Moderator: David Quigley

gravatar for David Quigley
David Quigley11k
Reputation:
10,840
Status:
Trusted
Location:
San Francisco
Website:
http://quigleylab.ucsf...
Last seen:
2 months, 3 weeks ago
Joined:
10 years, 3 months ago
Email:
d**************@gmail.com

David Quigley has been working in cancer genetics since 2006, with a particular focus on prostate cancer and DNA repair. Dr. Quigley has co-authored over 40 journal articles and has led studies published in Nature, Cell, and Cancer Discovery. Dr. Quigley received his undergraduate degree in Computer Science from Carleton College and worked as a software developer in industry for five years before complating a Masters degree in Biomedical Informatics at Columbia University, and a PhD at the University of Oslo.

Posts by David Quigley

<prev • 434 results • page 1 of 44 • next >
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Job: Postdoctoral scholar studying tumor genetics and epigenetics at UCSF
... **Postdoctoral positions for computational biologists are available in the [lab of David Quigley][1].** The Quigley laboratory is part of the Department of Urology at the University of California, San Francisco School of Medicine and the UCSF Helen Diller Family Comprehensive Cancer Center. We are a ...
next-gen epigenetics job rna-seq written 12 weeks ago by David Quigley11k
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Comment: C: spreadsheet tools alternative
... Renesh's comment is not correct. Try the following: Open a worksheet. Type "MAR7". You'll see "7-Mar" as Excel formats your text as a date. Now correct the formatting to "text" (Format|Cells). You will see "7-Mar" become a number. On my Macintosh it's 42801. There is no way to recover the original t ...
written 3.1 years ago by David Quigley11k
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... As of September 2017 the gem-mappability binary is missing from the GEM build. The note on the GEM wiki dated 2012 states "mappability tools are still in the process of being migrated to the new mapping engine. The mappability will come back online shortly." ([wiki for the GEM library][1]). There is ...
written 3.1 years ago by David Quigley11k
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Answer: A: BinGo customerized work flow
... The ontology file describes the structure of the ontology tree. It has three root nodes (Biological Process, Molecular Function, Cellular Compartment) and gets more specific from there, e.g. "M phase mitosis". It does not link any particular gene to an ontology entry. The Annotation file indicates w ...
written 4.7 years ago by David Quigley11k • updated 2.1 years ago by RamRS30k
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Job: UCSF Bioinformatics Junior Specialist, Helen Diller Cancer Center
... University of California, San Francisco Department of Obstetrics, Gynecology, and Reproductive Sciences Division of Gynecologic Oncology Junior Specialist Search The UCSF Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Gynecologic Oncology, is recruiting for Non-Faculty ...
immunology next-gen job rna-seq written 4.8 years ago by David Quigley11k
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Comment: C: bioinformatics conference ranking
... [(days distant from winter solstice) x latitude x (distance in km from college roommate)] / [(registration cost) * (number of concurrent tracks)] ...
written 4.8 years ago by David Quigley11k
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Answer: A: EGFR and KRAS expression
... If you don't specifically need RNA-seq data, there's a very large amount of retrospective transcriptome data on GEO, e.g. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40967 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68468 http://www.ncbi.nlm.nih.gov/gds/?term=colon%20cancer You c ...
written 4.9 years ago by David Quigley11k
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Comment: C: Identify somatic mutations in cancer exome without a matched pair.
... Thanks for these notes, very helpful. ...
written 4.9 years ago by David Quigley11k
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Comment: C: Is the PAM50 subtype available for TCGA BRCA data?
... @kanwarjag: I assume your answer is meant as a comment to my answer above; if so, please leave it as a comment next time rather than posting an answer to the question. What I mean by "somewhat different results for edge case tumors" is that, in practice, when you use genefu to assign PAM50 classes, ...
written 4.9 years ago by David Quigley11k • updated 11 months ago by RamRS30k
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Answer: A: Get number of variations in a huge VCF using Tabix?
... Heng Li says no, and he should know: > Dear Heng, > We are wondering if there's a fast approach to use tabix or any other hack to get the total number of variants that a VCF has without actually reading the whole vcf file and counting the lines. I assume that the total number of rows is some ...
written 4.9 years ago by David Quigley11k • updated 11 months ago by RamRS30k

Latest awards to David Quigley

Epic Question 2.2 years ago, created a question with more than 10,000 views. For Bulk Download Of Ncbi Gene "Summary" Field
Great Question 2.2 years ago, created a question with more than 5,000 views. For How Many Reads In A Bam File Are Aligned To An Arbitrary Region
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Looking for gene expression data from cultured human cells treated with drugs
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Scholar 2.2 years ago, created an answer that has been accepted. For A: R library/package for pairwise differential expression for microarray data?
Great Question 2.2 years ago, created a question with more than 5,000 views. For Reproducible Research: A More General Sweave?
Pundit 2.2 years ago, created a comment with more than 10 votes. For C: What Are Phased And Unphased Genotypes?
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: When It'S A Sequence And When It'S Not?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Looking for gene expression data from cultured human cells treated with drugs
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For What are the output values for PICNIC when called from the binary build?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For What are the output values for PICNIC when called from the binary build?
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: When It'S A Sequence And When It'S Not?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Great Question 3.2 years ago, created a question with more than 5,000 views. For How Many Reads In A Bam File Are Aligned To An Arbitrary Region
Popular Question 3.3 years ago, created a question with more than 1,000 views. For What are the output values for PICNIC when called from the binary build?
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Gold Standard 3.3 years ago, created a post with more than 25 bookmarks. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Microarray Dataset Formats: What Should My Program Know How To Read?
Good Question 3.6 years ago, asked a question that was upvoted at least 5 times. For Alternatives To Caarray For Microarray Storage
Appreciated 3.6 years ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals

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