Postdoc in biostatistics or bioinformatics
Icahn School of Medicine at Mount Sinai
See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoc-in-biostatistics-or-bioinformatics/?feed_id=67067
🤔 I took a #DNA test to see if #genetic testing could make me a better #cyclist - here's what I found https://www.cyclingweekly.com/fitness/could-genetic-testing-make-you-a-better-cyclist-i-took-a-dna-test-and-heres-what-i-found #fitness #health #genetics
From 04 Dec: Hackers stole ancestry data of 6.9 million users, 23andMe finally confirmed - EnlargeBloomberg / Contributor Bloomberg It’s now been confirmed that an addi... https://arstechnica.com/tech-policy/2023/12/hackers-stole-ancestry-data-of-6-9-million-users-23andme-finally-confirmed/ #23andme #ancestry-data #dna-relatives #dna-test-kit #dna-testing #genetics-testing #hackers #online-privacy #policy #relative-finder #security
Dishevelled binding antagonist of beta catenin 1 (Genetics 🧬)
Dishevelled binding antagonist of beta catenin 1 is a protein that in humans is encoded by the DACT1 gene. Dact1 was originally described in 2002 as a negative regulator of Wnt signaling by binding and destabilizing Dishevelled. More recent investigation into the molecular function of Da...
Peptide PACAP’s Key Role in Alcohol Addiction
Source: Boston University
Alcohol is the most common addictive substance in the world. Every year in the U.S. excessive alcohol use costs $249 billion and causes approximately 88,000 deaths, as well as various chronic diseases and social issues.
UK Biobank releases half a million whole-genome sequences for biomedical research
The release more than doubles the size of an earlier data set and will help reveal new links between DNA, health, and disease, geneticists say
#JohnSnyder and his wife #KatherineSnyder ‘adopted’ 5 orphaned babies from #China to be abused captives for years in their Hamilton County, #Ohio #BasketOfDeplorables , killing one of them when he was 8 years old. They will now spend decades in prison. https://www.huffpost.com/entry/john-katherine-snyder-sentenced-son-death_n_656a5c26e4b07b937ff4b225
"Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events."
Sarno S, Boattini A, Carta M, Ferri G, Alù M, et al. (2014) An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy. PLOS ONE 9(4): e96074. https://doi.org/10.1371/journal.pone.0096074 #OpenAccess #OA #Research #Article #Science #STEM #Population #Genetics #PopulationGenetics #Italy #Sicily #DNA #Paleogenetics #Europe #Anthropology #Biology #Academia @science @biology @anthropology
RNA’s Pivotal Role in Fear Memory and PTSD Treatment
“Understanding the complex world of RNA is a rapidly emerging area of neuroscience research, where we are constantly learning more about how different classes of RNA control the communication between and within brain cells,” Professor Bredy said.
We have published several research articles along this line. It is one of my research projects that is purely based on my personal interest😉
Because acetaldehyde damages DNA, people (especially individual with heterozygous for this allele) shouldn't be drinking a lot. But people with homozygous for this mutation are not able to drink alcohol at all, so they never become alcoholic, which seems to be a positive effect🤔
Triple IPA - 11.5% alcohol 🤔
I like this bitterness and light citrus flavor. But I feel alcohol a lot, thinking about acetaldehyde, the primary metabolite of alcohol, although my enzyme (ALDH2) that detoxifies acetaldehyde has no mutation 😉
About half of East Asian people have a mutation in this enzyme. I am looking forward to seeing our kids’ genotypes 🤔
According to this study, reduction in the activity of the INPP5D gene in microglia (immune regulating cells in the brain) leads to increased neuroinflammation, potentially contributing to the progression of Alzheimer’s disease, paving the way for targeted treatments.
