Dmitry (@meleshko_da) profile picture

Dmitry

@meleshko_da

PhD student in Weill Cornell Medical College

 Saint Petersburg, Russia
Joined April 2013
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  • Following83
  • Followers98
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Photo by Dmitry (@meleshko_da)Photo by Dmitry (@meleshko_da)Photo by Dmitry (@meleshko_da)
My small contribution into case study of 13q Deletion Syndrome mdpi.com/1422-0067/26/19/930…
13q Deletion Syndrome Presenting with Lymphopenia Detected Through Newborn Screening for Primary...

13q Deletion Syndrome Presenting with Lymphopenia Detected Through Newborn Screening for Primary...

The expanded newborn screening (NBS) program in the Russian Federation, launched in 2023, includes the detection of severe forms of T- and B-cell immunodeficiencies via TREC/KREC quantification. We...

mdpi.com
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I'm glad I did not table it. Finish your papers:)
Iman Hajirasouliha (@hajirasouliha) profile pictureIman Hajirasouliha@hajirasouliha4 Jul 2025
Our latest work on SV detection is now published. Congratulations @meleshko_da my former PhD student @cbm_student for leading this! Blackbird: structural variant detection using synthetic and low-coverage long-reads academic.oup.com/bioinformat…
Blackbird: structural variant detection using synthetic and low-coverage long-reads

Blackbird: structural variant detection using synthetic and low-coverage long-reads

AbstractMotivation. Recent benchmarks show that most structural variations, especially within 50–10,000 bp range cannot be resolved with short-read sequenc

academic.oup.com
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Doing some science about marine inhabitants while in Russia: mdpi.com/1422-0067/25/23/129…
Structure and Biosynthetic Gene Cluster of Sulfated Capsular Polysaccharide from the Marine...

Structure and Biosynthetic Gene Cluster of Sulfated Capsular Polysaccharide from the Marine...

Vibrio sp. KMM 8419 (=CB1-14) is a Gram-negative bacterium isolated from a food-net mucus sample of marine polychaete Chaetopterus cautus collected in the Sea of Japan. Here, we report the structure...

mdpi.com
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My final piece of work in US as a graduate student. Life is so different right now
Iman Hajirasouliha (@hajirasouliha) profile pictureIman Hajirasouliha@hajirasouliha19 Nov 2024
Our latest manuscript led by @cbm_student alumni @meleshko_da @WeillCornellGS @WCMEnglanderIPM , Blackbird: structural variant detection using synthetic and low-coverage long-reads biorxiv.org/content/10.1101/…
Blackbird: structural variant detection using synthetic and low-coverage long-reads

Blackbird: structural variant detection using synthetic and low-coverage long-reads

Motivation Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot...

biorxiv.org
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Our latest manuscript led by @cbm_student alumni @meleshko_da @WeillCornellGS @WCMEnglanderIPM , Blackbird: structural variant detection using synthetic and low-coverage long-reads biorxiv.org/content/10.1101/…
Blackbird: structural variant detection using synthetic and low-coverage long-reads

Blackbird: structural variant detection using synthetic and low-coverage long-reads

Motivation Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot...

biorxiv.org
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SPAdes 4.0 is released! github.com/ablab/spades/rele… Since 2022 SPAdes is not related to any institution and is maintained by the SPAdes team - an international group of volunteers. Although this might be the last major release, we strongly intend to continue supporting our users!
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My favourite collaboration with @hagentilgner and Andrey Prjbelski
Iman Hajirasouliha (@hajirasouliha) profile pictureIman Hajirasouliha@hajirasouliha23 Jan 2024
Our latest "accepted" manuscript led by recently-graduated @cbm_student @WeillCornellGS Dr. Meleshko of the lab. Fruitful collaboration with my dear friend @hagentilgner! cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data academic.oup.com/bioinformat…
cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data

cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data

AbstractMotivation. Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-re

academic.oup.com
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Our new methods paper, Ariadne, is just out @GenomeBiology ! Led by my incredible Ph.D. student @cbm_student @WeillCornell Lauren Mak - with contributions from several other current or former students including @meleshko_da @dcdanko genomebiology.biomedcentral.…
Ariadne: synthetic long read deconvolution using assembly graphs

