Results 11 to 20 of about 2,767,093 (282)

PhyloRef: A Semi‐Automated Workflow for eDNA Reference Database Curation via Phylogenetic Anomaly Detection [PDF]

Ecology and Evolution
Environmental DNA (eDNA) analysis depends critically on high‐quality reference databases. However, widely used public repositories (e.g., NCBI) frequently suffer from annotation error, species misidentification, and sequence contamination, leading to ...
Yan Mai, Chenhong Li
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MultiTax-human: an extensive and high-resolution human-related full-length 16S rRNA reference database and taxonomy [PDF]

Microbiology Spectrum
Considering that the human microbiota plays a critical role in health and disease, an accurate and high-resolution taxonomic classification is thus essential for meaningful microbiome analysis.
Zhiwei Bao, Bin Zhang, Jianhua Yao, Ming D. Li   +3 more
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RESCRIPt: Reproducible sequence taxonomy reference database management. [PDF]

PLoS Computational Biology, 2021
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys.
Michael S Robeson, Devon R O'Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich   +6 more
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A Reference Database of Standardised Continuous Lumbar Intervertebral Motion Analysis for Conducting Patient-Specific Comparisons [PDF]

Frontiers in Bioengineering and Biotechnology, 2021
Lumbar instability has long been thought of as the failure of lumbar vertebrae to maintain their normal patterns of displacement. However, it is unknown what these patterns consist of.
Alexander Breen, Diana De Carvalho, Martha Funabashi, Martha Funabashi, Greg Kawchuk, Isabelle Pagé, Arnold Y. L. Wong, Alan Breen, Alan Breen   +8 more
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Mare-MAGE curated reference database of fish mitochondrial genes [PDF]

BMC Genomic Data, 2023
Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems.
Yassine Kasmi, Erik Eschbach, Reinhold Hanel   +2 more
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Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease

Frontiers in Molecular Biosciences, 2023
Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized.
Mangesh Suryavanshi, Jose Agudelo, Aaron Miller, Aaron Miller   +3 more
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Human Protein Reference Database--2009 update [PDF]

Nucleic Acids Research, 2009
Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation ...
Keshava Prasad, T. S., Goel, Renu, Kandasamy, Kumaran, Keerthikumar, Shivakumar, Kumar, Sameer, Mathivanan, Suresh, Telikicherla, Deepthi, Raju, Rajesh, Shafreen, Beema, Venugopal, Abhilash, Balakrishnan, Lavanya, Marimuthu, Arivusudar, Banerjee, Sutopa, Somanathan, Devi S., Sebastian, Aimy, Rani, Sandhya, Ray, Somak, Harrys Kishore, C. J., Kanth, Sashi, Ahmed, Mukhtar, Kashyap, Manoj K., Mohmood, Riaz, Ramachandra, Y. L., Krishna, V., Rahiman, B. Abdul, Mohan, Sujatha, Ranganathan, Prathibha, Ramabadran, Subhashri, Chaerkady, Raghothama, Pandey, Akhilesh   +29 more
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Human protein reference database--2006 update [PDF]

Nucleic Acids Research, 2006
Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived ...
Mishra, Gopa R., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, Shubha, Bala, P., Shivakumar, K., Anuradha, N., Reddy, Raghunath, Raghavan, T. Madhan, Menon, Shalini, Hanumanthu, G., Gupta, Malvika, Upendran, Sapna, Gupta, Shweta, Mahesh, M., Jacob, Bincy, Mathew, Pinky, Chatterjee, Pritam, Arun, K. S., Sharma, Salil, Chandrika, K. N., Deshpande, Nandan, Palvankar, Kshitish, Raghavnath, R., Krishnakanth, R., Karathia, Hiren, Rekha, B., Nayak, Rashmi, Vishnupriya, G., Kumar, H. G. Mohan, Nagini, M., Kumar, G. S. Sameer, Jose, Rojan, Deepthi, P., Mohan, S. Sujatha, Gandhi, T. K. B., Harsha, H. C., Deshpande, Krishna S., Sarker, Malabika, Prasad, T. S. Keshava, Pandey, Akhilesh   +41 more
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Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

Environmental DNA, 2020
Background and Aims Environmental DNA (eDNA) metabarcoding provides a highly sensitive method of surveying freshwater fish communities, although studies to date have largely been restricted to temperate ecosystems.
Christopher J. Doble, Helen Hipperson, Walter Salzburger, Gavin J. Horsburgh, Chacha Mwita, David J. Murrell, Julia J. Day   +6 more
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BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata

Methods in Ecology and Evolution, 2023
DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high‐quality sequences to maximize ...
Sarah Wiechers, Lara Marie Kösters, Dietmar Quandt, Thomas Borsch, Susann Wicke, Kai Frank Müller   +5 more
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