Mohammed Alser 🇵🇸
@mealser@USC🇺🇸 | @ETH🇨🇭, @BilkentUniv @BilkentCompGen @Tubitak fellow 🇹🇷, @UCLA @zarlab🇺🇸, @tudresden_de🇩🇪, @Petronas🇲🇾 | Dad of two
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@_onurmutlu_
@SAFARI_ETH_CMU
@ProjectBioPIM
@EMBO
@damlasenolcali
@calkan_cs
@BilkentCompGen
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@Franc0Fernand0
@pashadag
@MAG2ART
@Voulnet
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@JSheltzer
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1/n It is fascinating to see how sequencing technologies shape algorithms over last 33 years. Check out our latest paper on developments in read alignment algorithms since 1988 (my birth 😅) until now @GenomeBiology: doi.org/10.1186/s13059… @_onurmutlu_ @SAFARI_ETH_CMU @CSatETH
It is always wonderful reconnecting and reminiscing with positive people, my academic father @calkan_cs, @RayanChikhi, and @crashius
We are at the @UCLA_CGSI Can presented @ProjectBioPIM, and Klea presented her project. We also met the leaders in bioinformatics, and one of our alumni, @mealser
Have low abundance microbes in your metagenomic sample and don't know if it's due to noise or not? We present YACHT: a statistical test to detect microbial presence/absence. No more hard thresholding: be statistically confident in your inferences! biorxiv.org/content/10.110…
🎉Happy to share our paper on using long seed sketches for alignment has been published in @genomeresearch! A big thank you to our amazing collaborators @alexmeterez, @akkah21, and @gxr Check out the paper: bit.ly/long_seed_sket…
We had a fantastic time @RECOMBconf! Thanks to all the organizers, participants & speakers at our #BIOArch workshop, panelists & @ProjectBioPIM We look forward to #RECOMB2024! @_onurmutlu_ @FirtinaC @mealser @el1goluj @damlasenolcali @lindegger_joel @iremboybat @RayanChikhi
The @ProjectBioPIM Team is at the @RECOMBconf! We organized the first BIO-Arch Workshop that we aim to launch as a Satellite Meeting next year, and the Panel on Hardware Acceleration of Bioinformatics Workloads.
Join us this evening for a panel on Hardware Acceleration of Bioinformatics Workloads, 17PM at the Marriott Hotel Sisli. Program: safari.ethz.ch/recomb23-arch-… @_onurmutlu_ Panelists: @mealser, @iremboybat @IBMResearch, @damlasenolcali @bionanogenomics, @RayanChikhi @institutpasteur
Our first Keynote Speaker of the day @ewanbirney is presenting "A Jumble of Keywords" at @RECOMBconf
At 16:20, our Mahmud Sami Aydın will present the SABER algorithm for pairwise alignment under block edit distance at @RECOMBseq
Some insightful afternoon talks at our BIO-Arch: Workshop on Hardware Acceleration of Bioinformatics Workloads w/ Banu Cavlak @damlasenolcali @mealser @lindegger_joel Program: safari.ethz.ch/recomb23-arch-… Livestream: youtube.com/live/2rCsb4-nL… @_onurmutlu_ @FirtinaC @RECOMBconf
We had some great talks this morning in our #BIOArch workshop w/ @_onurmutlu_ @GaganGdas Leonid Yavits @mealser Izzat El Hajj & @nika_mgh Join us live, back after lunch at 13:45! Program: safari.ethz.ch/recomb23-arch-… Livestream: youtube.com/watch?v=2rCsb4… @FirtinaC @RECOMBconf
We're looking forward to our upcoming #BIOArch workshop, with an exciting program! safari.ethz.ch/recomb23-arch-… For those not in Istanbul, join us live online: youtube.com/watch?v=2rCsb4… @_onurmutlu_ @RECOMBconf @FirtinaC @mealser @damlasenolcali @nika_mgh @lindegger_joel @GaganGdas
We're happy to share the release of Scrooge, a high-performance pairwise sequence aligner for CPUs, GPUs and ASICs based on the GenASM algorithm. Code: github.com/CMU-SAFARI/Scr… Preprint: arxiv.org/abs/2208.09985 w/ @_onurmutlu_ @damlasenolcali @mealser @el1goluj @nika_mgh
Scrooge is a fast pairwise genomic sequence aligner.. For long reads the CPU version of Scrooge we observe a 15x and 1.7x speedup over KSW2 and Edlib, respectively. github.com/CMU-SAFARI/Scr…
Talk by @p_peterlongo on indexing sequencing data in low RAM. Showing how all existing tools (reviewed by @CamilleMrcht) are inadequate
Talk by @mealser "Genome on Diet" using spaced seeds-like genome sparsification. See last slide as to how it differs from spaced seeds.
#DSB2023 Data structures in bioinformatics workshop is starting in Delft, program: dsb-meeting.github.io/DSB2023/
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Who to follow
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Onur Mutlu
@_onurmutlu_ -
SAFARI Research Group
@SAFARI_ETH_CMU -
BioPIM Project
@ProjectBioPIM -
EMBO
@EMBO -
Damla Şenol Çalı
@damlasenolcali -
Can Alkan
@calkan_cs -
Bilkent CompGen
@BilkentCompGen -
Zülal Bingöl
@zulal_b -
Fernando 🇮🇹🇨🇭
@Franc0Fernand0 -
PM @[email protected] @pashadag.bsky.social
@pashadag -
Dylan Burnette
@MAG2ART -
Mohammed Aldoub م.محمد الدوب
@Voulnet -
Can Fırtına
@FirtinaC -
Jason Sheltzer
@JSheltzer -
euan ashley
@euanashley
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