Sökresultat - "sequence analysis"

MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.

Patsakis M; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Provatas K; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Karatzikos A; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Koilakos C; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Mouratidis I; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA. ioannis.mouratidis@psu.edu.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA. ioannis.mouratidis@psu.edu., Georgakopoulos-Soares I; Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA. izg5139@psu.edu.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA. izg5139@psu.edu.

Journal Article , 2025

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

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.

Journal Article; Comparative Study , 2025

Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat.

Zhao J; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China., Wang Y; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China., Kamalibieke J; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China., Gong P; Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China., Zhang F; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China., Shi H; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China., Wang W; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China., Luo J; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China. luojun@nwafu.edu.cn.

Journal Article , 2025

From dual nucleic acid co-extraction to co-sequencing: A highly integrated next-generation forensic DNA and RNA sequencing experimental workflow.

Miao L; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. Electronic address: 947676188@qq.com., Lou DN; School of Forensic Medicine, Shanxi Medical University, Jinzhong 030600, China. Electronic address: loudani@163.com., Kang KL; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China. Electronic address: kang_kl@yeah.net., Zhao YX; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China. Electronic address: 18146501798@163.com., Zhang C; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China. Electronic address: jannychina@126.com., Zhao J; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China. Electronic address: zhao_jie95@163.com., Hu S; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China. Electronic address: hsheng2018@163.com., Wang L; Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; School of Forensic Medicine, Kunming Medical University, Kunming 650500, China. Electronic address: wangle_02@163.com.

Journal Article , 2025

Comparison of the BluePoint MoldID oligonucleotide array and Bruker Biotyper MALDI-TOF MS for the identification of filamentous fungi.

Chou C-H; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan., Chao Q-T; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan., Lu Y-S; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan., Lee T-F; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan., Hsueh P-R; Division of Infectious Diseases, Department of Internal Medicine, China Medical University, School of Medicine, Taichung, Taiwan.; Department of Laboratory Medicine, China Medical University, School of Medicine, Taichung, Taiwan., Huang Y-T; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan., Liao C-H; School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.; Division of Infectious Diseases, Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan.

Journal Article; Comparative Study; Evaluation Study , 2025

Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).

Weng Z; School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China., Li J; School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China., Wu Y; School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China., Xiu X; School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China., Wang F; School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China., Zuo X; School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China. zuoxiaolei@sjtu.edu.cn.; Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. zuoxiaolei@sjtu.edu.cn., Song P; School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China. songpingsjtu@sjtu.edu.cn., Fan C; School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China. fanchunhai@sjtu.edu.cn.

Journal Article , 2025

Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets.

Meng Y; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Zhang W; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Cheng Y; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Wu Y; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Wu H; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., He M; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Chen S; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Man C; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Gao H; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Du L; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China., Chen Q; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China. chenqiaoling@hainanu.edu.cn., Wang F; Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Engineering Key Laboratory of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan Province, China. 990805@hainanu.edu.cn.

Journal Article , 2024

Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing.

Santos R; Department of Biostatistics & Health Informatics, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK., Lee H; Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK., Williams A; Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK., Baffour-Kyei A; Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK., Lee SH; Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK., Troakes C; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, 5 Cutcombe Rd, London SE5 9RX, UK., Al-Chalabi A; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, 5 Cutcombe Rd, London SE5 9RX, UK., Breen G; Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK., Iacoangeli A; Department of Biostatistics & Health Informatics, Institute of Psychiatry Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AB, UK.; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, 5 Cutcombe Rd, London SE5 9RX, UK.; Perron Institute for Neurological and Translational Science, Ground RR Block QE II Medical Centre Ralph & Patricia Sarich Neuroscience Building, 8 Verdun St, Nedlands, WA 6009, Australia.; NIHR Maudsley Biomedical Research Centre (BRC), South London and Maudsley NHS Foundation Trust, 16 De Crespigny Park, London SE5 8AF, UK.

Journal Article , 2025

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.

Kovaka S; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. skovaka1@jhu.edu., Hook PW; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Jenike KM; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA., Shivakumar V; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA., Morina LB; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Razaghi R; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Timp W; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA., Schatz MC; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.

Journal Article , 2025

Efficient TF-IDF method for alignment-free DNA sequence similarity analysis.

Delibaş E; Department of Computer Engineering, Faculty of Engineering, Sivas Cumhuriyet University, 58140, Sivas, Turkey. Electronic address: edelibas@cumhuriyet.edu.tr.

