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Mouse genome annotation by the RefSeq project

Kelly M. McGarvey, Tamara Goldfarb, Eric Cox, Catherine M. Farrell, Tripti Gupta, Vinita S. Joardar, Vamsi K. Kodali, Michael R. Murphy, Nuala A. O'Leary, Shashikant Pujar, Bhanu Rajput, Sanjida H. Rangwala (+5 others)
2015 Mammalian Genome  
Quantitative RNA-seq intron features data are displayed in this view. d Shown here is a subset of the links and related information displayed in the sidebar of each Gene record RefSeq nucleotide and  ...  RefSeq (NM_) 27,401 28,881 5 Model RefSeq (XM_) 48,123 47,250 -2 RefSeq, non-coding Known RefSeq (NR_) 3923 4276 9 Model RefSeq (XR_) 19,731 25,771 31 CCDS IDs 23,093 c 23,880 d  ... 
doi:10.1007/s00335-015-9585-8 pmid:26215545 pmcid:PMC4602073 fatcat:h7gzfdaghzeith7en6ejocoksi

RefSeq: an update on mammalian reference sequences

Kim D. Pruitt, Garth R. Brown, Susan M. Hiatt, Françoise Thibaud-Nissen, Alexander Astashyn, Olga Ermolaeva, Catherine M. Farrell, Jennifer Hart, Melissa J. Landrum, Kelly M. McGarvey, Michael R. Murphy, Nuala A. O'Leary (+17 others)
2013 Nucleic Acids Research  
curated d Percent ncRNA e 1 5 126 980 68 7 <1 38 556 na 50 22 <1 6 10 79 686 41 17 <1 28 176 na 23 42 <1 12 19 158 111 65 11 <1 29 490 na 18 50 1 18 28 263 628  ...  Release a Taxa b Mammalian records Human records Total transcripts Percent models c Percent curated d Percent ncRNA e Total transcripts Total genes f Percent models c Percent  ... 
doi:10.1093/nar/gkt1114 pmid:24259432 pmcid:PMC3965018 fatcat:wid54lruqrdzndb4oghwltdrqa

Current status and new features of the Consensus Coding Sequence database

Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen Aken, Susan M. Hiatt, Adam Frankish (+31 others)
2013 Nucleic Acids Research  
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of proteincoding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the
more » ... me Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.
doi:10.1093/nar/gkt1059 pmid:24217909 pmcid:PMC3965069 fatcat:go2bm4timjdhzc6ecp42w77k7m

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox (+25 others)
2017 Nucleic Acids Research  
doi:10.1093/nar/gkx1031 pmid:29126148 pmcid:PMC5753299 fatcat:xlfpwnmezjejtbg7dyatdwspvi

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin (+43 others)
2015 Nucleic Acids Research  
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http:// www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences.
more » ... he RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
doi:10.1093/nar/gkv1189 pmid:26553804 pmcid:PMC4702849 fatcat:2bm7d5coyvfotaj23hnj3mce6m

Page 947 of Quiver Vol. 53, Issue [page]

1918 Quiver  
Riddick, Mrs Cyril Bengough, Mrs. J]. E. Wilson, Mrs. Whittington, Miss V Mabel Cumming’s Pupils, M. Scott, Mrs. F. Burtenshaw, FE. M. Wakeman, Mrs. D. Lindsay, Mrs. Sugg, Mrs.  ...  Young, *‘ Henley,’’ Miss D. M. English, Mrs. Edward Hopkinson, Miss Winifred Jordan, Miss Lillian C. Hume, Sister Madeline’s pupils (Jamaica), Mrs. Horne, Mrs. Simpson, Mrs. Hamilton, Mrs. Amies, A.  ... 

Page 19 of History Vol. 11, Issue Index [page]

1982 History  
The Name of Brooke: The End of White Rajah Rule in Sarawak (Riddick) Reeves, A. C. Lancastrian Englishmen (Theilmann) Reid, Robert L., editor Battleground: The Auto- biography of Margaret A.  ...  Coast Guard Cutters & Craft of World War JI (Johnson) Schlereth, Thomas J., editor Material Culture Studies in America (Kahler) Schlissel, Lillian Women’s Diaries of the Westward Journey (Pickens) Schmitt  ... 

Page 728 of JAMA: The Journal of the American Medical Association Vol. 38, Issue 11 [page]

1902 JAMA: The Journal of the American Medical Association  
Seneca D. Powell. 95 Notes from the Clinics. Dr. Caille, William B. DeGarmo, Samuel G. Gant, and D. B. St. John Roosa. Robert T.  ...  (Contin- Lillian <A. Medical Examiner and Practitioner (N. Y.), February. 83 Modern Life Insurance—Does Its Medical Selection Reflect the Scientific Advance of the Past Century? Charles L.  ... 

