Sam Modlin

Principal Bioinformatics Software Engineer, Roche |
Data-centric views of the natural world

[Sam Modlin @sam_modlin]

Our work on DNA methylation in M. tuberculosis is finally out in @eLife! https://t.co/mhwsrXJxcE Using sequencing kinetics and @PacBio long reads, we fully assembled DNA methylomes from 93 phylogeographically diverse clinical Mycobacterium tuberculosis complex isolates. (1/7)

[Sam Modlin @sam_modlin]

12/ Immense gratitude to Dr. Monica Espinoza, Derek Conkle-Gutierrez, @FaramarzValafar, and our @SDSUResearch colleagues for turning this curious observation into a paper that raises exciting questions and new hypotheses. #TBResearch #epigenetics #sequencing

[Sam Modlin @sam_modlin]

1/ �� Excited to share our lab’s latest work: “Intercellular mosaic methylation in fast-growing Mycobacterium tuberculosis clinical isolates,” now published in @NAR_Open Molecular Medicine: https://t.co/eGuEUbYLrZ

Huge thanks to my co-first author, Maryam Ahmadi Jeshvaghane!

[Sam Modlin @sam_modlin]

11/ This work highlights how integrating biological domain knowledge with @PacBio long-read sequencing can uncover hidden information about bacterial states directly from sequencing reads. 🔎🧬➡️🧠

[Paulina Mayell @MayellPaulina]

Our first research paper on the genomic epidemiology of drug resistant Tuberculosis in Mexico just published! 🧬🇲🇽 Grateful for the incredible team who made this possible @cliconac, @IndGenomics, @rozecu05, Dr. Julio, Dr. Enciso #WGS

https://t.co/y4O2h22Ag0

[Sam Modlin @sam_modlin]

@adrien_meur Appreciate the shout-out, Adrien! Thanks!

[Sam Modlin @sam_modlin]

Very happy to have our latest work published in Drug Resistance Updates. It highlights an interesting, clinically important case where targeted molecular diagnostics fail to correctly classify drug-resistant TB due to primer evasion.

[Faramarz Valafar @FaramarzValafar]

Proud of latest article from @Valafarlab led by @sam_modlin, published by Drug Resistance Updates. We show how minority PZA-susceptible #TB population in a sample can prevent detection of the majority resistant population by targeted molecular diagnostics. https://t.co/SAhTIb2HTv

[Faramarz Valafar @FaramarzValafar]

I am proud to announce the latest article from @Valafarlab led by @0xaf1f, published by @OxfordJournals. Here, we evaluate syntenic block detection strategies, build a combined rearrangement/SNP tree for comprehensive phylogeny of clinical #tuberculosis. https://t.co/VuzkG8KOqI

[Prof. Nikolai Slavov @slavov_n]

Humans excel at science when they are emotionally detached from the subjects under investigation.

Emotions can pose a challenge even for self-aware people aiming for objectivity.

Protein to RNA correspondence seems to engender enough feelings to challenge objectivity. 🧵🧵🧵

[Hesper Rego @Rego_Lab]

@Kuldeep_R_Gupta, working together with @celenagwin, discovered that a protein of unknown function in mycobacteria (PgfA) is recruited to one side of the cell by our favorite protein LamA, where it coordinates lipid trafficking and fast polar growth

[Will Blevins @willblev]

A few of us from the Single Cell Genomics team went to a stained glass workshop @ColorGlassShop. I asked the friendly sequencing lab techs in the @cnag_eu to save the used @illumina flow cells, and here is my first attempt at sci-art 🧪🎨. It could be a flower, or the sun, or...?

[Sam Modlin @sam_modlin]

Join us in San Diego! 🌅🔬🦭🧫🐠💻🐟 Work with high-quality long read sequencing data and other cutting edge profiling of interesting TB samples. And exciting opportunities in the wet-lab to improve on current methods and test data-driven hypotheses! DM me or @FaramarzValafar

[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