Biostar

697 results • Page 2 of 14

jayajit-das. Recent publications from the group can be found at, https://www.ncbi.nlm.nih.gov/pubmed/?term=jayajit+das . Das lab has access to a state of the art computer cluster over 120 INTEL processors. Resources at the

assembly

updated 11 months ago • jayajit

CPM`? Are these two different scale factors? Thanks [1]: https://www.ncbi.nlm.nih.gov/pubmed/30361341

Deeptools ATAC-seq

updated 11 months ago • Zeel

Apply Now!][9]** [3]: https://www.nature.com/articles/ng.3774 [4]: https://www.ncbi.nlm.nih.gov/pubmed/30311370 [5]: https://www.biorxiv.org/content/10.1101/700179v1?rss=1 [6]: https://www.biorxiv.org/content/10.1101/783134v1

civic biocuration cancer genomics

updated 11 months ago • Obi Griffith

Dear Biostars, Most of the students/researchers use PubMed in order to find publications relative to their work or the field of interest. Although Pubmed, most of the time, includes

arrayexpress GEO SRA

updated 11 months ago • Konstantinos Yeles

to requisite laboratory and analytical skills, the successful candidate will have high quality pubmed listed publications and a track record of productivity appropriate for their stage of training. The ability to begin

Research-Associate Postdoc Graduate-student

updated 11 months ago • matthew.stratton

206-667-4700. [1]: https://gavinhalab.org/people/Gavin-Ha/ [2]: https://www.ncbi.nlm.nih.gov/pubmed/29909985 [3]: https://www.ncbi.nlm.nih.gov/pubmed/29109393 [4]: https://www.ncbi.nlm.nih.gov/pubmed/25060187 [5]: https://careers

seattle

updated 11 months ago • Fred Hutch (Recruiting)

Cellosaurus release 30 is available on the ExPASy server: https://web.expasy.org/cellosaurus/ **1) Statistics** - 112983 cell lines (84432 human, 19675 mouse, 2075 rat) - 625 species represented - 73553 synonyms - 331707 cross-references to 85 ontologies, databases, catalogs, etc. - 104057 references to 17422 distinct publications (papers, patents, theses, etc.) - 17769 web links - 6482 human, …

database cell-line

updated 11 months ago • Amos Bairoch

Hi I would like to write a edirect query to extract number of publications per gene per year. The group I am interested in is Viridiplantae. So for all species under this group, given a date range, I would like to get the publication count for each gene in that species. The final output that I am looking for is something like YEAR Genus_Species Gene_Symbol Publication_Count 1970 Arabido…

eutilities

updated 11 months ago • abhijit.synl

html/CoexpressionNetwork/Rpackages/WGCNA/ [10]: https://www.ncbi.nlm.nih.gov/pubmed/20338053 [11]: https://www.ncbi.nlm.nih.gov/pubmed/31258543

time-course RNA-Seq time-series

updated 11 months ago • Anand Rao

and subclonal populations using WGS (for reference, please read: https://www.ncbi.nlm.nih.gov/pubmed/29093439), as well as subclonal phenotype and pathway activity using single cell sequencing data. - He/she will assist

R python perl

updated 11 months ago • alung

cnb/faculty_berrettini.html [3]: https://www.geisinger.org/ [4]: https://www.ncbi.nlm.nih.gov/pubmed/?term=geisinger [5]: https://www.geisinger.org/mycode [6]: https://www.geisingeradmi.org/ [7]: https://lewisburgpa.com

