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In memoriam –Scott Federhen (October 21, 1952 - May 5, 2016)

Conrad L. Schoch, Ilene Karsch-Mizrachi, James M. Ostell
2016 Standards in Genomic Sciences  
Scott Federhen will be remembered as an adventurous eater, kind colleague and devoted Red Sox fan with an exceptionally broad intellectual range.  ...  Born in 1952, Scott obtained a MS degree in Computer Science, focused on denotational semantics of AI languages, from University of Maryland in 1980.  ... 
doi:10.1186/s40793-016-0160-z fatcat:guhwdsqsunhxnhnfay7ibwpfiu

Replication is Recursion; or, Lambda: the Biological Imperative [article]

Scott Federhen
2015 bioRxiv   pre-print
Graphics by Erica Federhen. false = λx.λy.y true = λx.λy.x and = λx.λy. (xy) false or = λx.λy. (x true) y not = λx. (x false) true if-then-else = λx.λy.λz.(xy)z pair = λx.λy.λz.  ...  computation, axiomatic semantics akin to production systems, and denotational semantics based on the lambda calculus model of computation together with the lattice theory as a model for data objects (Scott  ... 
doi:10.1101/018804 fatcat:oazpd46fs5hz5nxvt6juebtaci

Type material in the NCBI Taxonomy Database

Scott Federhen
2014 Nucleic Acids Research  
Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database (http: //www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. This has important implications for many NCBI resources, some of which are outlined below.
doi:10.1093/nar/gku1127 pmid:25398905 pmcid:PMC4383940 fatcat:mvhne3nzlvfk7lndskpvy7ckf4

Update on RefSeq microbial genomes resources

Tatiana Tatusova, Stacy Ciufo, Scott Federhen, Boris Fedorov, Richard McVeigh, Kathleen O'Neill, Igor Tolstoy, Leonid Zaslavsky
2014 Nucleic Acids Research  
NCBI RefSeq genome collection http://www.ncbi. nlm.nih.gov/genome represents all three major domains of life: Eukarya, Bacteria and Archaea as well as Viruses. Prokaryotic genome sequences are the most rapidly growing part of the collection. During the year of 2014 more than 10 000 microbial genome assemblies have been publicly released bringing the total number of prokaryotic genomes close to 30 000. We continue to improve the quality and usability of the microbial genome resources by
more » ... easy access to the data and the results of the precomputed analysis, and improving analysis and visualization tools. A number of improvements have been incorporated into the Prokaryotic Genome Annotation Pipeline. Several new features have been added to RefSeq prokaryotic genomes data processing pipeline including the calculation of genome groups (clades) and the optimization of protein clusters generation using pan-genome approach.
doi:10.1093/nar/gku1062 pmid:25510495 pmcid:PMC4383903 fatcat:52oqwfkoircovp4jgymgm4nhry

Comment on 'Birdstrikes and barcoding: can DNA methods help make the airways safer?'

SCOTT FEDERHEN
2011 Molecular Ecology Resources  
Correspondence: Scott Federhen, Fax: 301 402 9651; federhen@ncbi.nlm.nih.gov. Mol Ecol Resour. Author manuscript; available in PMC 2011 November 27.  ... 
doi:10.1111/j.1755-0998.2011.03054.x pmid:21899722 pmcid:PMC3224856 fatcat:wtkerjm5argabp3k4ujzk7fgsq

Statistics of local complexity in amino acid sequences and sequence databases

John C. Wootton, Scott Federhen
1993 Computers and Chemistry  
The results of such statistical and functional classification of low-complexity segments is reported separately (Wootton & Federhen, 1993; and unpublished work) .  ...  A recent study that analyzed amino acid sequence databases globally (Wootton & Federhen, 1993) found that approx. 40% of sequence entries contain at least one such cluster and approx. 15 % of the residues  ... 
doi:10.1016/0097-8485(93)85006-x fatcat:w6y2bvfc2zgenlebljx2vqk4su

Comments on the paper by Pleijel et al. (2008): Vouching for GenBank

Scott Federhen, Carol Hotton, Ilene Mizrachi
2009 Molecular Phylogenetics and Evolution  
doi:10.1016/j.ympev.2009.04.016 pmid:19410006 pmcid:PMC2739410 fatcat:6hviuyv2mjgfvjqek3dqr5s34y

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

Scott Federhen, Karen Clark, Tanya Barrett, Helen Parkinson, James Ostell, Yuichi Kodama, Jun Mashima, Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-Mizrachi
2014 Standards in Genomic Sciences  
Microbial genome sequence submissions to the International Nucleotide Sequence Database Collaboration (INSDC) have been annotated with organism names that include the strain identifier. Each of these strain-level names has been assigned a unique 'taxid' in the NCBI Taxonomy Database. With the significant growth in genome sequencing, it is not possible to continue with the curation of strain-level taxids. In January 2014, NCBI will cease assigning strain-level taxids. Instead, submitters are
more » ... uraged provide strain information and rich metadata with their submission to the sequence database, BioProject and BioSample.
doi:10.4056/sigs.4851102 pmid:25197497 pmcid:PMC4149001 fatcat:lcwotk75g5amdejrgb55s3cu34

Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)

Scott Federhen, Ramon Rossello-Mora, Hans-Peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel Brown, David Labeda, David Ussery, George M. Garrity, Rita R. Colwell, Nur Hasan (+19 others)
2016 Standards in Genomic Sciences  
This project spans many groups at the NCBI, including taxonomy (Scott Federhen & Sean Turner), GenBank (Ilene Karsch-Mizrachi), WGS (Karen Clark), SRA (Chris O'Sullivan) 16S rRNA (Rich McVeigh), BLAST  ...  Federhen et al. Standards in Genomic Sciences (2016) 11:15 Workshop was held at the NCBI in Bethesda MD on 12-13 May, 2015.  ... 
doi:10.1186/s40793-016-0134-1 fatcat:ymjljz5pxzbd5aojvgl3bylfwa

Database resources of the National Center for Biotechnology Information

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer (+28 others)
2009 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities,
doi:10.1093/nar/gkp967 pmid:19910364 pmcid:PMC2808881 fatcat:duzfi6ea4rdvvb5wbhr7z2mbpq

The Global Registry of Biodiversity Repositories: A Call for Community Curation

David Schindel, Scott Miller, Michael Trizna, Eileen Graham, Adele Crane
2016 Biodiversity Data Journal  
This article is dedicated to the memory of Scott Federhen, head of NCBI's taxonomy database and a tireless champion for data integration in biology.  ...  Thiers, Roger Hyam, and Scott Federhen for agreeing to merge the contents of Index Herbariorum, Biodiversity Collections Index and the NCBI institution and collection tables to create GRBio.  ... 
doi:10.3897/bdj.4.e10293 pmid:27660523 pmcid:PMC5018115 fatcat:jfwasoegfjhvbbiklhj7cs3ikm

Reviewer acknowledgement 2013

Irene Pala
2014 BMC Genomics  
Jian-Bing Fan USA Longjiang Fan China David Fang USA Gang Fang USA Cathy Sj Fann Taiwan Kerrie Farrar UK Paul Farrell UK Marianna Fasoli Italy Mathias Faure France Herbert Federhen  ...  Diaconu USA Fernando Diaz Spain Oscar Diaz Horta USA Thomas Dick Singapore Giorgio Dieci Italy Sarah Diermeier USA Christoph Dieterich Germany Rod Dimaline UK Emmanuel Dimont USA Scott  ... 
doi:10.1186/1471-2164-15-205 pmcid:PMC3986690 fatcat:axrve6wj5nagph3n32wbb53pre

Page 54 of Charleston Medical Register 1803 Vol. 38, Issue 888 [page]

1892 Charleston Medical Register 1803  
Fales, Hall, Foster and Federhen; builder, Chicago, Il). — Frank Rowe, four-st’y hotel, Sixty- Columbian Endeavor Association, four-st’y hotel METAL CEILINGS, rai?2ls"s*sSos.  ...  Dowling, 8 two-st’y brick buildings, e s Cross St., w Paca St.; and 26 two-st’y brick buildings, es Scott St., s Cross St. P. D. Della, 10 two-st’y brick buildings,s s Fort Ave., e Covington St. S.  ... 

GenBank and PubMed: How connected are they?

Holly Miller, Catherine N Norton, Indra N Sarkar
2009 BMC Research Notes  
Acknowledgements The authors wish to thank Sheldon Kotzin (NLM), Lou Knecht (NLM), Scott Federhen (NCBI/NLM) and Mark Cavanaugh (NCBI/NLM) for their valuable insights and explanations pertaining to the  ...  -Scott Federhen & Mark Cavanaugh/NCBI/April 4, 2008). ). Where PMIDs are not available, DOIs may be an alternative solution.  ... 
doi:10.1186/1756-0500-2-101 pmid:19508734 pmcid:PMC2704225 fatcat:q5dms4qpjvfqxfh52snw7lapk4

Page 844 of Forest and Stream; A Journal of Outdoor Life, Travel, Nature Study, Shooting, Fishing, Yachting Vol. 44, Issue 26 [page]

1895 Forest and Stream; A Journal of Outdoor Life, Travel, Nature Study, Shooting, Fishing, Yachting  
Kenerson, “Herbert” (Federhen), Pit- kin and Mascrofi 29, Jones (W:W. Bennett) 28.  ...  Federhen, Quincy; F. E. Bennett, Boston; William Allison, Hingham; Pitkin, Hartford; C. H. Burbridge, Hartford; J. F. Maseroft, Sutton. = = of the home club, including A. W. Walls, W. L.  ... 
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