#science #research #openaccess #naturecommunicationsjournal #neurology #alzheimersdisease #immunology #genetics #inpp5d
Evo-devo gene toolkit (Genetics 🧬)
The evo-devo gene toolkit is the small subset of genes in an organism's genome whose products control the organism's embryonic development. Toolkit genes are central to the synthesis of molecular genetics, palaeontology, evolution and developmental biology in the science of evolutionary developmental biology. Many of them are ancient and highly conserved...
Dr. Chris Ponting talked about the DecodeME study in a recent NIH webinar titled "ME/CFS Genetics/Genomics." This is part of a series of NIH webinars about ME/CFS research.
Dr. Ponting's talk runs from 11:57 - 49:35 in this video:
A while back I asked for references about gene regulatory network models and how they relate to neural networks and others.
I'm still exploring this topic, but I wanted to share back a really cool paper I found: https://sci-hub.st/10.1111/evo.12337
This paper argues that "gene networks evolve like neural networks learn," and has some very fun examples demonstrating how to do traditional machine learning using model gene regulatory networks as a medium.
It's hardly the final word on the topic, but I'm excited to see folks actively exploring how learning theory might apply to genetics! Seems very promising.
Looking to start your week with some science and great stories? In this new podcast episode, Dr. Alexis “Lekki” Wood discusses her research examining the links between food, genetics, and health. She also gives us a glimpse into her favorite activities outside of science, the twists and turns of her career path, and some of her most meaningful successes and failures.
@markjamesadams ‘Reality is an overwhelmingly immense spiderweb of causes, with a myriad downstream consequences. Wherever you choose a node in this web to mess around with – whether it be a genetic variant or a type of political system – the resulting ripples are not going to stay neatly within the confines of any crude conception of “environment” vs. “biology”.’
#genetics #GxE #causation #GvsE #environment
I do not know enough about evolutionary biology or genetic mutation to have a sense of the applicability to this to people born to brown-eyed ancestrally homologous families who are the single solitary person to have blue eyes in their family for at least three or four generations. Grateful for evolutionary biologists out there to explain.
In this study, researchers have developed an algorithm called FLSHclust for mining publicly available genomic data and have found 188 genetic clusters associated with undiscovered and rare CRISPR systems, including one that targets RNA.
#science #research #crispr #genetics
"The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th–14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor."
Zhabagin, M., Sabitov, Z., Tarlykov, P. et al. The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan. BMC Genet 21 (Suppl 1), 87 (2020). https://doi.org/10.1186/s12863-020-00897-5 #OpenAccess #OA #Science #Research #Article #Human #Genetics #Medieval #Kazakh #Mongol @science
"The primary objectives of this study were to assess the paternal genetic variation in Altaian Kazakh populations and their population histories, to understand the paternal origins of Kazakhs, and to elucidate the process by which this ethnic group formed."
Dulik MC, Osipova LP, Schurr TG (2011) Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions. PLOS ONE 6(3): e17548. https://doi.org/10.1371/journal.pone.0017548 #OpenAccess #OA #Science #Research #Article #Kazakh #Population #Genetics #PopulationGenetics #Asia @science
Come work with us! I have a PhD position available to help understand which mutations in the non-coding parts of coding transcripts have functional consequences in Stem Cells.
We will using genome wide mesaurement of the effect of variation in miRNA binding sites to address when vairation causes changes in regulation and when it doesn't.
Mixed wetlab, bioinformatics and statistics project.
The world's 1st CRISPR therapy has just been approved.
U.K. regulators have approved the use of a CRISPR therapy called Casgevy to treat two inherited blood disorders.
Research reveals that children of mothers experiencing high stress, anxiety, or depression during pregnancy may have a greater risk of mental health and behavior issues throughout childhood and adolescence. #neurobiology #physiology #BrainScience #maternity #development #pregnancy #genetics #stress https://neurosciencenews.com/maternal-stress-child-mental-health-25225/
I once heard Julius Marmur say
You can go from physics or math to biology, but not the other way around
[ pause ]
I know of only one physicist who has made a real contribution to biology
I think he might have mean't Seymour Benzer
1) Deciphering roles of rare genetic variants in developmental speech/language disorders. This project studies impacts of pathogenic gene disruptions by integrating data from clinical & speech/language profiles of affected patients with lab-based analyses in human neuronal models (e.g. brain organoids).