Neuroimaging genomics

updated 12 months ago • Rm

past work for example) : ai@rednalabs.com / ai at rednalabs.com [1]: https://www.ncbi.nlm.nih.gov/pubmed/28053114 [2]: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky567/5050624#118596216 [3]: http://data.snu.ac.kr

neural-networks lncRNA RNN FEELnc

updated 12 months ago • sieva1

To apply**: Send CV to Matthew Maurano at: [maurano@nyu.edu][3]. [1]: http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Maurano+MT%5Bau%5D [2]: http://www.med.nyu.edu/research/systemsgenetics [3]: mailto:maurano@nyu.edu

python synthetic-biology illumina R

updated 12 months ago • maurano

VCF

updated 12 months ago • Shyam

curation of participants' health data. - Perform searches of relevant scientific databases (e.g. PubMed, Google Scholar) to identify published papers, databases, etc. - Assist in the development of health reports and longitudinal

big-data biostatistics data-curator

updated 12 months ago • asmi.shah

4] - [Feinstein Institute of Medical Research][5] - Dr. Hajizadeh's recent publications at [PubMed][6] - Dr. Khader's recent publications at [Google Scholar][7] [1]: https://www.feinsteininstitute.org/programs-researchers

postdoc artificial-intelligence data-science

updated 12 months ago • Khader Shameer

Want to know which potential treatment targets have been linked to a specific syndrome in the literature? Want to check which components of a signalling pathway already have a protein structure available? Interested if a particular chemical is reported in the methods section of particular papers? Extract valuable facts hidden in the millions of scientific papers: access text-mined literature evid…

text-mining ontology pubmed

updated 12 months ago • Maria_Levchenko

will be different, but it'd be nice to base it on something. [1]: http://www.ncbi.nlm.nih.gov/pubmed/20167110 [2]: http://www.genetics.org/cgi/rapidpdf/genetics.110.114983v1 [3]: http://tophat.cbcb.umd.edu/ [4]: http://cufflinks.cbcb.umd.edu

pipeline next-gen-sequencing rna rna-seq

updated 12 months ago • brentp

I'm a doctor expert in fertility and especially in endometriosis. I saw good examples on how text mining on pubmed database and genes understanding could help. This disease remains very difficult to understand and the average delay...expert in fertility and especially in endometriosis. I saw good examples on how text mining on pubmed database and genes understanding could help. This disease rem…

text-mining fertility pubmed

updated 12 months ago • jeromebouaziz

https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/?campaign=twitter-11022017 > If you regularly use the E-utilities API, we have important news for you: NCBI is now providing API keys for the E-utilities! After May 1, 2018, NCBI will limit your access to the E-utilities unless you have one of these keys. Obtaining an API key is quick, and simple, and will allow…

pubmed eutils ncbi api

updated 12 months ago • Pierre Lindenbaum

0 my_list = open('my_list.txt', 'r') for ID in my_list: handle = Entrez.efetch(db="pubmed", id=ID, rettype ='medline', retmode = 'gb') medRecords=Medline.parse(handle) for rec in medRecords: counterAB+=1 print('counterAB

biopython entrez

updated 12 months ago • Xylanaser

The paper is available at **https://academic.oup.com/hmg/article-lookup/doi/10.1093/hmg/ddx203** and [**pubmed**][1] ![Human Brain Project][2] [1]: https://www.ncbi.nlm.nih.gov/pubmed/?term=28575308 [2]: http://mirlab.sysu.edu.cn/brain/brainImg.png

Parkinson lncRNA Alzheimer brain transcriptome

updated 12 months ago • lsp03yjh

format vcf --input_file tests/test.vcf --output_file tests/test.vep.vcf --offline --pubmed --fork 4 --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory Any help would be appreciated. Thanks in advance

vcf2maf

updated 12 months ago • Winson

has just reported criticisms of the paper also, and the article appears with a critical comment on [pubmed][5]. [1]: https://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4293.html [2]: https://medium.com/@GaetanBurgio/should-we-be...amp;_hsmi=53166887 [5]: https://www.ncbi.nlm.nih.gov/pubmed/?term=Unexpected%20mutations%20after%20CRISPR-Cas9%20editing%20in%20vivo

off-target CRISPR

updated 12 months ago • BioinfGuru

Salary Range: £31,498 to £39,729, plus excellent benefits. The Wellcome Trust Sanger Institute are seeking to recruit a Data Scientist who can facilitate the scientific work of the Jones group by leading the computational data analysis support for the team and their collaborators. The group, led by Phil Jones, studies pre-cancer, how mutant cells evolve into cancers in humans and model systems …