Journal Article , 2025

The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers.

Zajac N; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland., Vlachos IS; Spatial Technologies Unit, Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Cancer Center and Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Sajibu S; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland., Opitz L; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland., Wang S; Spatial Technologies Unit, Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Cancer Center and Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Chittur SV; Center for Functional Genomics, University at Albany, State University of New York, Albany, NY, USA., Mason CE; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.; The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA., Knudtson KL; Genomics Division, Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA., Ashton JM; Genomics Research Center, University of Rochester, Rochester, NY, USA.; Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA., Rehrauer H; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland. hubert.rehrauer@fgcz.ethz.ch., Aquino C; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland. catharine.aquino@fgcz.ethz.ch.

Journal Article , 2025

A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.

Wang H; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; The Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK., Mennea PD; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Chan YKE; LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China., Cheng Z; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Neofytou MC; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Mechanisms and Biomarkers Research Group, School of Life Sciences, University of Westminster, London, W1 W 6UW, UK., Surani AA; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Vijayaraghavan A; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Ditter EJ; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Bowers R; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Eldridge MD; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Shcherbo DS; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; The Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK., Smith CG; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Markowetz F; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK., Cooper WN; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.; The Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK., Kaplan T; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.; Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel., Rosenfeld N; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. n.rosenfeld@qmul.ac.uk.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. n.rosenfeld@qmul.ac.uk.; The Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK. n.rosenfeld@qmul.ac.uk., Zhao H; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. hui.zhao@cruk.cam.ac.uk.; Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. hui.zhao@cruk.cam.ac.uk.; The Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK. hui.zhao@cruk.cam.ac.uk.

Journal Article , 2025

Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing.

Longtin A; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.; Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America., Watowich MM; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.; Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America., Sadoughi B; School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.; Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America., Petersen RM; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.; Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America., Brosnan SF; Departments of Psychology & Philosophy, Neuroscience Institute, Center for Behavioral Neuroscience, and the Language Research Center, Georgia State University, Atlanta, GeorgiaUnited States of America., Buetow K; School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.; Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America., Cai Q; Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America., Gurven MD; Department of Anthropology, University of California, Santa Barbara, California, United States of America., Higham JP; Department of Anthropology, New York University, New York, New York, United States of America.; New York Consortium in Evolutionary Primatology, New York, New York, United States of America., Highland HM; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America., Huang YT; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America., Kaplan H; Institute for Economics and Society, Chapman University, Orange, California, United States of America., Kraft TS; Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America., Lim YAL; Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.; Centre for Malaysian Indigenous Studies (CMIS), Universiti Malaya, Kuala Lumpur, Malaysia., Long J; Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America., Melin AD; Department of Anthropology & Archaeology, University of Calgary, Calgary, Alberta, Canada.; Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.; Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada., Montague MJ; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America., Roberson J; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America., Ng KS; Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia., Platt ML; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.; Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.; Marketing Department, Wharton School of Business, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America., Schneider-Crease IA; Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America.; School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America., Stieglitz J; Department of Social and Behavioral Sciences, Toulouse School of Economics, Institute for Advanced Study in Toulouse, Université Toulouse Capitole, Toulouse, France., Trumble BC; Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America.; School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America.; Institute of Human Origins, Arizona State University, Tempe, Arizona, United States of America., Venkataraman VV; Department of Anthropology & Archaeology, University of Calgary, Calgary, Alberta, Canada., Wallace IJ; Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America., Wu J; Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America., Snyder-Mackler N; School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.; Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America.; School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America., Jones A; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America., Bick AG; Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America.; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.; Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America., Lea AJ; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.; Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America.; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

Cayo Biobank Research Unit

Journal Article , 2025

Low-cost generation of clinical-grade, layperson-friendly pharmacogenetic passports using oligonucleotide arrays.