2) Mapping language-relevant genetic effects on brain variability using normative modelling. Here, we apply normative modelling to large-scale imaging & DNA data from the general population, to uncover heterogeneous effects of language-relevant genetic variants.
3) Genetic architecture of the human language network. In this project, we employ advanced neuroimaging techniques to map neural circuits involved in language processing, characterize interindividual differences in their properties, & associate them with DNA variation in unique cohorts.
Applications due before Jan 8th 2024. More info here: https://www.mpi.nl/imprs-phd-fellowships-2024
Data from three health repositories show a simple blood test reveals inherited and acquired genetic indicators, analyzed with artificial intelligence, to detect coronary heart disease.
Apparently it’s #FlyDay or #DrosophilaDay in honour of the day Drosophila melanogaster, the common fruit fly or vinegar fly line w1118 (the first variant with the white eyes) was isolated, so enjoy some #drosophila #sciart! This linocut print highlights the model organism with a hand-printed ring of 5 of the different eye colour genetic mutations on lovely handmade Japanese washi paper with flecks of bark inclusions. 🧵
"certain kinds of important high-dimensional geometric features are, unfortunately, mathematically impossible to represent in the 2D Euclidean plane, no matter what method is used, leading to distorted visualizations and missed geometric, and potentially biological, insights at both local and global scales."
Wang et al. What cannot be seen correctly in 2D visualizations of single-cell ’omics data? Cell Syst. 2023 Sep 20;14(9):723–731. DOI: https://doi.org/10.1016/j.cels.2023.07.002
"Polygenic risk scores performed poorly in population screening, individual risk prediction, and population risk stratification. Strong claims about the effect of polygenic risk scores on healthcare seem to be disproportionate to their performance."
Hingorani et al. Performance of polygenic risk scores in screening, prediction, and risk stratification: secondary analysis of data in the Polygenic Score Catalog. BMJ Medicine. 2023 Oct 1;2(1). DOI: https://doi.org/10.1136/bmjmed-2023-000554
We are looking for talented junior scientists to join our International Max Planck Research School for Language Sciences in Nijmegen, the Netherlands. Two fully-funded 4-year #PhD fellowships (2024-2028) are available to carry out cutting-edge research on #genetics and #development of human #language, with several innovative projects to choose from, co-supervised by leading researchers at the Max Planck Institute and our partners at the Radboud University. Projects include investigating rare #DNA variants in genes that cause developmental speech/language disorders, and neuroimaging #genomic analyses of language circuits in the brain.
Application portal opens Dec 4th 2023 and closes Jan 8th 2024. Full information and FAQ can be found here: https://www.mpi.nl/imprs-phd-fellowships-2024
Boosts much appreciated!
This study reveals that inhibiting a specific enzyme, USP30, in a mouse model can protect dopamine-producing neurons. This finding halts the disease’s progression and opens the door to new therapeutic possibilities for the 10 million people affected by Parkinson’s worldwide.
#science #research #openaccess #naturecommunications #parkinsonsdisease #usp30 #genetics #neurology
"In a world first, the UK medicines regulator has approved a therapy that uses CRISPR gene editing as a treatment for diseases. The decision marks another high point for a biotechnology that has regularly been lauded as revolutionary in the decade since its discovery."
And here's our coverage of the FDA's concerns about potential off-target edits as it considers Casgevy for US approval by Dec 8:
Today the UK approved the first CRISPR-based treatment: A gene-editing treatment for beta thalassemia and sickle cell disease
We've been reporting on CRISPR for years @STAT. Here are the answers to your questions about Casgevy:
From 11 Nov: Mummified baboons point to the direction of the fabled land of Punt - Enlarge / Drawing of a trade expedition to Punt during the reign of Queen Hatshepsut. Note... https://arstechnica.com/science/2023/11/mummified-baboons-point-to-the-direction-of-the-fabled-land-of-punt/ #ancient-dna #ancient-egypt #archeology #baboon #dna #egypt #egyptian-mummies #genetics #science
Untangling the genetics that underlie our facial features.