Perl Python Linux R

updated 12 months ago • Recruit

of annotation to which is the best tool) Thank you all. [1]: https://www.ncbi.nlm.nih.gov/pubmed/22955621

enhancer annotation

updated 12 months ago • BioinfGuru

I am trying to use Entrez to search and parse publication records from PubMed. The parse function used to work until recently, but a few days ago it started failing. I started getting the following...py from Bio import Entrez Entrez.email = "Your.Name.Here@example.org" handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml") records = Entrez.parse(handle) for record in record…

biopython pubmed entrez

updated 12 months ago • apiljic

of-drugs-and-disease [3]: http://repurposedb.dudleylab.org/ [4]: https://www.ncbi.nlm.nih.gov/pubmed/25579574 [5]: https://www.ncbi.nlm.nih.gov/pubmed/27080087 [6]: http://dudleylab.org/ [7]: http://repurposedb.dudleylab.org

precision-medicine drug-repositioning

updated 12 months ago • Khader Shameer

guidance from our experienced trainers. Topics Covered: Understanding NCBI and other databases- PUBMED, MESH Proteomics Understanding sequence alignment and its application Genomics Primer Designing Chemical databases

RASA

updated 12 months ago • Info

Salary Range: £31,498 to £39,729, plus excellent benefits. The Wellcome Trust Sanger Institute are seeking to recruit a Senior Bioinformatician who can facilitate the scientific work of the Jones group by leading the computational data analysis support for the team and their collaborators. The group, led by Phil Jones, studies pre-cancer, how mutant cells evolve into cancers in humans and model …

computer-science genome Unix Perl

updated 13 months ago • Recruit

**City, country**: Ostrava, Czech Republic **Laboratory and Institution information**: The University of Ostrava is the fastest developing University in Czech Republic. Laboratory of Molecular protozoology at the Life Science Research Centre is focused on molecular biology and functional genomics of Trypanosomatidae. There are two main research directions in the laboratory: i) studies of biodiv…

PhD

updated 13 months ago • kostygov

extra connections between this collection of genes? Thanks [1]: https://www.ncbi.nlm.nih.gov/pubmed/18671248 [2]: http://link.springer.com/article/10.1007/s10288-008-0073-9 [3]: http://www.robertolucchetti.com/public/uploads

game-theory RNA-Seq DEG

updated 13 months ago • Farbod

After I run my esearch in pubmed I return a list of IDs for publications. I found the following info by running einfo on pubmed" # {'Name': 'pubmed_protein_weighted...Links to protein', 'DbTo': 'protein'} # {'Name': 'pubmed_snp', 'Menu': 'SNP Links', 'Description': 'PubMed to SNP links', 'DbTo': 'snp'} # {'Name': 'pubmed_protein_refseq', 'Menu': 'Protein (RefSeq) Links', 'Description…

protein fasta Biopython Entrez

updated 13 months ago • m.brathwaite

How to get ftp direct links for pmids except those are in ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/file_list.pdf.txt. Thank you

pubmed pmc

updated 13 months ago • anithanagaraj93

by local walk and jump, which is faster than Smith-Waterman extension (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual

blast ncbi short-read mapper hts

updated 13 months ago • Pierre Lindenbaum

1]: http://cb2.uahs.arizona.edu/employment-opportunities [2]: http://www.ncbi.nlm.nih.gov/pubmed/?term=yves%20lussier [3]: http://www.ncbi.nlm.nih.gov/pubmed/?term=roberta%20brinton [4]: https://www.whitehouse.gov/the

precision-medicine biomedical-informatics postdoc

updated 13 months ago • joanneberghout

M. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print] [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/27288499) | [Bioinformatics Journal](https://doi.org/10.1093/bioinformatics/btw325...www.biostars.org/u/11013/ [8]: https://github.com/genome/gms [9]: http://www.ncbi.nlm.nih.gov/pubmed/26563128 [10]: http://clincancerres.aacrjournals.org/content/e…

