GenBank

Benson, D. A.; Cavanaugh, Mark; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W

doi:10.1093/nar/gks1195

Cited by 2,920 publications

(2,090 citation statements)

References 13 publications

Supporting

Mentioning

1,957

Contrasting

Unclassified

Order By: Relevance

“…The human genome assembly and annotated proteins (all isoforms) were obtained from GenBank (v. 37.3) (Benson et al , 2013). For MXE candidate validation, we selected data from 515 publically available samples comprising 31 tissues and organs, 12 cell lines and seven developmental stages (Barbosa‐Morais et al , 2012; Djebali et al , 2012; Tilgner et al , 2012; Xue et al , 2013; Yan et al , 2013; Fagerberg et al , 2014) amounting to over 15 billion RNA‐Seq reads.…”

Section: Methodsmentioning

confidence: 99%

“…Allora currently contains 94,148 PDB entries (derived from the RCSB Protein Data Bank, http://www.rcsb.org, Rose et al , 2015) with 247,959 chains, of which 120,665 represent unique sequences. Based on the database references in the PDB entries, the full‐length proteins were fetched from UniProt KB (UniProt Consortium, 2015) or GenBank (Benson et al , 2013) and the corresponding gene structures of the eukaryotic proteins reconstructed with WebScipio (Hatje et al , 2013). In Allora, all PDBs belonging to the same UniProt or GenBank entries are connected.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

View full text Add to dashboard Cite

Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

View full text Add to dashboard Cite

show abstract

“…Among the ~400 proteins that matched known proteins in GenBank (nr) (Benson et al, 2013) (Evalue < 10 -10 ), > 80% corresponded to known mitochondrial components (data not shown).…”

Section: Protein Extractsmentioning

confidence: 99%

“…MS and MS/MS queries were performed either against the GenBank protein database (nr) (Benson et al, 2013) or against a database of conceptually translated E. gracilis sequences assembled from contigs of 454 genomic reads and from contigs of public ESTs (see below). Precursor tolerance of 150 ppm for MS spectra and 0.1 Da fragment tolerance for MS/MS spectra were allowed.…”

Section: Mass Spectrometry (Ms) Analysesmentioning

confidence: 99%

The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae

et al. 2014

View full text Add to dashboard Cite

The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential therapeutic target. Recently, numerous additional subunits of the respiratory-chain complexes have been described in Trypanosoma brucei and Trypanosoma cruzi. Since these subunits had apparently no counterparts in other organisms, they were interpreted as potentially associated with the parasitic trypanosome lifestyle. Here we used two complementary approaches to characterise the subunit composition of respiratory complexes in Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes. First, we developed a phylogenetic pipeline aimed at mining sequence databases for identifying homologs to known respiratory-complex subunits with high confidence. Second, we used MS/MS proteomics after two-dimensional separation of the respiratory complexes by Blue Native-and SDS-PAGE to both confirm in silico predictions and to identify further additional subunits. Altogether, we identified 41 subunits that are restricted to E. gracilis, T. brucei and T. cruzi, along with 48 classical subunits described in other eukaryotes (i.e. plants, mammals and fungi). This moreover demonstrates that at least half of the subunits recently reported in T. brucei and T. cruzi are actually not specific to Trypanosomatidae, but extend at least to other Euglenozoa, and that their origin and function are thus not specifically associated with the parasitic lifestyle. Furthermore, preliminary biochemical analyses suggest that some of these additional subunits underlie the peculiarities of the respiratory chain observed in Euglenozoa.Liège, february 06 th 2014Dear Editor, Please find the fully revised version of our manuscript "The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae."We are grateful to you for having encouraged us to resubmit a modified manuscript. We have addressed all the comments raised by the reviewers on our first submission. A point to point answer has been submitted along with the manuscript. Main changes are : (i) additional explanations about the phylogenic/bioinformatic strategy including some phylogenetic trees (supplemental figures 1 and 2); (ii) all data that were previously not shown (mass spectrometry data, in vivo respiratory assays) are now included in the manuscript as supplemental figures/tables.We hope that we have now significantly improved our manuscript so you'll find it suitable for publication in the special issue of Mitochondrion dedicated to "Plant Mitochondria Biology". R: Primary MS data are now given in Supplemental Table 3 for each polypeptide for which the score was > 60. (BLAST alignments, Evalues, etc.) are actually presented in the paper to support the inference that a particular E. gracilis protein is a true homolog of a given kinetoplastid protein. The most important conclusion of t...

show abstract

“…Scientists who publish in most microbiological journals are required to deposit genomic sequence data supporting their conclusions to publicly accessible databases such as GenBank (Benson et al, 2013), although these databases do not cover the full range of microbiological data produced by deep subseafloor biosphere scientists. No similar requirement to deposit exists for complementary physical science data.…”

Section: Improving Curation Of Extant Datamentioning

confidence: 99%

Ship space to database: emerging infrastructures for studies of the deep subseafloor biosphere

Darch

Borgman

2016

PeerJ Computer Science

View full text Add to dashboard Cite

Background. An increasing array of scientific fields face a ''data deluge.'' However, in many fields data are scarce, with implications for their epistemic status and ability to command funding. Consequently, they often attempt to develop infrastructure for data production, management, curation, and circulation. A component of a knowledge infrastructure may serve one or more scientific domains. Further, a single domain may rely upon multiple infrastructures simultaneously. Studying how domains negotiate building and accessing scarce infrastructural resources that they share with other domains will shed light on how knowledge infrastructures shape science. Methods. We conducted an eighteen-month, qualitative study of scientists studying the deep subseafloor biosphere, focusing on the Center for Dark Energy Biosphere Investigations (C-DEBI) and the Integrated Ocean Drilling Program (IODP) and its successor, the International Ocean Discovery Program (IODP2). Our methods comprised ethnographic observation, including eight months embedded in a laboratory, interviews (n = 49), and document analysis. Results. Deep subseafloor biosphere research is an emergent domain. We identified two reasons for the domain's concern with data scarcity: limited ability to pursue their research objectives, and the epistemic status of their research. Domain researchers adopted complementary strategies to acquire more data. One was to establish C-DEBI as an infrastructure solely for their domain. The second was to use C-DEBI as a means to gain greater access to, and reconfigure, IODP/IODP2 to their advantage. IODP/IODP2 functions as infrastructure for multiple scientific domains, which creates competition for resources. C-DEBI is building its own data management infrastructure, both to acquire more data from IODP and to make better use of data, once acquired. Discussion. Two themes emerge. One is data scarcity, which can be understood only in relation to a domain's objectives. To justify support for public funding, domains must demonstrate their utility to questions of societal concern or existential questions about humanity. The deep subseafloor biosphere domain aspires to address these questions in a more statistically intensive manner than is afforded by the data to which it currently has access. The second theme is the politics of knowledge infrastructures. A single scientific domain may build infrastructure for itself and negotiate access to multi-domain infrastructure simultaneously. C-DEBI infrastructure was designed both as a response to scarce IODP/IODP2 resources, and to configure the data allocation processes of IODP/IODP2 in their favor.

show abstract

GenBank

Cited by 2,920 publications

References 13 publications

The landscape of human mutually exclusive splicing

The landscape of human mutually exclusive splicing

The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae

Ship space to database: emerging infrastructures for studies of the deep subseafloor biosphere

Contact Info

Product

Resources

About