Pinboard (arthegall)
https://pinboard.in/u:arthegall/public/
recent bookmarks from arthegallHome - Inflection Medicine2026-02-23T12:45:17+00:00
https://inflectionmedicine.com/
arthegalljob genomics sequencing saving-babies inflmhttps://pinboard.in/https://pinboard.in/u:arthegall/b:1d0b45d49438/Identity inference of genomic data using long-range familial searches | Science2020-02-28T17:20:50+00:00
https://science.sciencemag.org/content/362/6415/690
arthegallyaniv-erlich genomics privacy research-article familial-searcheshttps://pinboard.in/https://pinboard.in/u:arthegall/b:5f802aad8c50/Bray, Pimentel, Melsted, Pachter, "Near-optimal probabilistic RNA-seq quantification"2020-02-20T09:54:51+00:00
http://diytranscriptomics.com/Reading/files/Kallisto.pdf
arthegallgenomics probabilistic-genomics research-article lior-pachterhttps://pinboard.in/https://pinboard.in/u:arthegall/b:b38555c681d9/A Flow Procedure for the Linearization of Genome Sequence Graphs. | bioRxiv2019-02-14T09:53:46+00:00
https://www.biorxiv.org/content/10.1101/101501v1
arthegalllinearization graph-genomes bioinformatics preprint research-article david-haussler benedict-paten genomics sequence-analysishttps://pinboard.in/https://pinboard.in/u:arthegall/b:250d2f92aeda/Fast and accurate genomic analyses using genome graphs | Nature Genetics2019-02-04T12:45:29+00:00
https://www.nature.com/articles/s41588-018-0316-4#code-availability
arthegallgenomics licensing seven-bridges graph-genomes softwarehttps://pinboard.in/https://pinboard.in/u:arthegall/b:e3c8a69babd3/hammerlab/pileup.js: Interactive in-browser track viewer2016-11-30T18:48:05+00:00
https://github.com/hammerlab/pileup.js
arthegallhammerlab bioinformatics genomics visualization software opensource githubhttps://pinboard.in/https://pinboard.in/u:arthegall/b:e220abd80e71/Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms | bioRxiv2016-11-30T18:41:25+00:00
http://biorxiv.org/content/early/2016/10/17/081596
arthegallbioinformatics sequence-analysis genomics research-article bioarxiv preprinthttps://pinboard.in/https://pinboard.in/u:arthegall/b:8fbd959b7121/genome-source.cse.ucsc.edu Git - kent.git/blob - src/inc/bbiFile.h2016-09-26T14:40:36+00:00
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/inc/bbiFile.h
arthegallbigwig genomics file-format sequence-analysishttps://pinboard.in/https://pinboard.in/u:arthegall/b:8e5f2a0d29c1/Eugene Myers, "The fragment assembly string graph" Bioinformatics (2005)2016-09-26T14:36:44+00:00
http://bioinformatics.oxfordjournals.org/content/21/suppl_2/ii79.abstract
arthegallgenomics graphs research-article eugene-myershttps://pinboard.in/https://pinboard.in/u:arthegall/b:2c17b9b73985/Which Chip Seq Peak Callers Do You Use? (Biostars)2016-09-26T14:15:30+00:00
https://www.biostars.org/p/725/
arthegallchip-seq bioinformatics software list genomics sequence-analysis chromatinhttps://pinboard.in/https://pinboard.in/u:arthegall/b:eb9d91ba6e85/Chin, Hahn, Meyerson, "Making sense of cancer genomic data" (2013)2016-08-25T02:09:33+00:00
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059829/#!po=1.13636
arthegallreview-article cancer-genomics genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:f2bdc3fe07d9/A new algorithm for finding a visual center of a polygon | Mapbox2016-08-15T15:38:24+00:00
https://www.mapbox.com/blog/polygon-center/
arthegallgenomics maps mapbox algorithm labeling placement approximationhttps://pinboard.in/https://pinboard.in/u:arthegall/b:431e22eb3772/Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes | bioRxiv2016-06-28T04:08:22+00:00
http://biorxiv.org/content/early/2016/06/22/060186
arthegallreference-free genomics compression hashing bioinformatics bioarxiv research-articlehttps://pinboard.in/https://pinboard.in/u:arthegall/b:a80e1761cfbf/Comparison of somatic mutation calling methods in amplicon and whole exome sequence data | BMC Genomics | Full Text2016-05-24T11:21:01+00:00
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-244
