Biostar

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canon". Here are some of the papers that I use for teaching to start the ball rolling: Altschul et al. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10. http://www.ncbi.nlm.nih.gov/pubmed/2231712 Myers...et al. A whole-genome assembly of Drosophila. Science. 2000 Mar 24;287(5461):2196-204. http://www.ncbi.nlm.nih.gov/pubmed/10731133

literature papers history

updated 3.8 years ago • Casey Bergman

from Bio import SeqIO import glob import random import time print time.time() FNS=glob.glob("/home/et/Desktop/PP15_META/01Geneious/R1/*") for FN in FNS: SEQ_INDEX=SeqIO.index(FN,"fastq") SELECTED_SEQ_INDEX=random.sample(SEQ_INDEX...The 2nd script (slow): ``` import time import glob from Bio import SeqIO FNS_R2=glob.glob("/home/et/Desktop/PP15_META/01Geneious/*2.fastq") FNS_R1=glob.glob("…

Biopython

updated 2.4 years ago • jincheng.wang1986

I am attaching a figure from [Mabel et al., 2024](https://doi.org/10.1038/s41467-024-49349-z). ![][1] How can I create circos plots like this? I've seen these plots used in multiple

Visualization Circos Sequence

updated 5 months ago • Jaykumar

of standard errors graphed. Basically, I want some conceptually similar to this plot from Allentoft et al. 2015 (http://www.nature.com/nature/journal/v522/n7555/fig_tab/nature14507_SF2.html

updated 2.5 years ago • devenvyas

alpha = 0.05, lfcThreshold=1`. But there are more than 6000 DGEs, if you use edgeR, DEGSeq or GFOLD et al. Would you like to tell me where is wrong? Or which soft package is more fit to do this analysis (with different replicates

different-replicate DESeq RNA-Seq

updated 3.2 years ago • robertorun

I am running [Paradigm][1] on a matrix of mRNA expression. I read ***Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM." Bioinformatics

gene-expression pathway paradigm mrna

updated 2.7 years ago • fbrundu

VL03F635, WE02491 IDs: EF104615, AY557140, AY556740 ``` References: Wiemers, 2003; Wiemers et al., 2010 It's not difficult to write a python script for that aim, but the problem is in GenBank records. Years and authors appear

python sequencing

updated 3.2 years ago • Alice

search. In particular, I would like you to explain me how did you organize your search in Pubmed et similia, as I failed to find something by my self

algorithm literature transcription binding

updated 12.8 years ago • Anima Mundi

A knowledge-based approach for interpreting genome-wide expression profiles" by Subramaniana et al. Here, it says ranking genes based on the expression difference, but I found in the Fig.1A that there are multiple attributes

gene enrichment

updated 6.6 years ago • jin.k.koo

showed that more than two replicates did not significantly improve site discovery (Rozowsky et al. 2009) Paper Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/ But do we really need more than two biological

ChIP ChIP-Seq RNA-Seq

updated 7.3 years ago • sakibthegreat

The idea is to see if combined value of 5 miRNAs can differentiate Groups A and B ? Zeng X, et al. (2012) Circulating miR-17, miR-20a, miR-29c, and miR-223 combined as non-invasive biomarkers in nasopharyngeal carcinoma

edgeR mirna DE molecular signature

updated 6.6 years ago • Björn

Biology and Respiratory Clinical Discovery (*PDF or graduate student led papers)** 1. *Wang Z et al. 2016. Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations. European Respiratory Journal...47:1082-92. 2. *Saha S et al. 2016. Human microbial metabolites as a source of new drugs. Drug Discovery Today. 21: 692-698. 3. Brown JR et al. 2013 Translating...the human micro…

microbiome postdoc

updated 21 months ago • Ashutosh Pandey

include: - Super-enhancers delineate disease-associated regulatory nodes in T cells. Vahedi G, et al. Nature. 2015 Apr 23;520(7548):558-62. doi: 10.1038/nature14154. Epub 2015 Feb 16. - STATs shape the active enhancer landscape...of T cell populations. Vahedi G, et al. Cell. 2012 Nov 21;151(5):981-93. doi: 10.1016/j.cell.2012.09.044. A qualified candidate will be a strongly motivated individu…