bioconductor graphics R genvisr

updated 13 months ago • Obi Griffith

p/7126/#191667 9 Common metrics to measure tissue specificity: http://www.ncbi.nlm.nih.gov/pubmed/26891983 Bayesian tool for methylation analysis: https://en.wikipedia.org/wiki/Bayesian_tool_for_methylation_analysis

gallery

updated 13 months ago • Shicheng Guo

Hi, I'm interested in computational prediction of miRNAs in bees. To my understanding there are two methods to predict miRN: comparative and non-comparative. I am interested in learning how to conduct either of them. As I'm beginning with my PhD and I don't know much about bioinformatics yet (I've only used BLAST, PUBMED, uniprot, etc. a little). The amount of information out there (tutorials, …

miRNA

updated 13 months ago • Nuria_bl

chromatin state genomic co-ordinates of C.elegans reported in the paper http://www.ncbi.nlm.nih.gov/pubmed/21177976. All I found was Chip-Seq data but not chromatin states. Any suggestions? Thanx in advance

c.elegans chromatin-states

updated 14 months ago • biorepine

EDIT**: MeDUSA is still offline (as of 1/22/2015). [1]: http://www.ncbi.nlm.nih.gov/pubmed/23587164

MeDUSA methyl-seq

updated 14 months ago • Bohdan Khomtchouk

Hi. I am wondering is there any *python module* that allows to download paper by its doi? I am familiar with SciHub module (https://github.com/zaytoun/scihub.py) but there is a problem with *captchas*. Probably you know other methods of downloading papers using some API. I'm ready to pay some money to avoid *captchas* but personally I don't know any resource that offers this option. Thank you…

pubmed python scihub

updated 14 months ago • akarazeev

Does anybody has a new link to download the same? [1]: https://www.ncbi.nlm.nih.gov/pubmed/27466620

plasmidSPAdes

updated 14 months ago • lakhujanivijay

protein NCBI

updated 14 months ago • enriqp02

flowering and Asterid evolution JOURNAL Nature 546 (7656), 148-152 (2017) PUBMED 28538728 REFERENCE 2 (bases 1 to 195042445) AUTHORS Gouzy,J., Langlade,N. and Munos,S. TITLE Helianthus annuus Genome sequencing

Biopython

updated 14 months ago • abu

download data from there? I hope someone can help me. Thanks! [1]: https://www.ncbi.nlm.nih.gov/pubmed/25108458 [2]: http://image.ibb.co/dptixo/imagem.png

SNP hapmap

updated 14 months ago • williamtenoriotenorio

Hello! I was hoping someone here could help me with something. I have been using this code to scrape metadata from articles written by certain authors. However, I have been encountering some difficulty trying to scrape MeSH terms (as you will see, the code for the mesh_terms is incomplete. I will still provide the code that did not work for me). Would anyone know or have any suggestions for how t…

Python Entrez Scraping

updated 14 months ago • Arnau

Entrez def search(query): Entrez.email = 'example@mail.com' handle = Entrez.esearch(db='pubmed', sort='pub date', retmax='10', retmode='xml', term=query) results = Entrez.read(handle) print(results['Count']) return results def...ids = ','.join(id_list) Entrez.em…

biopython pubmed python3.x Esearch python

updated 14 months ago • yz

data: RPKM measure is inconsistent among samples". Wagner GP, Kin K, Lynch VJ. _Theory Biosci._ 2012. [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/22872506) ## Firstly create the coordinate of all of the exons Download the file: ``CCDS.20160908.txt

bam RNA-Seq bedtools rpkm

updated 14 months ago • jmzeng1314

overall survival in breast cancer in [doi: 10.1016/j.cca.2018.05.041](https://www.ncbi.nlm.nih.gov/pubmed/29800557), whilst high expression of *MMP10* was associated with ***poor*** prognosis in colon cancer in [doi: 10.1186/s12885

cox gene-expression survival-analysis geo

updated 14 months ago • Kevin Blighe

697 results • Page 2 of 14

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