jhu.edu.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. shicks19@jhu.edu.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. shicks19@jhu.edu.; Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA. shicks19@jhu.edu.

Source: BMC genomics [BMC Genomics] 2025 May 01; Vol. 26 (1), pp. 433. Date of Electronic Publication: 2025 May 01.

Publication Type: Journal Article

Journal Info: 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 Terms: Software* , Cell Size* , Gene Expression Profiling*/methods , Computational Biology*/methods, Algorithms ; Humans ; Sequence Analysis, RNA ; Animals

Unveiling the immune microenvironment of complex tissues and tumors in transcriptomics through a deconvolution approach.

Authors: Chen SH; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 250 Wu-Xing Street, Taipei, Taiwan., Yu BY; Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo, 153-8904, Japan., Kuo WY; Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan., Lin YB; Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan., Su SY; Department of Smart Computing and Applied Mathematics, Tunghai University, Taichung City, 407224, Taiwan., Chuang WH; Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan., Lu IH; Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan., Lin CY; Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan. cylin@iis.sinica.edu.tw.; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan. cylin@iis.sinica.edu.tw.; Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan. cylin@iis.sinica.edu.tw.

Source: BMC cancer [BMC Cancer] 2025 May 01; Vol. 25 (Suppl 1), pp. 733. Date of Electronic Publication: 2025 May 01.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100967800 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2407 (Electronic) Linking ISSN: 14712407 NLM ISO Abbreviation: BMC Cancer Subsets: MEDLINE

MeSH Terms: Tumor Microenvironment*/immunology , Tumor Microenvironment*/genetics , Gene Expression Profiling*/methods , Transcriptome* , Neoplasms*/genetics , Neoplasms*/immunology , Head and Neck Neoplasms*/immunology , Head and Neck Neoplasms*/genetics, Humans ; Computational Biology/methods ; Algorithms ; Single-Cell Analysis/methods ; Software ; Melanoma/immunology ; Melanoma/genetics ; Sequence Analysis, RNA ; RNA-Seq ; Lymphocytes, Tumor-Infiltrating/immunology

Integrated transcriptomics and metabolomics reveal the molecular characteristics and metabolic regulatory mechanisms among different muscles in Minxian black fur sheep.

Authors: Wang H; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China., Liu Z; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China., Yang H; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China., Bai Y; Animal Husbandry Technology Extension Station of Gansu Province, Lanzhou, 730030, China., Li Q; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China., Qi X; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China., Li D; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China., Zhao X; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China.; College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China., Ma Y; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China. yjma@gsau.edu.cn.; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China. yjma@gsau.edu.cn.

Source: BMC genomics [BMC Genomics] 2025 Apr 29; Vol. 26 (1), pp. 412. Date of Electronic Publication: 2025 Apr 29.

Publication Type: Journal Article

Journal Info: 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 Terms: Metabolomics* , Gene Expression Profiling* , Transcriptome* , Muscle, Skeletal*/metabolism , Metabolome*, Animals ; Sheep/genetics ; Sheep/metabolism

Comparative transcriptome analysis provides a glance into the regulation of the Krüppel homolog 1 on the reproduction and diapause of the predatory ladybeetle, Coccinella septempunctata.

Authors: Chen J; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China., Liu X; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China., Han S; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China., Zhang M; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China., Liu Z; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China., Li Y; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China. liyuyan@caas.cn., Zhang L; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Natural Enemy Insects, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing, 100193, P. R. China. zhangleesheng@163.com.; Key Laboratory of Animal Biosafety Risk Prevention and Control (North) of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China. zhangleesheng@163.com.

Source: BMC genomics [BMC Genomics] 2025 Apr 29; Vol. 26 (1), pp. 414. Date of Electronic Publication: 2025 Apr 29.