Lanting P; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, the Netherlands., Warmerdam R; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, the Netherlands., Slager J; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Brugge H; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Ochi T; Groningen Research Institute of Pharmacy, Unit of PharmacoTherapy, Epidemiology & Economics, University of Groningen, Groningen, the Netherlands., Benjamins M; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Lopera-Maya E; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Jankipersadsing S; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Gelderloos-Arends J; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Teuben D; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Hendriksen D; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Genomics Coordination Center, Groningen, the Netherlands., Charbon B; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Genomics Coordination Center, Groningen, the Netherlands., Johansson L; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Genomics Coordination Center, Groningen, the Netherlands., Munnink TO; Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., de Boer-Veger N; Service Apotheek Boterdiep, Groningen, the Netherlands., Wilffert B; Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Groningen Research Institute of Pharmacy, Unit of PharmacoTherapy, Epidemiology & Economics, University of Groningen, Groningen, the Netherlands., Swertz M; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Genomics Coordination Center, Groningen, the Netherlands., Touw D; Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Deelen P; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, the Netherlands., Knoers N; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Dekens J; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Center for Development and Innovation, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands. Electronic address: j.a.m.dekens@umcg.nl., Franke L; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Oncode Institute, Utrecht, the Netherlands. Electronic address: l.h.franke@umcg.nl.

Lifelines NEXT Cohort Study, Lifelines Cohort Study

Journal Article , 2025

iSeqSearch: incremental protein search for iBlast/iMMSeqs2/iDiamond.

Yoo H; Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America., Refahi M; Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America., Polikar R; Electrical and Computer Engineering, Rowan University, Glassboro, NJ, United States of America., Sokhansanj BA; Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America., Brown JR; Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America., Rosen GL; Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.

Journal Article , 2025

Optimizing Cost-Effective gene expression phenotyping approaches in cattle using 3' mRNA sequencing.

Mohamed RI; Genome Science and Technology Program, Bredesen Center, University of Tennessee, Knoxville, TN, USA., Ault-Seay TB; Department of Animal Science, University of Tennessee Institute of Agriculture (UTIA), Knoxville, TN, USA., Moisá SJ; Department of Animal Science, University of Tennessee Institute of Agriculture (UTIA), Knoxville, TN, USA., Beever JE; Genome Science and Technology Program, Bredesen Center, University of Tennessee, Knoxville, TN, USA.; Department of Animal Science, University of Tennessee Institute of Agriculture (UTIA), Knoxville, TN, USA., Ríus AG; Department of Animal Science, University of Tennessee Institute of Agriculture (UTIA), Knoxville, TN, USA., Rowan TN; Genome Science and Technology Program, Bredesen Center, University of Tennessee, Knoxville, TN, USA. trowan@utk.edu.; Department of Animal Science, University of Tennessee Institute of Agriculture (UTIA), Knoxville, TN, USA. trowan@utk.edu.

Journal Article , 2025

Return of Clinically Actionable Pharmacogenetic Results From Molecular Tumor Board DNA Sequencing Data: Workflow and Estimated Costs.

Koo H; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.; Department of Pharmacy Practice, Purdue University College of Pharmacy, West Lafayette, Indiana, USA., Smith TB; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA., Callaghan JT; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA., Osei W; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.; Department of Pharmacy Practice, Purdue University College of Pharmacy, West Lafayette, Indiana, USA., Bray SM; LifeOmic, Inc., Indianapolis, Indiana, USA., Tillman EM; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA., Tran MT; Indiana University Health, Indianapolis, Indiana, USA., Fausel CA; Indiana University Health, Indianapolis, Indiana, USA., Schneider BP; Division of Hematology and Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA., Shugg T; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA., Skaar TC; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA.; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA.

Journal Article , 2025

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Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features.

Kim Y; Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC V5Z 0B4, Canada; Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 0B4, Canada., Saville L; Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC V5Z 0B4, Canada; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., O'Neill K; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 0B4, Canada., Garant JM; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 0B4, Canada., Liu Y; Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC V5Z 0B4, Canada; Department of Experimental Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Haile-Merhu S; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 0B4, Canada., Ghashghaei M; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Hoang QA; Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC V5Z 0B4, Canada; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Louwagie A; Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC V5Z 0B4, Canada; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Park YP; Faculty of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Jones SJM; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 0B4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address: sjones@bcgsc.ca., Vu LP; Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, BC V5Z 0B4, Canada; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address: lvu@bccrc.ca.

Journal Article , 2025

TORC: Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq.

Wei X; Department of Biostatistics, Brown University, Providence, USA., Ma W; Department of Biostatistics, University of Michigan-Ann Arbor, Ann Arbor, USA., Wu Z; Department of Biostatistics, Brown University, Providence, USA. zhijin_wu@brown.edu., Wu H; Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, China. wuhao@suat-sz.edu.cn.; Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. wuhao@suat-sz.edu.cn.

Journal Article , 2025