arthegallgenomics somatic-variation cancer bioinformatics research-article concordancehttps://pinboard.in/https://pinboard.in/u:arthegall/b:9f99a83030a1/A Market Framework for Eliciting Private Data2016-05-06T04:34:05+00:00
https://papers.nips.cc/paper/5995-a-market-framework-for-eliciting-private-data
arthegallmarkets data genomics nips research-article machinelearninghttps://pinboard.in/https://pinboard.in/u:arthegall/b:12cebe976ecc/Unravelling the human genome-phenome relationship using phenome-wide association studies : Nature Reviews Genetics : Nature Publishing Group2016-04-27T03:40:20+00:00
http://www.nature.com/nrg/journal/v17/n3/full/nrg.2015.36.html
arthegallphenome genomics gwas genotyping bioinformatics research-articlehttps://pinboard.in/https://pinboard.in/u:arthegall/b:f5f7ef9ee9b4/Biofinysics: How does bowtie2 assign MAPQ scores?2016-04-27T03:37:49+00:00
http://biofinysics.blogspot.com/2014/05/how-does-bowtie2-assign-mapq-scores.html
arthegallbioinformatics genomics alignmenthttps://pinboard.in/https://pinboard.in/u:arthegall/b:6e652c3f8f5e/Improved genome inference in the MHC using a population reference graph : Nature Genetics : Nature Publishing Group2016-04-27T03:35:37+00:00
http://www.nature.com/ng/journal/v47/n6/abs/ng.3257.html
arthegallresearch-article reference-graphs genomics population-geneticshttps://pinboard.in/https://pinboard.in/u:arthegall/b:9309f389a567/Home · Steven-N-Hart/VariantDB_Challenge Wiki2016-04-12T05:24:43+00:00
https://github.com/Steven-N-Hart/VariantDB_Challenge/wiki#challenge-2-the-continuous-integration-problem
arthegallvariantdb sequence-analysis genomics bioinformatics future challenge work berkeleyhttps://pinboard.in/https://pinboard.in/u:arthegall/b:52a4f72305eb/The real cost of sequencing: scaling computation to keep pace with data generation | Genome Biology | Full Text2016-04-12T05:23:55+00:00
http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0917-0
arthegallsequencing costs genomics research-article mark-gersteinhttps://pinboard.in/https://pinboard.in/u:arthegall/b:e4baf3556cc0/Ester, Kriegel, Sander, Xu, "A Density-based Algorithm for Discovering Clusters in Large Spatial Databases with Noise" (1996)2016-03-30T20:53:43+00:00
https://www.aaai.org/Papers/KDD/1996/KDD96-037.pdf
arthegallgenomics databases research-article clustering dbscanhttps://pinboard.in/https://pinboard.in/u:arthegall/b:3a8599d610d6/Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory : Genetics in Medicine : Nature Publishing Group2016-03-30T15:16:06+00:00
http://www.nature.com/gim/journal/v16/n7/full/gim2013183a.html
arthegallsequencing genomics research-article sanger-sequencinghttps://pinboard.in/https://pinboard.in/u:arthegall/b:8271e3b3a94d/Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants2016-03-30T15:15:50+00:00
http://www.clinchem.org/content/62/4/647.abstract
arthegallsequencing validation genomics bioinformatics sanger-sequencinghttps://pinboard.in/https://pinboard.in/u:arthegall/b:69ef35ac0fe4/Pathway and Network Analysis of Cancer Genomes2016-03-27T11:16:51+00:00
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717906/
arthegallbioinformatics software via:ryan-williams genomics cancerhttps://pinboard.in/https://pinboard.in/u:arthegall/b:21fd8390ae21/GenAp: a distributed SQL interface for genomic data2016-03-24T09:54:48+00:00
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741060/
arthegallregion-join adam spark sql research-article genomics bioinformaticshttps://pinboard.in/https://pinboard.in/u:arthegall/b:23d29189f561/BMC Medical Informatics and Decision Making | Full text | FORESEE: Fully Outsourced secuRe gEnome Study basEd on homomorphic Encryption2016-02-11T11:26:52+00:00
http://www.biomedcentral.com/1472-6947/15/S5/S5
arthegallprivacy workshop-proceedings genomics bioinformatics via:hannu homomorphic-encryptionhttps://pinboard.in/https://pinboard.in/u:arthegall/b:ef4715f9af6f/BMC Medical Informatics and Decision Making | Full text | Secure Distributed Genome Analysis for GWAS and Sequence Comparison Computation2016-02-11T11:25:24+00:00
http://www.biomedcentral.com/1472-6947/15/S5/S4