Epigenetics

updated 2.4 years ago • vahedilab.jobs

2 y = y[isexpr,keep.lib.sizes=FALSE] y <- calcNormFactors(y) y <- estimateDisp(y) et <- exactTest(y) summary(decideTests(et)) exactTest result: 1+2 Down 31 NotSig 12512 Up 42 design: > design group1 group2 1 1 0

R RNA-Seq edgeR

updated 4.3 years ago • thancy

y) > design <- model.matrix(~group) > y <- estimateDisp(y,design) > et <- exactTest(y) > topTags(et) logFC logCPM PValue FDR hsa-mir-3613 0.9061035 8.5155819 0.001912410 1 hsa-mir-6825 2.3963572

RNA-Seq edgeR FDR

updated 5.7 years ago • silas008

population genetics statistics gene by gene, such as Ka, Ks, the ratio of Ka and Ks, Pi, Fst, Theta et al. So i am troubled that how to deal with the heterozygous SNP and missing data? 1.For each gene or SNP loci, should i calculate...the character (such as pi, theta, Fst et al.) for each pairwise in sub-population and then get the average of this gene or SNP loci? I think so, but i am not sure.…

SNP rna-seq

updated 8.8 years ago • robertorun

genome (version 38, EnsEMBL 90 transcript annotations) using the STAR read aligner (2.5.3a)(Dobin et al., 2013)** Is there any EnsEMBL 90 transcriptome based annotation file? Can someone help me to understand this

GTF cgat RNA-Seq

updated 5 months ago • PK

distance matrices for 25-SNP sliding windows across the genome. This is shown in figure 1D in Chan et al 2012. http://linkinghub.elsevier.com/retrieve/pii/S0960982212002680 My questions are: - Can this be minimized to a simpler

SNP sliding-window

updated 2.4 years ago • serpalma.v

can upload the figure. I have read documentation of tool as well as original refereed paper of Diaz et al 2012. Could any member point me to a source where it is mentioned what these x and Y axis matrices are plotted or generated

Figure ChIP-Seq quality

updated 2.4 years ago • rob.costa1234

Hi, I am new to Music when find significant mutated genes in my data. There three test to calculate significant p value of gene, and I am confused which test should be chosen or all three test should be considered together? Another question: The q value threshold is limited at 0.01 as paper (Kandoth, Cyriac, et al. "Mutational landscape and significance across 12 major cancer types." *Nature* 5…

SMG Music cancer-genome

updated 3.1 years ago • wangjiaqian

ordering, the exons were complete and used the usual splice donor and acceptor sites." (Jeck et al. 2014). My question is: why do we need an extra tool for the circRNA identification like find_circ? Why can't normal alignment

sequencing rna-seq RNA-seq circRNA circular RNA

updated 3.2 years ago • gudetama2001

were obtained from alignment to full-length HOR sequences that were previously described (Hayden et al. 2013). But I can't find it in [referenced][2] article as well. [1]: http://genome.cshlp.org/content/24/4/697.full [2]: http://mcb.asm.org

hor alpha-satellite fasta

updated 7.8 years ago • bbb

Dear All I am a user of clinvar database. (ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20181028.vcf.gz) which downloaded from ftp site, while I noted that these variations with high review status level can be searched in clinvar website with have high review status level. Some examples were listed as follows: 37861, 229653, et al. So, my question is which source can be used in my r…

Clinvar

updated 6.1 years ago • cginsea

group) > design <- model.matrix(~group) > y <- estimateDisp(y,design) > et <- exactTest(y) Thank very much for any help