Publication Type: Journal Article; Comparative Study

Journal Info: 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 Terms: Coleoptera*/genetics , Coleoptera*/physiology , Kruppel-Like Transcription Factors*/genetics , Kruppel-Like Transcription Factors*/metabolism , Insect Proteins*/genetics , Insect Proteins*/metabolism , Gene Expression Profiling* , Diapause, Insect*/genetics , Transcriptome* , Diapause*/genetics, Animals ; Reproduction/genetics ; Female ; RNA Interference

Gene expression profiling, prognosis, and immune microenvironment of KLF4 in malignancies.

Authors: Yu S; Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.; Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America., Qian L; Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Tong T; Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Ma X; Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Source: PloS one [PLoS One] 2025 Apr 29; Vol. 20 (4), pp. e0322523. Date of Electronic Publication: 2025 Apr 29 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Kruppel-Like Transcription Factors*/genetics , Kruppel-Like Transcription Factors*/metabolism , Neoplasms*/genetics , Neoplasms*/immunology , Neoplasms*/pathology , Neoplasms*/mortality , Gene Expression Profiling* , Tumor Microenvironment*/genetics , Tumor Microenvironment*/immunology, Kruppel-Like Factor 4 ; Humans ; Prognosis ; Gene Expression Regulation, Neoplastic ; Mutation

HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.

Authors: Liberati F; Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Università s.n.c., 01100, Viterbo, Italy., Pose Marino TM; Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy., Bottoni P; Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy., Canestrelli D; Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Università s.n.c., 01100, Viterbo, Italy., Castrignanò T; Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Università s.n.c., 01100, Viterbo, Italy. tiziana.castrignano@unitus.it.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Apr 28; Vol. 26 (1), pp. 113. Date of Electronic Publication: 2025 Apr 28.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Software* , Transcriptome* , Gene Expression Profiling*/methods, Sequence Analysis, RNA/methods ; Computational Biology/methods ; Databases, Genetic ; RNA-Seq/methods

Transcriptome-based analysis reveals relationship between duck eggshell color and eggshell strength.

Authors: Wang L; Chinese Academy of Agricultural Sciences, Institute of Animal Science, Beijin, China.; College of Animal Science & Technology, Northwest A&F University, Shaan'xi, Yangling, China., Liu H; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan, China., Yu S; Chinese Academy of Agricultural Sciences, Institute of Animal Science, Beijin, China., Lu M; Chinese Academy of Agricultural Sciences, Institute of Animal Science, Beijin, China., Zhang Y; Chinese Academy of Agricultural Sciences, Institute of Animal Science, Beijin, China., Wang S; Chinese Academy of Agricultural Sciences, Institute of Animal Science, Beijin, China., Hou S; Chinese Academy of Agricultural Sciences, Institute of Animal Science, Beijin, China. houss@263.net.; College of Animal Science & Technology, Northwest A&F University, Shaan'xi, Yangling, China. houss@263.net.

Source: BMC genomics [BMC Genomics] 2025 Apr 28; Vol. 26 (1), pp. 410. Date of Electronic Publication: 2025 Apr 28.

Publication Type: Journal Article

Journal Info: 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 Terms: Ducks*/genetics , Egg Shell*/metabolism , Egg Shell*/physiology , Egg Shell*/chemistry , Gene Expression Profiling* , Transcriptome*, Animals ; Liver/metabolism ; Gene Regulatory Networks ; Color

metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.

Authors: He L; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China., Zou Q; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China.; Macao Polytechnic University, Macau Peninsula Gomes Street, Macau, 999078, China., Wang Y; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China. wangyansu@uestc.edu.cn.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Apr 26; Vol. 26 (1), pp. 111. Date of Electronic Publication: 2025 Apr 26.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Metagenomics*/methods , Software* , Gene Expression Profiling*/methods , Microbiota*, Computational Biology/methods ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation

Expression profiles analysis and roles in immunity of transient receptor potential (TRP) channel genes in Spodoptera frugiperda.

