@BKille

PhD student and former software engineer in the Treangen lab at Rice University. MS in computer science from UIUC.

 Houston, TX
Joined December 2019
  • Tweets18
  • Following412
  • Followers140
3Media
In a new preprint, @curious_coding and I led the derivation of a new lower bound, g’ (red), on k-mer sampling scheme density: - our bound appears to be tight for k ≡ 1 (mod w). - existing schemes are nearly optimal! - mod-minimizers are optimal for large sigma for k ≡ 1 (mod w)
Comparison of existing schemes to lower bounds with practical parameters. Densities are calculated by applying each scheme to a random sequence of 10 million characters over an alphabet of size σ = 4 (dotted lines) and are compared with the corresponding proportion of sampled k-mers on the human Y chromosome (Rhie et al., 2023) (soft lines). The window sizes 5 and 19 are the default window sizes for Kraken2 (Wood et al., 2019) and minimap2 (-ax hifi) (Li, 2018), respectively. For SSHash, w = 12 was the window size used when indexing the human genome (Pibiri, 2022).

ALT Comparison of existing schemes to lower bounds with practical parameters. Densities are calculated by applying each scheme to a random sequence of 10 million characters over an alphabet of size σ = 4 (dotted lines) and are compared with the corresponding proportion of sampled k-mers on the human Y chromosome (Rhie et al., 2023) (soft lines). The window sizes 5 and 19 are the default window sizes for Kraken2 (Wood et al., 2019) and minimap2 (-ax hifi) (Li, 2018), respectively. For SSHash, w = 12 was the window size used when indexing the human genome (Pibiri, 2022).

bioRxiv Bioinfo@biorxiv_bioinfo11 Sep 2024
A near-tight lower bound on the density of forward sampling schemes biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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It’s been an honor to work on such a popular tool and meet so many great scientists in the process. Thank you @aphillippy for the opportunity! I couldn’t have asked for a more ideal project, it was the perfect balance of algorithmics, probability, and high performance computing.
Adam Phillippy@aphillippy18 May 2023
Our latest methods paper "Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation" (aka MashMap3) is out with @BKille @erikgarrison @traingene! There's an interesting backstory here 🧵 \ biorxiv.org/content/10.1101/…

Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation

Motivation The Jaccard similarity on k -mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations,...

biorxiv.org
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While I expected to learn a lot about MashMap-related content over the last year, I truly underestimated the sheer amount of general research skills I’d take away from the project, particularly thanks to @aphillippy's mentorship, as well as @traingene's and @erikgarrison's.
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With all of this wrapped up, I’m looking forward to whatever comes next, especially if it involves hopping on the Rust bandwagon (:
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Happy to announce an open postdoctoral research scientist position in my group @RiceCompSci focused on exciting research questions related to metagenomics & protein structure prediction. Joint position with the amazing @KavrakiLab Interested? apply today! careers.iscb.org/jobs/view/8…
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Bryce Kille retweeted
Tiancheng@txu_teapot13 Aug 2022
The problem was really fun to work on! And as someone knowing little about genomes at the beginning, I was blessed to have invaluable support & guidance from @traingene @beleafsTX @BKille @SapovalNicolae @fuyilei96! And thank you very much @RiceCompSci for the spotlight! 😁🙏
Rice University Computer Science@RiceCompSci12 Aug 2022
Rice CS PhD student Tiancheng Xu has developed a new hardware accelerator that speeds up genome variant analysis, processing #SARSCoV2 data in minutes. He recently presented this new tool at #FCCM22 alongside his advisors Alan Cox and Scott Rixner. bit.ly/3zNdypw
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This was by far the largest and most collaborative project I’ve ever worked on and what a rewarding experience it was. Thanks to everyone who helped make it happen!
Todd J Treangen@traingene21 Jun 2022
Very happy to share the latest paper from my group, SeqScreen, just published in @GenomeBiology. SeqScreen was led by my @RiceCompSci PhD students @AdvaitBalaji & @BKille, spanning 5 fruitful years of collaboration with Signature Science LLC @SigSci genomebiology.biomedcentral.… 1/n

SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning

Genome Biology - The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open...

link.springer.com
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