arthegallprivacy workshop-proceedings genomics bioinformatics via:hannu distributed-computing gwashttps://pinboard.in/https://pinboard.in/u:arthegall/b:86d3220fc8a9/BMC Medical Informatics and Decision Making | Full text | Private Genome Analysis through Homomorphic Encryption2016-02-11T11:25:11+00:00
http://www.biomedcentral.com/1472-6947/15/S5/S3
arthegallprivacy workshop-proceedings genomics bioinformatics via:hannu homomorphic-encryptionhttps://pinboard.in/https://pinboard.in/u:arthegall/b:26c30b95ffd3/BMC Medical Informatics and Decision Making | Full text | Privacy-Preserving GWAS Analysis on Federated Genomic Datasets2016-02-11T11:24:49+00:00
http://www.biomedcentral.com/1472-6947/15/S5/S2
arthegallprivacy workshop-proceedings genomics bioinformatics via:hannu distributed-computing federated-analysishttps://pinboard.in/https://pinboard.in/u:arthegall/b:453af82605aa/BMC Medical Informatics and Decision Making | Full text | Privacy-preserving Genome-wide Association Studies on Cloud Environment using Fully Homomorphic Encryption2016-02-11T11:24:37+00:00
http://www.biomedcentral.com/1472-6947/15/S5/S1
arthegallprivacy workshop-proceedings genomics bioinformatics via:hannu homomorphic-encryptionhttps://pinboard.in/https://pinboard.in/u:arthegall/b:bd43e72b4c18/The Zones Algorithm for Finding Points-Near-a-Point or Cross-Matching Spatial Datasets - Microsoft Research2016-01-07T19:12:26+00:00
http://research.microsoft.com/apps/pubs/default.aspx?id=64524
arthegalljim-gray databases relational-data bioinformatics genomics research-articlehttps://pinboard.in/https://pinboard.in/u:arthegall/b:9a66575f54c3/Preprint — mash 1.0 documentation2016-01-05T04:57:45+00:00
http://mash.readthedocs.org/en/latest/
arthegallminhash genomics tool software documentation metagenomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:1d5addccddcd/PCR duplicate models2015-10-16T04:01:45+00:00
http://lh3lh3.users.sourceforge.net/download/PCR-dup.pdf
arthegallpcr genomics sequencing heng-lihttps://pinboard.in/https://pinboard.in/u:arthegall/b:ef5d6f71004b/[1407.2812] Rate-Optimal Detection of Very Short Signal Segments2015-10-16T04:01:06+00:00
http://arxiv.org/abs/1407.2812
arthegallgenomics segmentation bioinformatics arxiv research-articlehttps://pinboard.in/https://pinboard.in/u:arthegall/b:76f91a4afef8/Genome Biology | Full text | The case for cloud computing in genome informatics2015-10-15T19:39:44+00:00
http://www.genomebiology.com/content/11/5/207
arthegallcloud-computing lincoln-stein bioinformatics genomics reviewhttps://pinboard.in/https://pinboard.in/u:arthegall/b:aa707b5d89a5/Poster about the Velvet Assembler2015-10-15T19:38:38+00:00
http://www.ebi.ac.uk/~zerbino/velvet/velvet_poster.pdf
arthegallgenomics assembly poster presentationhttps://pinboard.in/https://pinboard.in/u:arthegall/b:9073c1f0b1b0/Homer Software and Data Download2015-10-15T19:34:52+00:00
http://homer.salk.edu/homer/ngs/groseq/groseq.html
arthegallgro-seq data genomics via:robinhttps://pinboard.in/https://pinboard.in/u:arthegall/b:8025b57e31e1/Adam Roberts, "Imputation 1"2015-10-15T18:41:24+00:00
http://www.eecs.berkeley.edu/~yss/courses/fa12-cs294-81/slides/Imputation_1.pdf
arthegallimputation genomics gwas slideshttps://pinboard.in/https://pinboard.in/u:arthegall/b:350fbba60427/Yearly Demand for Whole Human Genome Sequencing – 400K New Genomes in 2015 ? | Genohub High Throughput Sequencing Blog2015-10-14T18:43:18+00:00
http://blog.genohub.com/yearly-demand-for-whole-human-genome-sequencing-400k-new-genomes-in-2015/
arthegallsequencing genomics industry predictionshttps://pinboard.in/https://pinboard.in/u:arthegall/b:e95c96bed690/Converting genetic variants to their minimal representation | MacArthur Lab2015-10-07T15:49:04+00:00
http://macarthurlab.org/2014/04/28/converting-genetic-variants-to-their-minimal-representation/
arthegallgenomics vcf representation data formattinghttps://pinboard.in/https://pinboard.in/u:arthegall/b:7a0076006eaf/atifrahman/AVIARY2015-10-01T13:29:48+00:00
https://github.com/atifrahman/AVIARY
