Literature DB >> 27008010

Genomic Annotation Resources in R/Bioconductor.

Marc R J Carlson1,2, Hervé Pagès3, Sonali Arora3, Valerie Obenchain3, Martin Morgan3.   

Abstract

Annotation resources make up a significant proportion of the Bioconductor project (Huber et al., Nat Methods 12:115-121, 2015). And there are also a diverse set of online resources available which are accessed using specific packages. Here we describe the most popular of these resources and give some high level examples on how to use them.

Keywords:  Annotation; Bioconductor; Genomics; Next-generation sequencing; R

Mesh：

Year:  2016        PMID： 27008010     DOI： 10.1007/978-1-4939-3578-9_4

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  10 in total

1.  Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth.

Authors:  Timothy P York; Shawn J Latendresse; Colleen Jackson-Cook; Dana M Lapato; Sara Moyer; Aaron R Wolen; Roxann Roberson-Nay; Elizabeth K Do; Susan K Murphy; Catherine Hoyo; Bernard F Fuemmeler; Jerome F Strauss
Journal:  Epigenetics       Date:  2020-05-24       Impact factor: 4.528

2.  Menin regulates the serine biosynthetic pathway in Ewing sarcoma.

Authors:  Laurie K Svoboda; Selina Shiqing K Teh; Sudha Sud; Samuel Kerk; Aaron Zebolsky; Sydney Treichel; Dafydd Thomas; Christopher J Halbrook; Ho-Joon Lee; Daniel Kremer; Li Zhang; Szymon Klossowski; Armand R Bankhead; Brian Magnuson; Mats Ljungman; Tomasz Cierpicki; Jolanta Grembecka; Costas A Lyssiotis; Elizabeth R Lawlor
Journal:  J Pathol       Date:  2018-05-28       Impact factor: 7.996

3.  An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer.

Authors:  Michail Sarafidis; George I Lambrou; Vassilis Zoumpourlis; Dimitrios Koutsouris
Journal:  Cancers (Basel)       Date:  2022-07-10       Impact factor: 6.575

4.  An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence.

Authors:  Eugen Dhimolea; Ricardo de Matos Simoes; Dhvanir Kansara; Aziz Al'Khafaji; Juliette Bouyssou; Xiang Weng; Shruti Sharma; Joseline Raja; Pallavi Awate; Ryosuke Shirasaki; Huihui Tang; Brian J Glassner; Zhiyi Liu; Dong Gao; Jordan Bryan; Samantha Bender; Jennifer Roth; Michal Scheffer; Rinath Jeselsohn; Nathanael S Gray; Irene Georgakoudi; Francisca Vazquez; Aviad Tsherniak; Yu Chen; Alana Welm; Cihangir Duy; Ari Melnick; Boris Bartholdy; Myles Brown; Aedin C Culhane; Constantine S Mitsiades
Journal:  Cancer Cell       Date:  2021-01-07       Impact factor: 31.743

5.  Epigenome-Wide Study of Posttraumatic Stress Disorder Symptom Severity in a Treatment-Seeking Adolescent Sample.

Authors:  Christina M Sheerin; Eva E Lancaster; Timothy P York; Jesse Walker; Carla Kmett Danielson; Ananda B Amstadter
Journal:  J Trauma Stress       Date:  2021-02-02

6.  Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos.

Authors:  Ilaria Lavagi; Stefan Krebs; Kilian Simmet; Andrea Beck; Valeri Zakhartchenko; Eckhard Wolf; Helmut Blum
Journal:  Sci Rep       Date:  2018-03-06       Impact factor: 4.379

7.  Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms.

Authors:  Phuc H Hoang; Sara E Dobbins; Alex J Cornish; Daniel Chubb; Philip J Law; Martin Kaiser; Richard S Houlston
Journal:  Leukemia       Date:  2018-04-09       Impact factor: 11.528

8.  Identifying Hepatocellular Carcinoma Driver Genes by Integrative Pathway Crosstalk and Protein Interaction Network.

Authors:  Wenbiao Chen; Jingjing Jiang; Peizhong Peter Wang; Lan Gong; Jianing Chen; Weibo Du; Kefan Bi; Hongyan Diao
Journal:  DNA Cell Biol       Date:  2019-08-29       Impact factor: 3.311

9.  Exploiting gene dependency to inform drug development for multiple myeloma.

Authors:  Molly Went; Phuc H Hoang; Philip J Law; Martin F Kaiser; Richard S Houlston
Journal:  Sci Rep       Date:  2022-07-26       Impact factor: 4.996

10.  An epigenome-wide association study of early-onset major depression in monozygotic twins.

Authors:  Roxann Roberson-Nay; Dana M Lapato; Aaron R Wolen; Eva E Lancaster; Bradley T Webb; Bradley Verhulst; John M Hettema; Timothy P York
Journal:  Transl Psychiatry       Date:  2020-08-25       Impact factor: 6.222
  10 in total

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