Ariadne: synthetic long read deconvolution using assembly graphs

Genome Biology - Synthetic long read sequencing techniques such as UST’s TELL-Seq and Loop Genomics’ LoopSeq combine 3 $$'$$ barcoding with standard short-read sequencing to expand...

link.springer.com
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Our recent ccollaborative work with @hagentilgner ... led by the incomparable @meleshko_da @cbm_student @WeillCornell biorxiv.org/content/10.1101/…
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I have several open positions (at all levels) available in the lab in 2023. Please check the page for details and/or R/T :) physiology.med.cornell.edu/f…
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Our own @cbm_student @meleshko_da presents a new version of his blackbird algorithm for assembly of SVs using hybrid synthetic long reads and low coverage long reads. #GI2022
Image from Iman Hajirasouliha (@hajirasouliha)
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Our latest work is now online ... led by the great @cbm_student @meleshko_da :) Efficient detection and assembly of non-reference DNA sequences with synthetic long reads academic.oup.com/nar/advance…
Efficient detection and assembly of non-reference DNA sequences with synthetic long reads

Efficient detection and assembly of non-reference DNA sequences with synthetic long reads

Abstract. Recent pan-genome studies have revealed an abundance of DNA sequences in human genomes that are not present in the reference genome. A lion’s sha

academic.oup.com
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The difference between different linked-read platforms is pretty notable. 10X and stLFR have a heavy tail in molecule length distribution. stLFR has mean molecule coverage around 0.4X!
Image from Dmitry (@meleshko_da)
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Wow, my first Nature paper is here! And what a paper it is.
Rayan Chikhi (@RayanChikhi) profile pictureRayan Chikhi@RayanChikhi26 Jan 2022
Serratus is published in @Nature!🎉 Planetary viral discovery by analysis of all available RNA sequencing data. nature.com/articles/s41586-0…
Image from Rayan Chikhi (@RayanChikhi)
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Today I launched a bunch of "novel" bioinformatics tools to benchmark, and they all have something in common. They write random numbers into the console without any explanation.
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Мне нравится как с точки зрения секвенирования Россия похожа на некоторые страны Африки или Антарктиду. И единственное хорошо исследованное место - это Байкал. Требуем гранты на секвенирование всего и вся
Rayan Chikhi (@RayanChikhi) profile pictureRayan Chikhi@RayanChikhi15 Mar 2021
Replying to @RayanChikhi
The entire search was completed in 11-days wall-clock. All software is open-source and the data is freely available. Explore the Open Virome at serratus.io
Image from Rayan Chikhi (@RayanChikhi)
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Explore Earth’s Virome with Serratus. We uncover 130,000+ new species of RNA viruses, increasing the total known species by an order of magnitude. (Thread)
Image from Rayan Chikhi (@RayanChikhi)
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"Три дня не пить, налево не ходить", - напутствовала меня медсестра в поликлинике после вакцинации. Очень хорошо!
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Our new method for the recovery of RNA viruses (e.g. Coronaviruses) [led by incomparable @meleshko_da and @akorobeynikov] coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies biorxiv.org/content/10.1101/…
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies

coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies

The COVID-19 pandemic has ignited a broad scientific interest in coronavirus research. The identification of coronaviral species in natural reservoirs typically involves de novo assembly. However,...

biorxiv.org
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We developed a new tool for the coronavirus assembly using HMMs!
bioRxiv Bioinfo (@biorxiv_bioinfo) profile picturebioRxiv Bioinfo@biorxiv_bioinfo28 Jul 2020
coronaSPAdes: from biosynthetic gene clusters to coronaviral assemblies biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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