Authors: Su H; Department of Entomology, College of Plant Protection, South China Agricultural University, No. 483, Wushan Road, Tianhe District, Guangzhou, 510642, China., Dai Q; Department of Entomology, College of Plant Protection, South China Agricultural University, No. 483, Wushan Road, Tianhe District, Guangzhou, 510642, China., Teng F; Department of Entomology, College of Plant Protection, South China Agricultural University, No. 483, Wushan Road, Tianhe District, Guangzhou, 510642, China., Li Z; Department of Entomology, College of Plant Protection, South China Agricultural University, No. 483, Wushan Road, Tianhe District, Guangzhou, 510642, China., Qi Y; Department of Entomology, College of Plant Protection, South China Agricultural University, No. 483, Wushan Road, Tianhe District, Guangzhou, 510642, China. qiyixiang19880922@163.com., Lu Y; Department of Entomology, College of Plant Protection, South China Agricultural University, No. 483, Wushan Road, Tianhe District, Guangzhou, 510642, China. luyongyue@scau.edu.cn.

Source: BMC genomics [BMC Genomics] 2025 Apr 24; Vol. 26 (1), pp. 401. Date of Electronic Publication: 2025 Apr 24.

Publication Type: Journal Article

Journal Info: 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 Terms: Spodoptera*/genetics , Spodoptera*/immunology , Spodoptera*/growth & development , Transient Receptor Potential Channels*/genetics , Transient Receptor Potential Channels*/metabolism , Transient Receptor Potential Channels*/immunology , Gene Expression Profiling* , Insect Proteins*/genetics , Insect Proteins*/metabolism , Transcriptome*, Animals ; Phylogeny

An updated comparison of microarray and RNA-seq for concentration response transcriptomic study: case studies with two cannabinoids, cannabichromene and cannabinol.

Authors: Gao X; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA. xiugong.gao@fda.hhs.gov., Yourick MR; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA., Campasino K; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA., Zhao Y; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA., Sepehr E; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA., Vaught C; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA., Sprando RL; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA., Yourick JJ; Division of Toxicology, Office of Chemistry and Toxicology (OCT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program (HFP), U.S. Food and Drug Administration (FDA), Laurel, MD, 20708, USA.

Source: BMC genomics [BMC Genomics] 2025 Apr 23; Vol. 26 (1), pp. 392. Date of Electronic Publication: 2025 Apr 23.

Publication Type: Journal Article; Comparative Study

Journal Info: 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 Terms: Cannabinoids*/pharmacology , Cannabinoids*/toxicity , Gene Expression Profiling*/methods , RNA-Seq*/methods , Transcriptome*/drug effects , Oligonucleotide Array Sequence Analysis*/methods, Humans ; Sequence Analysis, RNA

Transfer learning of multicellular organization via single-cell and spatial transcriptomics.

Authors: Tan Y; Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China., Wang A; Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China., Wang Z; Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.; Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China., Lin W; Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.; Shanghai Artificial Intelligence Laboratory, Shanghai, China., Yan Y; Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China., Nie Q; Department of Mathematics, University of California Irvine, Irvine, California, United States of America., Shi J; Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.; Shanghai Artificial Intelligence Laboratory, Shanghai, China.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 21; Vol. 21 (4), pp. e1012991. Date of Electronic Publication: 2025 Apr 21 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: 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 Terms: Single-Cell Analysis*/methods , Single-Cell Analysis*/statistics & numerical data , Transcriptome*/genetics , Gene Expression Profiling*/methods , Machine Learning*, Animals ; Humans ; Mice ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Drosophila ; Neural Networks, Computer

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics.

Authors: Morin A; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.; Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada., Chu CP; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.; Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada., Pavlidis P; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.; Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Apr 21; Vol. 21 (4), pp. e1012962. Date of Electronic Publication: 2025 Apr 21 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: 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 Terms: Single-Cell Analysis*/methods , Transcriptome*/genetics , Gene Expression Profiling*/methods , Transcription Factors*/genetics , Transcription Factors*/metabolism, Animals ; Mice ; Humans ; Computational Biology ; Gene Regulatory Networks/genetics ; Gene Expression Regulation/genetics ; Sequence Analysis, RNA ; Chromatin Immunoprecipitation Sequencing ; RNA-Seq

Genome-wide identification and expression profiling of MYB transcription factors in Artemisia argyi.

