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#evolution#Genetics#genomics#PopulationHealth@mrcfnd#Wolfpack@CABNR#Bioinformatics#biologistpic.twitter.com/jaq3C4R3GR
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RT mike_schatz "jltsiren cHHillee JeffDean melanie_kirsche Cool! Hadn’t seen that one. Sapling is more specialized but I would put it into the same (extended) family of ideas"
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RT mike_schatz "RT DCGenomics: This may be my last tweet for a while about NCBI resources, but an important one for
#virologist colleagues. Please R/T! Here are the CoV sequences from Wuhan and US isolates: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Wuhan%20seafood%20market%20pneumonia%20virus,%20taxid:2697049&SeqType_s=Nucleotide … linsalrob JasonWilliamsNY jxtx nomad421 DoctorR…Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
RT mike_schatz "cHHillee JeffDean melanie_kirsche One major difference is showing a simple piecewise linear model is extremely effective (more effective?) but impossible to do a head to head comparison since they didn’t release anything"
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RT mike_schatz "cHHillee JeffDean melanie_kirsche Similar conceptual framework. If you check our github repo you will see we have been working on this >1 year before that was posted"
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RT mike_schatz "RT segal_eran: New perspective I wrote for nature where I argue that cohorts with rich molecular and physiological data may allow to prioritize human-relevant targets for drug development In some cases may allow to skip animal testing… pic.twitter.com/qARQ5l7OMa"
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RT mike_schatz "dreycey You are too kind"
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RT mike_schatz "acarroll_ATG Oh yes, this is just the first of many potential applications. The performance improvement grows with the size of the data, so are keen to apply to metagenomics and pangenomics"
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RT mike_schatz "melanie_kirsche tim_kraska JeffDean It is a classic CS space-time tradeoff, and with a tiny amount of space overhead (0.1%) we can double the performance over TheGeneMyers' optimal suffix array search algorithm. If we allow for more s… pic.twitter.com/qqUFgHBpdq"
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RT mike_schatz "BioMickWatson melanie_kirsche This was with 21-mers but is robust except if you use very short kmers. The function also becomes more complicated if you really skew the GC content but you have to go beyond anything that exists in nature pic.twitter.com/M5VGhIHVkA"
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RT mike_schatz "melanie_kirsche We were deeply inspired by The Case for Learned Index Structures by tim_kraska et al (plus conversations with JeffDean last year): https://arxiv.org/abs/1712.01208 . I see huge potential for these ideas in the future"
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RT mike_schatz "melanie_kirsche Real genomes are shockingly predictable with respect to the ordering of k-mers/suffixes pic.twitter.com/vc7zsDwXRy"
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RT mike_schatz "melanie_kirsche CS101 teaches us binary search is the best way to search through large datasets, but with a bit of data modeling we can substantially improve performance"
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RT mike_schatz "Introducing Sapling: Accelerating Suffix Array Queries with Learned Data Models with melanie_kirsche and http://arundas.org . https://www.biorxiv.org/content/10.1101/2020.01.29.925768v1 … pic.twitter.com/FmK8oOBHEg"
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RT mike_schatz "RobAboukhalil BenLangmead cc: BenLangmead"
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RT mike_schatz "RT aphillippy: HG002 data release from HumanPangenome. PacBio HiFi, CLR, nanopore PromethION, GridION, illumina Hi-C, Strand-seq, bionanogenomics opmaps... CC0-licensed. Benchmarking to inform production sequencing recipe https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0 …"
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RT mike_schatz "infoecho Very nice!"
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RT mike_schatz "dombraccia This is a old paper/method but would extend to more divergent samples. But IMHO building the graph is the easier step, need to use it to find interesting patterns that cannot otherwise be seen"
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RT mike_schatz "RT theNASciences: Congratulations Zachary B. Lippman of CSHLCareers HHMINEWS, recipient of the NAS Prize in Food and Agriculture Sciences! His work, which aims to improve crop production, helps to address the challenges of population … pic.twitter.com/1oNQauUyqy"
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RT mike_schatz "RobAboukhalil marianattestad anderspitman The wasm code is blazing fast!"
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RT mike_schatz "RT Magdoll: My Medium interview w sedlazeck MedhatHelmy7 is out! We cover SV calling w long reads, the life cycle of
#Bioinformatics tools, why it never hurts to ask for a postdoc you feel unqualified for, and the future for populatio… https://medium.com/@Magdoll/hidden-in-plain-sight-a-bioinformatics-journey-into-structural-variation-calling-in-the-long-da7183007764 …"Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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