Luis F. Soto-Ugaldi@LFSoto12

Bach. Genetics and Biotechnology Ph.D. student in Computational Biology at Fuchs Lab and Pe'er Lab RU/MSKCC

Joined October 2019
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Luis F. Soto-Ugaldi retweeted
The Fuchs lab@ElaineFuchsLab
Mar 26
Our paper is out in @ScienceMagazine Here we describe how stem cell retain epigenetic inflammatory memory long-term. Full text in the link below! Congratulations @chris_cowley14 @SairajSajjath @LFSoto12 and everyone else involved! science.org/doi/10.1126/scie…

Distinctive DNA sequence features define epigenetic longevity of inflammatory memory

Tissues harbor memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understo...

science.org
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Luis F. Soto-Ugaldi retweeted
Juan Fuxman Bass@fuxmanlab
31 May 2024
Exited to share our recent review on viral elements and their role in sensing cellular and environmental cues!!! Great work by @TheRealJRott @TommyTaslim5 @LFSoto12 @camilam59287155 and @Lumartcues
Trends in Genetics@TrendsGenetics
30 May 2024
Viral cis-regulatory elements as sensors of cellular states and environmental cues dlvr.it/T7d7nS
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Luis F. Soto-Ugaldi retweeted
Anna Berenson, Ph.D.@annaabananabell
16 Apr 2023
The @fuxmanlab is so excited to share our preprint, “Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors.” We explore the extensive functional relationships between TFs that affect DNA targeting. biorxiv.org/content/10.1101/…

Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcri...

Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for...

biorxiv.org
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Epitope-Intersection: Identification of epitopes recognized by many HLA alleles, which is relevant for immunological tests or vaccines. It also can be used to identify restricted epitopes recognized only by a selected set of HLA alleles.
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Location analysis shows that the loss and gain of epitopes are mainly due to mutations in the RBD region. Mutations in other regions have a lower impact on neoepitopes.
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Many thanks to Juan and David for helping me get this out. Check out the paper for more information journals.plos.org/plosone/ar… I am pleased to hear your feedback as I will constantly update this server. I hope this will be useful as a first step in analyzing predicted epitopes

Epitope-Evaluator: An interactive web application to study predicted T-cell epitopes

Multiple immunoinformatic tools have been developed to predict T-cell epitopes from protein amino acid sequences for different major histocompatibility complex (MHC) alleles. These prediction tools...

journals.plos.org
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Epitope-Evaluator is out! If you are working with predicted epitopes for immunological tests or vaccine design, or simply want to try any of these tools to analyze predicted T-cell epitopes, this thread 🧵can help!
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Epitope-Distribution: Identification of HLA alleles recognizing the least (and greatest) number of epitopes independent of the % rank cutoff selected. It also can be used to select a proper cutoff based on the expected number of predicted epitopes.
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Epitope-Evaluator contains 5 interactive tools: Epitope-Distribution, Epitope-Intersection, Epitope-Density, Epitope-Promiscuity, Epitope-Location, and Epitope-Conservation.
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Together with @fuxmanlab and @davidr_requena , we developed Epitope-Evaluator (fuxmanlab.shinyapps.io/Epito…), an interactive online program. It requires 1) a protein fasta file, and 2) the output prediction table of any predictor.
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Luis F. Soto-Ugaldi retweeted
Dr. Verónica Espinoza@Verukita1
27 Aug 2022
➡Two interesting tools, check them out! ➡bioicons.com/ ➡healthicons.org/ #neuroscience #Bioinformatics #RStats #AcademicTwitter #postdoc #OpenAccess #bibliometrics #Biology #PhD #Journal #datascience #AI
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When it’s Friday AND you got good news on a paper 🔉🎶 nitter.siddz.com/RahulkMex/status/15575…
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