Maria Chikina

Computational Biologist. University of Pittsburgh.

[Maria Chikina @ChikinaLab]

Voters expressed genuine grievances, and while change is rarely immediate, this outcome may still signal shifts that align the economy more closely with the needs of the people. And that’s an aspiration we can all share.

[Maria Chikina @ChikinaLab]

Many are feeling the weight of the election's outcome. As we process this, let's focus on what we can control: our work, connections with friends and family, and sources of personal fulfillment.

[Maria Chikina @ChikinaLab]

Democracy, though not always a direct reflection of our ideals, remains a system responsive to collective concerns, even if indirectly.

[Maria Chikina @ChikinaLab]

Our work benchmarking proportion estimation methods (https://t.co/oP2ZP7zbVU) finds BayesPrism (https://t.co/RnOxvSweBK) among the top performers. We introduce a fast re-implementation InstaPrism: same accuracy, orders of magnitude faster! https://t.co/4J34Pu7gE3

[Sasha Gusev @SashaGusevPosts]

A 🧵 on some of my intuitions/priors about the genetics of complex and molecular traits in humans (i.e. what I think of as typical), largely motivated by GWAS/QTL studies over the past decade [citing papers with nice figures where possible]

[Maria Chikina @ChikinaLab]

Can someone explain Fig 2 of https://t.co/kf5r1bBiLG. Why do some nascent RNA techniques give signal past the transcription end site and others don't.

[Maria Chikina @ChikinaLab]

@anshulkundaje But the slow and diligent approach is not incentivized. How might we be able to solve that problem?

[Maria Chikina @ChikinaLab]

@anshulkundaje @sara_mostafavi @LXandR_ We are not saying you need to replace the reference genome with another one but that you need more genome/output pairs. Clearly in the limit of variant memorization this *will* increase prediction accuracy but perhaps it can also be used to get a more biochemically aware model.

[Maria Chikina @ChikinaLab]

Hopefully this in depth evaluation will pave the way for more accurate personalized gene expression models. We will surely need more data and likely different models and training paradigms.

[Sara Mostafavi @sara_mostafavi]

Interested in using deep learning to predict the impact of genetic variation on gene expression? In our pre-print we investigate how well this can be done currently . Joint work with wonderful colleagues @ChikinaLab, Alex (@LXandR_ ), and others.

https://t.co/zKjGl4HErJ

[Maria Chikina @ChikinaLab]

In our new paper https://t.co/ORbPOrka87 we show that unlike gene expression methylation changes persist for months after infection and could be used to predict infection timing. Great effort by @WayneMao1.

[Maria Chikina @ChikinaLab]

If you need to deconvolve bulk RNAseq data and like BayesPrism (https://t.co/Nv7L3L1xoL) consider InstaPrism (https://t.co/MJmFA58nL2). Same results but much faster.

[Maria Chikina @ChikinaLab]

We just posted a new preprint on benchmarking deconvolution methods. With an appropriately realistic simulation we get highly counter-intuitive results. The problem is far from being completely solved! https://t.co/Tz6hk2twBc

[Nathan Clark nclark.bsky.social @NathanClark111]

Here Today, Gone Tomorrow: How (Some) Mammals Lost Their Body Hair
new release on lab publication from @KowalczykAmanda and @ChikinaLab
https://t.co/qs4OUahcuj via @UofUHealth

[Maria Chikina @ChikinaLab]

Our new paper with @NathanClark111 and @KowalczykAmanda looking at mammalian sparse hair phenotype is now online. https://t.co/JnTkwonfrs

[Wes Pegden @WesPegden]

New preprint with @ChikinaLab:
"The paradoxical nature of easily improvable evidence"

When trying to reason about available evidence which is filtered through the lens of publication bias, what you *don't* see can be as informative as what you do see.
1/2
https://t.co/UvMgI8LCKe

[Maria Chikina @ChikinaLab]

When considering doing a correlation analysis, a useful thought experiment is to imagine the conclusion for every possible outcome (+, -, NS). This avoids the trap of only accepting the results that reinforce one’s prior and discarding others with some post-hoc explanation.

[Wes Pegden @WesPegden]

This thread on a recent paper from @ProfEmilyOster and others is making the rounds.

It is an extremely critical thread employing strong language, questioning the basic judgement and statistical understanding of the authors.

A quick, polite thread with some comments on this.1/12

[Maria Chikina @ChikinaLab]

At a time when many comments from just a few months ago have aged badly this timeless quote from Bertrand Russell is both inspirational and comforting. Stick to the facts, respect those that disagree and you are sure to have few regrets.

[Wes Pegden @WesPegden]

Russell's "message to the future" was perhaps never timelier than now.

https://t.co/7A4IROtnxT

[Wes Pegden @WesPegden]

Happy to announce our recent paper with @ChikinaLab, @jcmattingly, and Alan Frieze on new Markov chain significance tests in the context of redistricting problems.

It includes examples from the 2019 Common Cause v. Lewis case in North Carolina.

https://t.co/u70GvOk6Zs

[David Sinclair @davidasinclair]

Alpha-ketoglutarate (AKG) is a chemical used by the cell to make amino acids, energy & reverse the "DNA methylation" clock. Feeding 18-month old female mice AKG reduced hair greying, frailty & extended median lifespan 10-16% 💪 Worked less well on boys 😒 https://t.co/YbvaIKzQhi