Authors: Peng S; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China., Zhang Q; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China., Yang Y; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China., Li Y; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China., Feng W; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China., Zhao D; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China., Huang B; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.; Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, 430065, China., Liu D; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China. liudahui@hbucm.edu.cn.; Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, 430065, China. liudahui@hbucm.edu.cn., Miao Y; School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China. miaoyh@hbucm.edu.cn.; Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, 430065, China. miaoyh@hbucm.edu.cn.

Source: BMC genomics [BMC Genomics] 2025 Apr 18; Vol. 26 (1), pp. 384. Date of Electronic Publication: 2025 Apr 18.

Publication Type: Journal Article

Journal Info: 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 Terms: Artemisia*/genetics , Artemisia*/metabolism , Transcription Factors*/genetics , Transcription Factors*/metabolism , Transcription Factors*/chemistry , Plant Proteins*/genetics , Plant Proteins*/metabolism , Plant Proteins*/chemistry , Gene Expression Profiling*, Gene Expression Regulation, Plant ; Phylogeny ; Flavonoids/biosynthesis ; Genome, Plant ; Multigene Family

Profiling the full-length transcriptome of plasma cell mastitis via nanopore sequencing.

Authors: Li S; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China. lisu11777@163.com., Chen H; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Fan Y; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Wang C; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., An L; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Xu Q; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Cai W; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Zhao S; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Tian T; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Zhang B; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Yang M; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China., Zhang L; Department of Thyroid and Breast Disease, Henan Provincial Hospital of Traditional Chinese Medicine, No.6 Dongfeng Road, Jinshui District, Zhengzhou, 450002, Henan Province, China.

Source: BMC genomic data [BMC Genom Data] 2025 Apr 16; Vol. 26 (1), pp. 29. Date of Electronic Publication: 2025 Apr 16.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101775394 Publication Model: Electronic Cited Medium: Internet ISSN: 2730-6844 (Electronic) Linking ISSN: 27306844 NLM ISO Abbreviation: BMC Genom Data Subsets: MEDLINE

MeSH Terms: Plasma Cells*/metabolism , Plasma Cells*/pathology , Transcriptome* , Nanopore Sequencing* , Gene Expression Profiling* , Mastitis*/genetics, Female ; Animals ; Cattle ; Humans

Redefining the high variable genes by optimized LOESS regression with positive ratio.

Authors: Xie Y; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.; BGI Research, Shenzhen, 518083, China.; BGI Research, Hangzhou, 310030, China., Jing Z; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.; BGI Research, Shenzhen, 518083, China.; BGI Research, Hangzhou, 310030, China., Pan H; BGI Research, Shenzhen, 518083, China., Xu X; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. xuxun@genomics.cn.; BGI Research, Shenzhen, 518083, China. xuxun@genomics.cn., Fang Q; BGI Research, Shenzhen, 518083, China. fangqi@genomics.cn.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Apr 15; Vol. 26 (1), pp. 104. Date of Electronic Publication: 2025 Apr 15.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Algorithms* , Single-Cell Analysis*/methods , Sequence Analysis, RNA*/methods , Gene Expression Profiling*/methods , Computational Biology*/methods, Transcriptome ; Humans ; Regression Analysis

Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.

Authors: Tombácz D; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Kakuk B; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Torma G; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Fülöp Á; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Dörmő Á; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Gulyás G; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Csabai Z; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary., Boldogkői Z; Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary.

Source: PloS one [PLoS One] 2025 Apr 15; Vol. 20 (4), pp. e0320439. Date of Electronic Publication: 2025 Apr 15 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Nanopore Sequencing*/methods , Transcriptome* , Gene Expression Profiling* , Herpesvirus 1, Equid*/genetics, Animals ; Horses ; Gene Expression Regulation, Viral