Medvedev Group News
@MedvedevGroupAccount for news from the research group of Paul Medvedev
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I've created a separate profile @MedvedevGroup which will contain big news from my research group, like threads about publications. If you want to follow my research but want only big updates and not "thoughts of the week", follow @MedvedevGroup instead of @pashadag
Penn State Libraries has a nice tradition that promoted faculty get to select a book that has shaped them as a faculty. I've selected "The Science of Computing: Shaping a Discipline" by Matti Tedre and here's what I wrote to explain my selection: @psulibs @PennStateEECS 1/2
I wrote a new blog post about managing the research process when juggling many projects and other commitments. From idea to paper: discretizing and optimizing the initial stages of the process. Feedback is appreciated. medvedevgroup.com/2022/08/17/fro…
A new paper and video: "Markov chains improve the significance computation of overlapping genome annotations." Askar Gafurof will present in person today at 4pm in #ISMB2022 @HiTSeq (Madison B). A 🧵 Paper: doi.org/10.1093/bioinf…. Video: youtube.com/watch?v=ra5RCN…. 1/5
I've posted a new preprint (arxiv.org/abs/2205.01785) on the limitations of the theoretical analysis of applied algorithms, focusing on examples from sequencing bioinformatics such as genome assembly, structural variation, and k-mer data structures. 1/6
I have a new preprint posted, "Theoretical analysis of edit distance algorithms: an applied perspective", arxiv.org/abs/2204.09535. 1/7
In a new paper with @amatur_r, we investigated how de Bruijn graph-based assemblers exhibit systematic mis- and under-assemblies that is inherent to unitigs. twitter.com/biorxiv_bioinf… 1/6
Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful biorxiv.org/cgi/content/sh… #biorxiv_bioinfo
In our new paper, we show that using a minimizer sketch to estimate the k-mer Jaccard similarity between two sequences is potentially problematic. This is joint work with Antonio Blanca, @RSHarrisPSU @DavidKoslicki, and Mahdi Belbasi. biorxiv.org/content/10.110… 1/5
I have been teaching a course on writing in computer science. Here's one lecture that I recorded about how to write a good introduction: Video: [bit.ly/3G3X6mt] Slides: [bit.ly/3o4mjXJ] @PennStateEECS @PSUEngineering #writingcommunity 1/3
This sheds light on terminology around dBGs. A dBG can be 𝑛𝑜𝑑𝑒-𝑐𝑒𝑛𝑡𝑟𝑖𝑐 or 𝑒𝑑𝑔𝑒-𝑐𝑒𝑛𝑡𝑟𝑖𝑐. A dBG can use 𝑘 to define the length of the nodes or the length of the edges. These two are unrelated properties and shouldn't be conflated. twitter.com/jnalanko/statu… 1/4
People who work on de Bruijn graphs: Could we all use the terms "nodemer" or "edgemer" instead of the generic "k-mer". This could prevent many bugs caused by confusion about whether the order k refers to node length or edge length. #Bioinformatics
I wrote a short blog post about one of the challenges of writing a logical argument in the introduction of a paper: medvedevgroup.com/2021/11/10/the…
It started as a blog post and is now published in @PLOSCompBiol What do Eulerian and Hamiltonian cycles have to do with genome assembly? medvedevgroup.com/2020/08/21/wha… journals.plos.org/ploscompbiol/a…
Our survey on k-mer data structures is now out in ACM Computing Surveys. Paper: dl.acm.org/doi/10.1145/34… Previous thread: twitter.com/pashadag/statu…
Together with Jan Holub and Rayan Chikhi, we've posted on arXiv our survey article on data structures to represent sets of k-mers. arxiv.org/abs/1903.12312
At the end of the day, we derived CIs and hypothesis tests from/for Nmut, n. islands, n. oceans, Jaccard, minhash Jaccard, and the CBER score from Jabba. The paper contains extensive validations and practical applications. Software available as well: bit.ly/3pL9Q9e 8/8
A highlight reel of our upcoming #recomb2021 paper (doi.org/fq3g) with @DavidKoslicki, @RSHarrisPSU, and Antonio Blanca. The mash distance estimates the avrg nucl. identity b/w two sequences from only their minhash sketches. However, its only a point estimate. 1/8
We have with @nanopore Applications Team and @pashadag developed a computational method (isONcorrect) to correct @nanopore cDNA transcriptome reads without reference achieving a median accuracy of 98.9-99.6% for cDNA R9 PCS109 data. nature.com/articles/s4146…
Our work with @krsahlin and @nanopore and on error correcting ONT transcriptomic reads reference-free (isONcorrect) is finally published. nature.com/articles/s4146… @BMB_PSU @PennStateEECS @huckinstitutes @PSUresearch @PSUScience @BioinformPSU
We have with @nanopore Applications Team and @pashadag developed a computational method (isONcorrect) to correct @nanopore cDNA transcriptome reads without reference achieving a median accuracy of 98.9-99.6% for cDNA R9 PCS109 data. nature.com/articles/s4146…
Our paper on fast whole-genome aligner for closely-related genomes SibeliaZ is finally out in Nature Communications: nature.com/articles/s4146…! SibeliaZ can align multiple mammalian-sized genomes on a single server allowing to scale comparative genomics when resources are limited.
For those who missed my talk today at @PangaiaProject, I've posted my slides, together with a draft of the paper, in a dropbox folder: dropbox.com/sh/ldhm0zu8m5w… The talk is about the theoretical analysis of sequencing bioinformatic algorithms.
On Monday 10am EST, I'll be presenting my recent investigation into the theoretical analysis of sequencing bioinformatics algorithms @PangaiaProject seminar series and I hope you can make it (pangenome.eu/news-event-pan…). Here's what I'll discuss: (1/n)
On Monday 10am EST, I'll be presenting my recent investigation into the theoretical analysis of sequencing bioinformatics algorithms @PangaiaProject seminar series and I hope you can make it (pangenome.eu/news-event-pan…). Here's what I'll discuss: (1/n)
We are glad to announce the first ever meeting in PANGAIA seminar series. Paul Medvedev, Penn State University The theoretical analysis of sequencing bioinformatics algorithms November 16, 2020 – 16:00pm CET pangenome.eu/news-event-pan… @CORDIS_EU
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