59 episodes

A podcast about computational biology, bioinformatics, and next generation sequencing.

the bioinformatics chat Roman Cheplyaka

    • Life Sciences
    • 4.8 • 23 Ratings

A podcast about computational biology, bioinformatics, and next generation sequencing.

    Proteomics calibration with Lindsay Pino

    Proteomics calibration with Lindsay Pino

    In this episode, Lindsay Pino discusses the
    challenges of making quantitative measurements in the field of proteomics.
    Specifically, she discusses the difficulties of comparing measurements across
    different samples, potentially acquired in different labs, as well as a method
    she has developed recently for calibrating these measurements without the need
    for expensive reagents. The discussion then turns more broadly to questions in
    genomics that can potentially be addressed using proteomic measurements.





    Links:


    Talus Bioscience
    Matrix-Matched Calibration Curves for Asssessing Analytical Figures of Merit in Quantitative Proteomics
    (Lindsay K. Pino, Brian C. Searle, Han-Yin Yang, Andrew N. Hoofnagle, William S. Noble, and Michael J. MacCross)

    • 48 min
    B cell maturation and class switching with Hamish King

    B cell maturation and class switching with Hamish King

    In this episode, we learn about B cell maturation and class switching from
    Hamish King. Hamish recently published a
    paper on this subject in Science Immunology, where he and his coauthors
    analyzed gene expression and antibody repertoire data from human tonsils.
    In the episode Hamish talks about some of the interesting B cell states he
    uncovered and shares his thoughts on questions such as «When does a B cell
    decide to class-switch?» and «Why is the antibody isotype correlated with its
    affinity?»






    Links:



    Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
    (Hamish W. King, Nara Orban, John C. Riches, Andrew J. Clear, Gary Warnes, Sarah A. Teichmann, Louisa K. James) (paywalled by Science Immunology)
    Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation
    (the preprint of the above Science Immunology paper)
    www.tonsilimmune.org: An immune cell atlas of the human tonsil and B cell maturation

    • 1 hr 29 min
    Enhancers with Molly Gasperini

    Enhancers with Molly Gasperini

    In this episode, Jacob Schreiber interviews Molly Gasperini about
    enhancer elements. They begin their discussion by talking about Octant Bio,
    and then dive into the surprisingly difficult task of defining enhancers and
    determining the mechanisms that enable them to regulate gene expression.






    Links:



    Octant Bio
    Towards a comprehensive catalogue of validated and target-linked human enhancers (Molly Gasperini, Jacob M. Tome, and Jay Shendure)

    • 46 min
    Polygenic risk scores in admixed populations with Bárbara Bitarello

    Polygenic risk scores in admixed populations with Bárbara Bitarello

    Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS)
    to predict the phenotype based on the genotype. However, the prediction
    accuracy suffers when GWAS from one population are used to calculate PRS within
    a different population, which is a problem because the majority of the GWAS
    are done on cohorts of European ancestry.


    In this episode, Bárbara Bitarello helps us
    understand how PRS work and why they don’t transfer well across populations.





    Links:



    Polygenic Scores for Height in Admixed Populations (Bárbara D. Bitarello, Iain Mathieson)
    What is ancestry? (Iain Mathieson, Aylwyn Scally)

    • 1 hr 30 min
    Phylogenetics and the likelihood gradient with Xiang Ji

    Phylogenetics and the likelihood gradient with Xiang Ji

    In this episode, we chat about phylogenetics with Xiang Ji. We start with a
    general introduction to the field and then go deeper into the likelihood-based
    methods (maximum likelihood and Bayesian inference). In particular, we talk
    about the different ways to calculate the likelihood gradient, including a
    linear-time exact gradient algorithm recently published by Xiang and his
    colleagues.






    Links:



    Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics
    (Xiang Ji, Zhenyu Zhang, Andrew Holbrook, Akihiko Nishimura, Guy Baele, Andrew Rambaut, Philippe Lemey, Marc A Suchard)
    BEAGLE: the package that implements the gradient algorithm
    BEAST: the program that implements the Hamiltonian Monte Carlo sampler and the molecular clock models

    • 57 min
    Seeding methods for read alignment with Markus Schmidt

    Seeding methods for read alignment with Markus Schmidt

    In this episode, Markus Schmidt explains how seeding in read alignment works.
    We define and compare k-mers, minimizers, MEMs, SMEMs, and maximal spanning seeds.
    Markus also presents his recent work on computing variable-sized seeds (MEMs,
    SMEMs, and maximal spanning seeds) from fixed-sized seeds (k-mers and
    minimizers) and his Modular Aligner.






    Links:



    A performant bridge between fixed-size and variable-size seeding
    (Arne Kutzner, Pok-Son Kim, Markus Schmidt)
    MA the Modular Aligner
    Calibrating Seed-Based Heuristics to Map Short Reads With Sesame
    (Guillaume J. Filion, Ruggero Cortini, Eduard Zorita) — another
    interesting recent work on seeding methods (though we didn’t get to discuss
    it in this episode)

    • 1 hr

Customer Reviews

4.8 out of 5
23 Ratings

23 Ratings

slinkerlee ,

great podcast!

This podcast has great interviews and in-depth coverage of new tools and techniques.

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