William Schierding (@SpaceGenome) profile picture

Bioinformatics - GWAS - Non-coding variation in disease - Interested in how distal regulation arises through Spatial Genomic Arrangement

Auckland City, New Zealand
Joined February 2016
Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)Photo by William Schierding (@SpaceGenome)
William Schierding retweeted
William Schierding et al. from the University of Auckland investigate structural and microstructural brain changes in glaucoma using multimodal magnetic resonance imaging across primary, secondary, and higher-order visual brain regions. doi.org/10.1167/iovs.67.8.34
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Hey @AmericanAir -cancelling my flight (because the flight crew timed out) then telling the lovely lady at the ticket counter that I’m on too poor man of a ticket book me on the next flight so I have to fly twice as long? This is how American works now? Did @elonmusk buy you too?
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William Schierding retweeted
Vision is expensive. One bit of information in a photo receptor costs 100x to 1000x more energy than in a synapse. This adds up to ~4% of the entire body's energy budget. A Story of Energy, Information, and Evolution (Thread 🧵)
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William Schierding retweeted
Why are ~10% of humans left-handed? (🙋‍♂️) Exome-wide association study of rare variants in UK Biobank identified alleles of the beta-tubulin gene TUBB4B. Could be related to cilia function, which has been linked to other left-right asymmetries. nature.com/articles/s41467-0…
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William Schierding retweeted
1/ 40 YouTube Channels Every Bioinformatician Should Follow buff.ly/3Pyi3gS
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William Schierding retweeted
Multi-omics: the next arena for big data in biology For the first time in history, we can measure life's ingredients at a large scale: DNA → genomics RNA → transcriptomics Protein → proteomics Can we unite these data modalities and understand them in context of one another?
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William Schierding retweeted
Starting the new year with an updated version of our database of funding opportunities for EARLY-CAREER RESEARCHERS/FACULTY. For each of the 496 entries, we provide description, link, deadline, amount, eligibility criteria Download for free here: research.jhu.edu/rdt/funding…
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William Schierding retweeted
Database of 316 funding opportunities/fellowships for POSTDOC fellows. For each entry, we provide description, link to funder, deadline, $ amount, discipline/field, and eligibility criteria (e.g. citizenship). Download it here: research.jhu.edu/rdt/funding…
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William Schierding retweeted
still one of the top christmas gifts i have ever received 🧬
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📣Our 🆕 paper Causal Inference is Not Just a Statistics Problem is out! @malco_barrett, @travisgerke, and I show that you can have 4 data sets with identical summary stats & visuals but very different data generating mechanisms-statistics alone can't tell you what to adjust for!
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🛫Travel Awards!!🛬 The AEpiA ECR reps would like to thank all applicants for the 2023 ECR Travel Awards. The high quality of submissions made for a difficult judgement process, and we have enjoyed reading about the wide range of epigenetics research undertaken by AEpiA members.
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Everyone needs to know about `easystats` in R It is so much fun to use and then share with students Teaching on regression and just used the check_model() function and look at this beautiful figure
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William Schierding retweeted
How do distal enhancers control transcription dynamics in living cells? Check out our latest work published in @MolecularCell!! We show that the dynamic assembly and disassembly of TF clusters at enhancers are a major source of transcriptional bursting. cell.com/molecular-cell/full…
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William Schierding retweeted
Me watching my supervisor edit my writing in real time on google docs
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Not enough people know about bioicons.com/ Open source vector graphics. Free alternatives to BioRender.
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William Schierding retweeted
You get your differentially expressed genes, now what? to make sense of them, use these 7 gene set enrichment analysis tools. 👇 🧵 #rstats #python #bioinformatics
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William Schierding retweeted
It was wonderful celebrating #sammies2023 honorees last evening at the Kennedy Center in DC! NHGRI was particularly proud of Adam Phillippy, Sergey Koren, and Arang Rhie for being Sammies finalists for their groundbreaking contributions to the Telomere-to-Telomere Consortium.
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William Schierding retweeted
📢Attention all scientists: interested in helping the NASA mission by being a part of the data processing team at GeneLab and OSDR? Then check out this latest open position for a Bioinformatics Program Devleoper. 🔗Apply here: bit.ly/48MoC7d
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William Schierding retweeted
Every Data Scientist needs to know these ideas. They will blow your mind. 1. Correlation vs Causation P(A | B) is the probability of A given B. It is the probability that we will observe A given that we have already observed B. P(A | do(B)) is the probability of A given do(B). It is the probability that we will observe A given that we have intervened to cause B to happen. In this context, an intervention simply means to take an action of some kind. Therefore do(B) means to take an action which causes B to happen. The expressions P(A | B) and P(A | do(B)) might seem very similar but they represent very different situations. 2. We can only learn P(A|B) from the data alone. Bob has an extremely accurate weather app and is always very good about bringing his umbrella when it rains. We observe Bob over several years and we find that whenever it rains, Bob always has his umbrella and he never brings his umbrellas on days when it doesn't rain. In the language of probability, we say P(Umbrella | Rain) = 1 and P(Rain | Umbrella) = 1 as well. What we can learn from this data alone is how to predict whether it rains with a 100% accuracy by checking whether Bob has an umbrella. We can also learn to predict with 100% accuracy whether Bob has an umbrella by checking if it's going to rain. What we cannot learn is what will happen if we give Bob an umbrella on a random day of our choosing. The answer to this question is P(Rain | do(Umbrella) ) and it's unknowable from the data alone. We need prior knowledge about how the world works to properly interpret the data we collected. We need to know that rain has an effect on Bob's behavior, but Bob's behavior has no effect on the rain. Information about the effects of interventions are simply not available in raw data unless it is collected by controlled experimental manipulation. 3. Scientific Experiments work because they produce a very special kind of data. You may have heard of what many people call a scientific experiment. Take a collection of objects, animals or people. Randomly split that collection into a control group and a treatment group. Apply your intervention to the treatment group while leaving the control group alone. If you observe any differences between the treatment group and the control group, it is logical to attribute these differences to the treatment. You can therefore say the differences were caused by the treatment. In statistics, the procedure I just described is called a Randomized Controlled Trial. It is a procedure for generating a specific kind of data where: P(Difference | Treatment) = P(Difference | do(Treatment) ) This is why traditional science experiments work. They are designed to capture causal information. This is not the case for vast majority of data that we collect in society. Without human guidance or access to real world knowledge, statistical algorithms and artificial intelligences can only learn P(A | B) from the raw data. This is a fundamental mathematical limitation on the use of data alone. That's it for now. This post is part of a series of posts about the concept of causal inference. They are based on the content of the Book of Why by Judea Pearl with lots of commentary from me. Follow me (@kareem_carr) so you don't miss out on the next post. Please show support by liking and retweeting the thread.
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