arthegallvia:twitter data sequencing bioinformatics genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:8b71f7972d8b/Genome Biology | Full text | <it>quantro</it>: a data-driven approach to guide the choice of an appropriate normalization method2015-08-04T17:03:23+00:00
http://www.genomebiology.com/2015/16/1/117
arthegallmicroarrays bioinformatics normalization statistics rafael-irizarry research-article genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:8c5a6de1b556/lh3/fermikit2015-08-04T15:14:39+00:00
https://github.com/lh3/fermikit
arthegallheng-li assembly genomics illumina bioinformaticshttps://pinboard.in/https://pinboard.in/u:arthegall/b:a70cdc85e1e4/Bauckhage, Kersting, and Hadiji, "Parameterizing the Distance Distribution of Undirected Networks"2015-07-15T16:57:24+00:00
http://auai.org/uai2015/proceedings/papers/62.pdf
arthegallprivacy genomics networks statistics via:cshalizi research-article uai distances graphs pathshttps://pinboard.in/https://pinboard.in/u:arthegall/b:ba16e2742414/Access : Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources : Nature Protocols2015-07-14T03:26:11+00:00
http://www.nature.com/nprot/journal/v4/n1/pdf/nprot.2008.211.pdf
arthegallgenomics proteomics research-article david listshttps://pinboard.in/https://pinboard.in/u:arthegall/b:fa2b2fc53190/Merging Structural Variant Calls from Different Callers · Simpson Lab Blog2015-07-14T03:23:38+00:00
http://simpsonlab.github.io/2015/06/15/merging-sv-calls/
arthegallgenomics variants variant-calling indels researchhttps://pinboard.in/https://pinboard.in/u:arthegall/b:2da59afc9701/Managing incidental findings and research results in genomic research involving biobanks and archived data sets : Genetics in Medicine : Nature Publishing Group2015-07-14T02:47:17+00:00
http://www.nature.com/gim/journal/v14/n4/abs/gim201223a.html
arthegallbiobanks incidental-findings genomics genetic-testinghttps://pinboard.in/https://pinboard.in/u:arthegall/b:0114b1bebe04/BamStats04 · lindenb/jvarkit Wiki2015-07-06T11:26:49+00:00
https://github.com/lindenb/jvarkit/wiki/BamStats04
arthegallcoverage work bioinformatics genomics roll-your-ownhttps://pinboard.in/https://pinboard.in/u:arthegall/b:1d1e70d76b07/DISSECT: A new tool for analyzing extremely large genomic datasets | bioRxiv2015-06-08T10:10:56+00:00
http://biorxiv.org/content/early/2015/06/05/020453
arthegallphenotypes mixed-linear-models genomics big-data bioarxiv preprint research-articlehttps://pinboard.in/https://pinboard.in/u:arthegall/b:8b941a13dcbf/BamHash and some insights from information theory | Bits of Bioinformatics2015-06-04T10:54:48+00:00
https://pmelsted.wordpress.com/2015/03/03/bamhash-and-some-insights-from-information-theory/
arthegallhashing genomics bamhash testinghttps://pinboard.in/https://pinboard.in/u:arthegall/b:0c569c0f43a8/Bandage by rrwick2015-05-28T14:22:50+00:00
http://rrwick.github.io/Bandage/
arthegallassembly genomics bioinformatics visualization graphshttps://pinboard.in/https://pinboard.in/u:arthegall/b:0850727a864e/Measuring the Contribution of Genomic Predictors to Improving Estimator Precision in Randomized trials | bioRxiv2015-05-25T19:28:56+00:00
http://biorxiv.org/content/early/2015/04/16/018168
arthegalljeff-leek genomics clinical-trials bioarxiv research-articlehttps://pinboard.in/https://pinboard.in/u:arthegall/b:d0cd7dad81b8/Lohse et al. "Strategies for calculating blockwise likelihoods under the coalescent" bioRxiv2015-05-25T19:23:48+00:00
http://biorxiv.org/content/early/2015/03/13/016469
arthegallbioarxiv coalescent likelihoods calculation preprint genetics genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:6d0aa1c55edb/Vassy et al. "A One-Page Summary Report of Genome Sequencing for the Healthy Adult"2015-05-25T19:17:33+00:00
http://www.genomes2people.org/wp-content/uploads/2015/01/Vassy-Public-Health-Genomics-2015.pdf
arthegallreport mgh heidi-rehm genomics clinical-genomics public-healthhttps://pinboard.in/https://pinboard.in/u:arthegall/b:14947e06f01f/SnpSift2015-05-25T19:14:19+00:00
http://snpeff.sourceforge.net/SnpSift.html
