Ph.D. student at University of Maryland at College Park. Research on Computational Biology.
Canada
Joined September 2012
- Tweets144
- Following140
- Followers210
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Fatemeh Almodaresi retweeted
After a long wait, the latest in large-scale indexing from @fataltes, @prashn_25, @scarecrow00007, @CSIdiotSavant, Rob Johnson, Mike Ferdman & I is published:academic.oup.com/bioinformat… (preprint biorxiv.org/content/10.1101/…). This work shows how to make Mantis incrementally updatable. 1/
Write a blind review so that if unexpectedly the reviewers’ names are disclosed, you’re the one who’s proud and not ashamed!
Fatemeh Almodaresi retweeted
Check out new #genomics work by Hongyu Zheng (CPCB Ph.D. student in @SCSatCMU) and Guillaume Marçais (at @CMUCompBio) on "polar sets" for sketching strings. It's a new way to construct minimizers that work well on specific sequences. biorxiv.org/content/10.1101/…
Fatemeh Almodaresi retweeted
Thanks to the #WomenInScience who are prominent on Twitter and have served as role models without even knowing it!
And more about discussing science .. 👩🎓👩💻👩🔬
I look forward to a day when discussions about being a woman in science are less about dealing with bias, harassment, bullying, sexism, self-doubt, invisible work, etc
And are more about discussing...science
#InternationalDayOfWomenInScience
Fatemeh Almodaresi retweeted
New research from CPCB Ph.D. student (@CMUCompBio in @SCSatCMU) Yutong Qiu @yutong_qiu on efficiently constructing smaller genome graphs using ideas from data compression. Can we make a genome graph using gzip? Someday, maybe. biorxiv.org/content/10.1101/…
Fatemeh Almodaresi retweeted
Interested in single cell genomics but need help getting started? Check out my lab's Single Cell Genomics Day on March 26. Talks will feature recent exciting computational and experimental advances and will be livestreamed at satijalab.org/scgd. Please RT/spread the word!
I can’t emphasize this enough.
Fatemeh Almodaresi retweeted
Fun to read about these milestones in genomics. I was a co-author on 3 of them, and my former lab members were co-authors on several more (@mike_schatz @traingene @aphillippy @BenLangmead @coletrapnell Mihai Pop/@umiacs) nature.com/immersive/d42859-…
Fatemeh Almodaresi retweeted
#HiTSeq2021 Keynote Speakers line up announced! Looking forward to hear from @TheBrooksLab @bvhalldorsson and @StevenSalzberg1
Third in Mantis product line, the dynamic Mantis can now be easily scaled to more samples without rebuilding the whole index and by just adding the new sample to an existing one.
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Fatemeh Almodaresi retweeted
The latest in the Mantis line of work, led by the inimitable @fataltes along with @scarecrow00007, @prashn_25, @abnicken, Mike Ferdman, Rob Johnson and myself. Here, we apply the Bentley-Saxe transform to dynamize Mantis; and idea suggested in the original paper 1/x
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Fatemeh Almodaresi retweeted
Very excited to share the preprint for cuttlefish (biorxiv.org/content/10.1101/…); a new method for constructing the compacted (colored) de Bruijn graph from (collections of) reference genomes. This work was led by @scarecrow00007 1/7
Fatemeh Almodaresi retweeted
Need to clear your mind a bit after the final presidential "debate"? Why not take a look at our latest preprint on cuttlefish; led by @scarecrow00007
Very excited to share the preprint for cuttlefish (biorxiv.org/content/10.1101/…); a new method for constructing the compacted (colored) de Bruijn graph from (collections of) reference genomes. This work was led by @scarecrow00007 1/7
Fatemeh Almodaresi retweeted
My productivity algorithm is something like:
* Start to do something
* Remember higher-priority thing, switch to doing that
* Remember that high-priority thing is hard
* Do nothing
Fatemeh Almodaresi retweeted
Metalign: efficient alignment-based metagenomic profiling via containment min hash genomebiology.biomedcentral.… github.com/nlapier2/Metalign
Fatemeh Almodaresi retweeted
HiCanu is published in @genomeresearch! Accurate assembly of segmental duplications, centromeres, and allelic variants from @PacBio HiFi reads w/ @sergeynurk @sergekoren @ArangRhie @mrvollger @glennis_logsdon @khmiga -> doi.org/10.1101/gr.263566.12…
Fatemeh Almodaresi retweeted
A great deep dive led by @k3yavi* and Laraib* with important contributions by @hrksrkr*, Mohsen and @fataltes*, and our collaborators @CSoneson, @mikelove and @ckingsford. Fun fact: co-authors with a * have all since graduated, so double congrats to them!
Srivastava, Malik, @nomad421 and co benchmark alignment and mapping algorithms for transcript abundance estimation from RNA-seq data. Based on results, they introduce selective alignment approach that is fast, but removes errors from lightweight alignment genomebiology.biomedcentral.…
Fatemeh Almodaresi retweeted
Nice write-up on our line of work being led by @fataltes & @prashn_25 (w/ important contributions by @scarecrow00007 & @abnicken in an imminent update). This is one of my favorite collaborations with Rob Johnson (@vmwareresearch), Mike Ferdman & Michael Bender (@sbucompsc).
Read how @UofMaryland computational biologist @nomad421 is developing fundamentally improved data structures and algorithms to enable large-scale sequence search across public repositories of genomic data. go.umd.edu/5RD #UMDdiscovers