RNA-Seq

updated 4.3 years ago • silas008

to find out the GO categories that rank on the very top (say, top 10), or as in the paper of Young et. al. 2010 in Genome Biology, can use GOseq to identify the top-ranked categories. My question is what are the criteria for ranking

gene statistics

updated 13.7 years ago • alittleboy

Does anyone have experience running the ddRAD pipeline of Peterson et al? I'm running on a MiSeq run of data and the amount of disk space it seems to require is huge. I modified one of the files so that

updated 12.0 years ago • DG

genomic coordinates. Basically, I want to generate something like this Figure 1A from Sankararaman et al. (2014) (http://www.nature.com/nature/journal/v507/n7492/fig_tab/nature12961_F1.html) except the Y-axis would be frequency

SNP allele

updated 8.4 years ago • devenvyas

analysis of GxE interaction across 5 cohorts. I'm going to use a joint meta-analysis of Mannig et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312394/) I know that the method needs SNP beta and SNP×E beta and covariance

SNP interaction

updated 4.6 years ago • Apprentice

Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq (Xiaoping Su et al, 2013 )", they counted expression level from viral transcript. But, in VirusSeq package that they used, they didn't used expression

virus rna-seq

updated 6.3 years ago • oghzzang

and genome data analysis skills are desirable. Some of our sample publications: - S. Li et al., Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation, Genome...Biology, 2019 - D. Huang et al., Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression, Genome Research

deep-learning genomics

updated 19 months ago • Sanjar

ChIP-Seq data of the 27 TFs from modencode][1]. However, the version is WS190. This paper (Cheng, C., et al. (2011). "Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data...has analyzed this data. And the data has not been updated for years. EDGEdb (Barrasa, M. I., et al. (2007). "EDGEdb: a transcription factor-DNA interaction database for th…

ChIP-Seq database c.elegans TFBS

updated 2.4 years ago • pengchy

Hi everyone, Has anyone successfully calculated delta K using the methods in Evanno et al using fastSTRUCTURE output, as opposed to STRUCTURE output, and if so, what did you use as the equivalent of the required...in the output? A little more detail: I'm trying to calculate delta K as outlined in Evanno et al (https://www.ncbi.nlm.nih.gov/pubmed/15969739). This requires taking the posterior p…

fastSTRUCTURE STRUCTURE deltaK

updated 6.1 years ago • Stephanie

exemplify what I'm after, I would like to be able to construct schemes like Figure 1 in Swiech et. al., Role of mTOR in physiology and pathology of the nervous system, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

visualization pathway

updated 12.0 years ago • Fredrik

and aberrant signalling properties associated with human diseases (see e.g. Trulsson F et al., 2022 Nat Comm; Barrio-Hernandez I et al., 2020 Genome Research; Akimov V et al., 2018 Nat Struct Mol Biol). **Qualifications/requirements

cell ubiquitylation proteomics signalling phosphorylation

updated 19 months ago • info

enter image description here*][1] This project is based on the results reported in Bradford et al., 2016, "Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumors and stromal...its outside microenvironment, is a challenging problem. The experimental study performed by Bradford et al. provided the data which allowed an essential step forward in this dir…

transcriptome pdx R ChIP-Seq

updated 20 months ago • Pine Biotech

stability. Recent exemplary project include comparison of transcriptome and proteome data (Dejung et al., PLOS Pathog 2016), large-scale temporal proteome data (Casas-Vila et al., Genome Res 2017) and integration of RNA-seq, ChIP-seq...and quantitative proteomics (Jahn et al., EMBO Rep 2017). **Job description** - Analysis of RNA-seq and ChIP-seq experiments using own and in-house provided pip…

R RNA-Seq ChIP-Seq

updated 20 months ago • f.butter

conducted by Dr Goel that exemplify the efforts of the lab can be found in the publications: Watt AC et al 2021 Nature Cancer, Goel et al 2017 Nature and Goel et al 2016 Cancer Cell. Importantly, Dr Goel has recently been awarded

