Qiyun Zhu
@zhuqiyunAssistant Professor @ Arizona State University, studying microbiomes, evolution and bioinformatics
MMseqs2-GPU has been introduced, showing a 177x speed improvement. Also, a GPU back-end for FoldSeek is coming! 🔥 The future of bioinfo will be rewritten in CUDA. I'm really grateful for the work of amazing scientist like @milot_mirdita and the lab of @thesteinegger
Have you ever wondered how evolution looks at the finest scale? Check out our new preprint on genotype networks of viral quasispecies. Huge thanks to my mentors @brigan_raman, Susanna Manrubia and collaborator @EsterLzaro1!
New preprint out on genotype networks of viral quasispecies: "Hierarchical genotype networks and incipient ecological speciation in Qβ phage quasispecies" arxiv.org/abs/2411.07110
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introduce "Logan Search" which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics 🧵👇
Wanted to announce we are looking for two graduate students to fill fully funded PhD positions from a @NIH @NIDDKgov R01 grant on #microbiome bile acid metabolism. Please share with any students looking for PhD programs.
Please retweet: @ASU is hiring a Teaching Assistant Professor in Microbiology/Immunology. Application Deadline: 8/16/25 Link to apply: apply.interfolio.com/157981 More about @asuSOLS: sols.asu.edu
Job Alert: Teaching Assistant Professor - Computational Life Sciences, Arizona State University: apply.interfolio.com/157209. #hiring #ASU
Happy to announce that our (me and @YunWilliamYu) metagenome profiler sylph (github.com/bluenote-1577/…) is now published in @NatureBiotech! 1/5
Rapid species-level metagenome profiling and containment estimation with sylph go.nature.com/3BBVqDC
Published in 2009, bwa-aln is one of the oldest short-read aligners. It remains a popular choice for aligning ancient DNA reads. The following blog post explains the algorithmic reasons. lh3.github.io/2024/09/28/why…
I am very happy to report that the review @BanfieldJill and I wrote on Modern Microbiology just appeared in @CellPressNews: cell.com/cell/abstract/… Our celebration of microbiology also made it to the cover of this issue and we hope you will find yourself in it, too.
Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB arxiv.org/abs/2409.00613
The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks nature.com/articles/s4159…
A little backstory for: "A Bioinformatician, Computer Scientist, and Geneticist lead bioinformatic tool development - which one is better?" doi.org/10.1101/2024.0… #1/9
Our protocols manuscript has been accepted🥳 I can't wait to share it with everyone once it is available in final form! x.com/jlsteenwyk/sta…
NEW preprint: #PhyKIT is a command-line tool for analyzing multiple sequence alignments and phylogenies. Here, we detail #protocols for using PhyKIT to build #phylogenomic supermatrices, quantifying biases/#errors therein, identifying putative radiations & so much more.
Slides from my #ISME19 presentation available at github.com/statdivlab/pre… . Looking forward to continuing the rest of the session in 1.4 at 2:30pm today! Joint work with @davidandacat @sarah_teichman @bejcal and @mikemc423
scikit-bio now offers an expanded and well-documented array of alpha diversity metrics, including new generalized and phylogenetic ones like abundance-weighted PD, Hill numbers, and Renyi entropy. scikit.bio/docs/latest/ge… #bioinformatics #microbiome #ecology
Welcome to join my research team. @sshsphmidsea
New RA position with @weiluo0001 NUS Geography to study the geographic spread of mosquito-transmitted viruses (i.e., dengue) under future climate change scenarios in Southeast Asia. Welcome application. careers.nus.edu.sg/NUS/job/ARTS-&… @theAAG @HealthGeography @cpgis_media
#hiring PhD student in Kraków! Join our efforts to understand the role of the human gut microbiome in health and disease by studying microbial protein structures and functions. An exciting project with @Joana_MPereira @TorstenSchwede more info and APPLY: sano.science/job-offers/san…
This paper probably won't make a big splash since it doesn't play into the "AI is going to take over the world" narrative, but the results are profound: *real* data is still limiting Unlikely models will continue to improve as they have for the last few years without a…
I'll be presenting at this free @NIH @genome_gov (National Human Genome Research Institute) Symposium on Exploring the Many Dimensions of Sex and Gender in the Genomics Era - this week. Registration is free! genome.gov/event-calendar…
Yang Lu talks about BLAST e-values and highlights that dependency on the database, depending on the db it either over or underestimates the e-value. To fix this they propose a SG-pvalue. #ISMB2024
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