Page 622 of Southern Medical Journal Vol. 13, Issue 8 [page]

1920 Southern Medical Journal  
D. Ferguson, Oklahoma City, died at Corpus Christi, Texas, June 11 following an illness of several years.  ...  Riddick, Raleigh, died recently from carcinoma of the throat. OKLAHOMA Dr. Fived I. El Reno, has move to Oklahoma City. Dr. Charles T. C. Buckner, Capt. M. C., U. S.  ... 

Page 44 of Virginia Medical Quarterly : VMQ Vol. 109, Issue 9 [page]

1982 Virginia Medical Quarterly : VMQ  
Hans RIDDICK JR, MD RIDDICK, MD, David Hayd RIDER, MD. Robt Edward RIDGWAY-HULL, MD, Duvah RIEMAN, MOD. G Fletcher RIFAAT, MD, Monira K RIGGINS JR, MD.  ...  Lillian Mariene PAYNE, MD. Sami O Brien PAYNE, MD. Thos Wm PAYNE, MD. William Duncan PAZ, MD. Alvaro Nwardc PEACH, MD, Wm Fennell PEACOCK JR, MD. JohnH PEARCE JR, MD. Carney C PEARCE, MD.  ... 

Page 4800 of Psychological Abstracts Vol. 83, Issue 11 [page]

1996 Psychological Abstracts  
Richard, 33069 Riddick, Annie, 35367 Riddle, Andrea S., 33682 Ridout, Deborah, 33568 Rieck, Angela, 32874 Riedel, W., 33555 Rieder, Ronald O., 34220 Riehle, Alexa, 33354 Riekkinen, M., 33556 Riekkinen,  ...  Rammisayer, Thomas, 33553 Ramos, Luis J., 33349 Ramsay, Michael C., 32846 Ranaldi, Robert, 33554 Ranchor, Adelita V., 34098 Randall, Patrick K.. 33588 Randall, Penny, 34437 Rangaswami, K., 34850, 35004 Range, Lillian  ... 

Page 446 of Chautauquan Vol. 7, Issue 7 [page]

1887 Chautauquan  
R.; Morris, Carrie E.; Phillips, Ella F.; Riddick, Mrs. Amelia P.; Roseberry, Ella; Smith, Willie V.; Standish, Mrs. Elvira E.; Warren, Mrs. Lucie Ransom; Willcox, Mrs. Virginia D. ; Will- <ox, R.  ...  Hitchcock, Irenaeus D. OHIO. Adams, N. B.; Adams, Mrs. Addie L.; Adair, Emmet M.; Allen, Davida. Andrews, Mrs. Lillian; Armstrong, Mrs. Ettie A.; Austin, L. O. F.: Bailey, Susie Morris; Baker, Mrs.  ... 

Page 685 of Psychological Abstracts Vol. 90, Issue 2 [page]

2003 Psychological Abstracts  
JR, 5445 Riddick, Barbara, 5423 Riddoch, M. Jane, 4562 Ridgway, Jim, 5417 Ridley, R.  ...  K., 4753 Rando, Teresa, 4539 Range, Lillian M., 5028 Rantala, Heikki, 5008 Raphling, David L., 4820 Rapoport, Amnon, 5436 Rapoport, Tamar, 3663 Rapp, Richar d C., 5166 Pc Paula, 3751 Rapport, Lisa J.,  ... 

Page 2184 of JAMA: The Journal of the American Medical Association Vol. 49, Issue 26 [page]

1907 JAMA: The Journal of the American Medical Association  
D., 163 medical, in Argentina, 1709 Reed, Jacob W., 2168 Stewart, H.  ...  Wilson, 1867 Stone, Winfield Scott, 619 Wroughton, John Henry, 2112 Richter, Martin Emil, 1797 Strausz, Philip Hurt, 710 Wurts, Charles Stewart, 798 Riddick, Thomas B., 799 Strong, Benjamin Grinell, 619  ... 

A systematic nomenclature for mammalian tropomyosin isoforms

Michael A. Geeves, Sarah E. Hitchcock-DeGregori, Peter W. Gunning
2014 Journal of Muscle Research and Cell Motility  
We thank Michael Murphy and Lillian Riddick at the NCBI for their assistance in verifying accession numbers and for including the proposed nomenclature in the NCBI website.  ...  Acknowledgments This work was supported by the following grants National Institutes of Health (USA): GM-093065 to SEH-D and Wellcome Trust Programme Grant 085309 to MAG.  ...  the four exons that vary in vertebrates can be designated by a four letter code; a.a.b.d indicates exon 1 is splice form a, exon 2 is splice form a, exon 6 is splice form b and exon 9 is splice form d.  ... 
doi:10.1007/s10974-014-9389-6 pmid:25369766 pmcid:PMC4426136 fatcat:xneeugyhpbhvdji5fmjff6yki4
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