ChIP-seq RNA-seq ATAC-seq

updated 23 months ago • ahnje770

variants to either the light or heavy strands of mitochondria, such as this excellent example by Ju et al. 2014: https://elifesciences.org/articles/02935#info In this and other instances, the authors filter out variants that...it and will post in response if I figure it out on my own. For reference, the methods of the Ju et al. paper are here: > We extracted mtDNA reads using Samtools (L…

variant calling mitochondria

updated 4.0 years ago • caearthworms

Hello all, I am processing the original ATAC-seq dataset from Buenrostro et al. 2013. After removing the adapters with cutadapt, where I set a minimum fragment size of 20, and mapping, I filter all the...Hello all, I am processing the original ATAC-seq dataset from Buenrostro et al. 2013. After removing the adapters with cutadapt, where I set a minimum fragment size of 20, and mapping, I filter…

ATAC-seq

updated 2.1 years ago • gen23crassus

Hi all, I'm reading this paper: Srinivasan et. al., (2020). Alzheimer's Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation. Cell reports, 31

pvalue

updated 2.1 years ago • TingAn

graphical representations used for experimental design, as seen in this [lecture][2]. [Kendziorski et al. PNAS 2005][3] is cited. If anyone knows (the course textbook used or similar), please let me know. Thankyou [1]: https://www.biostat.jhsph.edu

microarray

updated 2.0 years ago • atomic.supernatant

gt;Protein A HELIX 2 LPQIYQSGVVVLVITVLSSMGI >Protein B HELIX 1 LTYVAAVAVGMLGASYAAV ``` ... et cetera I have managed a workaround already that greps out non structural parts, but this is slow, somewhat rigid and labour

sequence protein uniprot

updated 2.9 years ago • Good Gravy

Has anybody used the [DNaseI footprint data from ENCODE][1]? In the corresponding article, [Neph et al., 2012][2] map the footprints to transcription factors by scanning the DNA sequences with motifs from TRANSFAC and JASPAR

Footprint genomics ENCODE TF dnase

updated 3.2 years ago • enricoferrero

about the sequencing and get for exemple : > Submitter,Date,Assembly method, Genome coverage et Sequencing technology. Acc_nb Sp_name Submitter Date Assembly_method Genome_coverage Sequencing_technology GCA_001442555.1

ncbi Assembly efetch

updated 4.8 years ago • Chvatil

I already used the correlated zygosity statistics for single genomes that was developped by [Lynch et al. 2014][1] and for which the software [mlRho][2] exists. However, I was wondering if there is any solution to calculate more conventional

linkage disequilibrium LD PLINK VCFtools

updated 5.1 years ago • KL_STKLBK

bcv <- 0.2 counts <- data y <- DGEList (counts=counts, group=1:2) et <- exactTest(y, dispersion=bcv^2) If I can adjust upon code to achieve my goal

edgeR no-replicated multiple sample RNA-Seq

updated 4.1 years ago • jimmy0958073736

Dear Colleague, I am processing the VCF files from thousands of samples from exome-sequencing. I would like to take the three steps as follows: 1. Identify the homozygous SNPs. 2. Identify the minor allele SNPs. 3. identify the SNP/InDel that have deleterious effects on protein function such as nonsynonymous mutations, frameshift, indels et. al. Ideally to find out all the SNPs and InDels that…

VCF SNP InDel Exome-Seq

updated 6.9 years ago • wangdp123

as described in An atlas of active enhancers across human cell types and tissues (Andersson et al, 2014). The file is composed by: - the genomic coordinates of the enhancer - the associated promoter (gene) - the distance between

enhacer promoters correlation CAGE

updated 6.0 years ago • daniele.avancini

how to annotate the probe, don't worry ! I know there's a CRLMM genotyping algorithm (Carvalho et al., 2007; Lin et al., 2008) , but it's too complex, I just want to know how to do it firstly. you can just recommend a package for me ,and

idat intensity illumina microarray

updated 5.0 years ago • jmzeng1314

download the ENCODE DNase I footprint data for the 41 human cell and tissue types described by Neph et al. (2012) Nature, 489:83-90. Here is an example to illustrate my question. Consider only a single human cell type, K562. The following...this number matches up exactly with the number of "Hotspot Regions" reported in Table S1 of the Neph et al. (2012) paper. What I am looking for, however, is…

encode

updated 10.9 years ago • joshualevipayne

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