arthegallvariant annotation genomics tool tutorial softwarehttps://pinboard.in/https://pinboard.in/u:arthegall/b:d4bf01566c53/Genome Biology | Full text | An integrated computational pipeline and database to support whole-genome sequence annotation2015-05-25T19:02:55+00:00
http://genomebiology.com/2002/3/12/research/0081
arthegallgenomics annotation pipeline research-article bioinformatics chris-mungallhttps://pinboard.in/https://pinboard.in/u:arthegall/b:29bc581bb386/BD2KGenomics/cgcloud2015-05-25T19:00:17+00:00
https://github.com/BD2KGenomics/cgcloud
arthegallwork genomics cgcloud bd2k ucschttps://pinboard.in/https://pinboard.in/u:arthegall/b:32db4ed38a32/ryanlayer/gqt2015-05-01T14:32:41+00:00
https://github.com/ryanlayer/gqt
arthegallgentoypes language query github opensource aaron-quinlan genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:24975fefc283/Homer Software and Data Download2015-04-20T13:43:15+00:00
http://homer.salk.edu/homer/
arthegallmotif-discovery software bioinformatics genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:2aadfb07e9e2/[1405.2350] Hypothesis testing at the extremes: fast and robust association for high-throughput data2015-03-16T15:12:16+00:00
http://arxiv.org/abs/1405.2350
arthegallvia:vaguery arxiv genomics hypothesis-testing research-article statistics generalized-linear-modelshttps://pinboard.in/https://pinboard.in/u:arthegall/b:44d507d2795d/Language Log » Reliability2015-03-15T18:51:29+00:00
http://languagelog.ldc.upenn.edu/nll/?p=17916
arthegallga4gh genetics mark-liberman nikete reproducibility genomics hard-to-taghttps://pinboard.in/https://pinboard.in/u:arthegall/b:5c9a9d1e0c5d/In RNA-Seq, 2 != 2: Between-sample normalization | The farrago2015-02-19T01:26:09+00:00
https://haroldpimentel.wordpress.com/2014/12/08/in-rna-seq-2-2-between-sample-normalization/
arthegallharold-pimentel rna-seq normalization genomics bioinformaticshttps://pinboard.in/https://pinboard.in/u:arthegall/b:9172fa4e2936/[1411.2664] Preserving Statistical Validity in Adaptive Data Analysis2015-01-29T13:58:56+00:00
http://arxiv.org/abs/1411.2664
arthegallarxiv cynthia-dwork statistics cross-validation genomics privacy differential-privacyhttps://pinboard.in/https://pinboard.in/u:arthegall/b:e55a48eb06f4/We can, and should, do clinical trials in rare diseases2015-01-21T15:10:47+00:00
http://www.cureffi.org/2014/11/24/we-can-and-should-do-clinical-trials-in-rare-diseases/
arthegallclinical-trials rare-diseases genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:36e689a62a3f/Quantification of rare allelic variants from pooled genomic DNA2015-01-19T13:00:04+00:00
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776647/
arthegallcombinatorial-testing research-article variant-calling sequence-analysis genomics poolinghttps://pinboard.in/https://pinboard.in/u:arthegall/b:b9e8d08d312d/Atallah et al. "Private Combinatorial Group Testing"2015-01-15T02:57:17+00:00
http://www.cse.nd.edu/~mblanton/papers/asiaccs08a.pdf
arthegallprivacy group-testing combinatorics research-article pooling genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:7fe77de14c14/RNA-seqlopedia2015-01-09T07:10:43+00:00
http://rnaseq.uoregon.edu/
arthegallrna-seq genomics outlinehttps://pinboard.in/https://pinboard.in/u:arthegall/b:5a0e4c338b2d/Scaling probabilistic models of genetic variation to millions of humans | bioRxiv2015-01-07T15:58:38+00:00
http://biorxiv.org/content/early/2014/12/24/013227
arthegallgenomics research-article association-testhttps://pinboard.in/https://pinboard.in/u:arthegall/b:f6778dab8fe0/Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods2014-12-29T11:04:50+00:00
http://bioinformatics.oxfordjournals.org/content/early/2014/12/04/bioinformatics.btu745.full
arthegallmetagenomics research-article genomicshttps://pinboard.in/https://pinboard.in/u:arthegall/b:cd32c560e47a/A comprehensive transcriptional portrait of human cancer cell lines : Nature Biotechnology : Nature Publishing Group2014-12-18T11:52:42+00:00
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3080.html
arthegalladam work rna-seq research-article genomics cancerhttps://pinboard.in/https://pinboard.in/u:arthegall/b:30e63f67c95b/