Valafar Lab

pathogen #genomics lab researching the genetic basis of antibiotic resistance in Mycobacterium #tuberculosis

[Faramarz Valafar @FaramarzValafar]

Happy to report a fruitful collaboration with @thekswenson, Siavash Mirarab, @0xaf1f, and Mathias Weller:

https://t.co/XFzVtQz9VJ

[Valafar Lab @Valafarlab]

Come join us!

[Faramarz Valafar @FaramarzValafar]

. @Valafarlab has several predoctoral & postdoctoral positions open. We are focused on Tuberculosis. We house a wet and a dry lab. Members work on all aspects of TB Research: mutagenesis, phenotyping, informatics, ML/AI, evolution, phylogeny, systems biology, metabolic modeling

[Faramarz Valafar @FaramarzValafar]

. @Valafarlab has several predoctoral & postdoctoral positions open. We are focused on Tuberculosis. We house a wet and a dry lab. Members work on all aspects of TB Research: mutagenesis, phenotyping, informatics, ML/AI, evolution, phylogeny, systems biology, metabolic modeling

[Conor Meehan @con_meehan]

Great insights into Mtb methylation patterns and diversity by @sam_modlin at #EMBOTB2022 . Some of the work is outlined here: https://t.co/Iz7jkCOIxH

[PacBio @PacBio]

Tuberculosis (TB) remains one of the deadliest global pathogens. @Sam_modlin and @FaramarzValafar measured #epigenetic diversity, identifying mosaic methylation patterns across TB isolates accounted for phenotypic variations.

Read more: https://t.co/Uia7PlOOUh

#PacBio

[Valafar Lab @Valafarlab]

@0xaf1f representing LPCDRP @ #ASMMicrobe2022 with his work developing Hybran, a tool for hybrid annotation of genomes. Interested in getting the most out of curated reference genomes while IDing genes in your sample absent from the reference? Check out his poster from 4-5 today!

[San Diego State University @SDSU]

SDSU researchers have identified rare genetic markers in tuberculosis that could improve early detection of drug-resistant strains of the disease. 🔬

More on their research. 👉 https://t.co/3AUePgk33a

[Valafar Lab @Valafarlab]

We proposed the orphan methyltransferase encoded by Rv2756c to be renamed to MamC (mamC for the gene), the specificity subunit of MamC encoded by Rv2761 to mamS/MamS (formerly hsdS/HsdS) and the specificity subunit fragment Rv2755 (formerly hsdS.1/HsdS.1) to mamS.1/MamS.1.

[Faramarz Valafar @FaramarzValafar]

Our new publication describes a novel rapid epigenetic phenomenon named Intercellular Mosaic Methylation (IMM). IMM, can lead to enhanced phenotypes (persistence, resistance) in tuberculosis. Publication also renames three genes to mamC, mamS, and mamS.1. https://t.co/MJMHUJIu8m

[Faramarz Valafar @FaramarzValafar]

I will be giving a talk on the epidemiology and molecular diagnostic challenges of drug resistance tuberculosis.

[Valafar Lab @Valafarlab]

Open Postdoctoral Fellow position at Valafar Lab.

[Faramarz Valafar @FaramarzValafar]

Check out this job from San Diego State University and University of California in San diego https://t.co/Y2pCUS7U1S

[Valafar Lab @Valafarlab]

Check out our latest pre-print, where we annotate hundreds of genes, cutting away at the M. tuberculosis "hypotheticome" https://t.co/6mzUxbUc0M

[Valafar Lab @Valafarlab]

New preprint, PBHoover and Cigar Roller: a method for confident haploid
variant calling on Pacific Biosciences data and its
application to heterogeneous population analysis #pacbio https://t.co/jwNyrpEvhW

[Valafar Lab @Valafarlab]

A big mistake indeed https://t.co/Rbjv5yj8kg

[PacBio @PacBio]

VF: Summarizing learnings to date - 'Ignoring structural variations, in my opinion, is a big mistake' #PBUGM @Valafarlab

[Valafar Lab @Valafarlab]

@mseetin @sam_modlin @PacBio To clarify, the 1,449 were annotated manually & w/structural homology and applied to PB assemblies. PB data may help annotate remaining

[gconcepcion.bsky.social @phototrophic]

FV: structural variation responsible for majority of genomic differences, not SNPs that most people focus on #PBUGM @PacBio

[Tyson Clark @tysonaclark]

FV: structural variations in Mtb clinical isolates with @PacBio. Some are associated with specific lineages, drug resistance. #PBUGM

[PacBio @PacBio]

VF: @Valafarlab study found prev study overstated genetic differences btwn the microbes due to seq error:

https://t.co/RwrGH00nGL #PBUGM

[gconcepcion.bsky.social @phototrophic]

FV: Illumina "blind" genome spots caused by more than just GC / repeat content #PBUGM @PacBio

[Sam Modlin @sam_modlin]

@Valafarlab illuminating the shortcomings of short read sequencing at the @PacBio UGM

[PacBio @PacBio]

FV: TB infects 9 mil ppl/yr, #1killer of infect. diseases - 4.4 Mb, 40% unannotated, large/small repeats, study mech. of resistance #PBUGM