@KnowableMag reports: "After turning up hundreds of genes with hard-to-predict effects, some scientists are now probing the grander developmental processes that shape face geometry."
Another interesting thing:
are you interested in researching the relationship between #vision and #sleep? we have a fully funded #PhD opportunity using classic #drosophila #genetics, #connectome and #scRNASeq to investigate! the student will be supervised by myself and Roberto Feuda @robertofeuda at @NeurogeneticsLeicester
please see further info here and BOOST!! #neuroscience
Looking for paper leads on: a genetic network w/ attractor states linked to brains
I'm fond of the approaches in this paper:
The gist here is to model a genetic network as a dynamical system with two attractor states (in this case, it's leukemia and the states are apoptosis on-versus-off).
I'm looking for leads to papers that apply this type of approach to model genetic networks (not neural circuits) that have something a bit more to do with the brain; ideally not cancer.
(This is not my field). Huntington's? Fragile X? Anything neuron related?
Thanks in advance!
I'd like to learn more about computational models of gene regulatory networks. Does anybody have pointers about that?
Boosts appreciated. :boost_requested:
To be more specific, I'm looking for something analogous to artificial neural networks. Something very simplified and easy to implement. Something that focuses on the causal / informational / computational properties of gene regulatory networks in general.
That's probably different from models of specific gene networks, or computational biology tools for studying the genes of real organisms.
How #Kelp Keeps a Record of Environmental Calamity https://undark.org/2023/10/31/bull-kelp-destruction/
Integrating kelp #genomics analyses and geological data to reveal ancient #earthquake impacts https://royalsocietypublishing.org/doi/10.1098/rsif.2023.0105
"On a coastal rock platform near #Rārangi, #NewZealand, the team stumbled on another pocket of odd kelp #genetics. The kelp, they found, shared the genes of a population from 300 kilometers away. Something had clearly happened here."
Some deaf children in China can hear after gene treatment
"Here’s the easy game Li Xincheng has been playing at home. Her mother says a few words. Then the six-year-old, nicknamed Yiyi, repeats what she heard. “Clouds, one by one, blossomed in the mountains,” says her mother, Qin Lixue, while covering her mouth so Yiyi can’t read her lips. “Clouds, one, one, blossomed..."
"He specialises in the study of sorghum, a popular source of food in Africa.
In 2009, Mr Ejeta won the prestigious World Food Prize for developing a sorghum hybrid that is resistant to both drought and the parasitic weed Striga, which commonly invades farms in Africa.
Sorghum is the fifth-most important cereal crop globally - after maize, wheat, rice and barley.
It is also the second-most important cereal in Africa” https://journa.host/@fulelo/111299738762399483
📢 My latest article has been published online ahead of print publication in Notes and Records: The Royal Society Journal of the History of Science.
'Mendel's Closet: Genetics, Eugenics and the Exceptions of Sex in Edwardian Britain' 🌈 🧬
Today's learning resource
Have you tried the CRISPR-based map that ties every human gene to its job function?
Supposed huge leak of 23andMe user data, stolen by hacker known as 'Golem'.
I and others did warn folk that this was bound to happen one day. So much of ourselves on other people's computers. Many plausible implications, if true.
🇵🇱 "Results showed that the level of differentiation within Polish population is quite low, but some differences were indicated. It was confirmed that the Polish population is characterized by a high degree of homogeneity, with only slight genetic differences being observed at the regional level."
Grochowalski, Ł. et al. (2020) 'Y-Chromosome Genetic analysis of modern Polish population,' Frontiers in Genetics, 11. https://doi.org/10.3389/fgene.2020.567309. #OpenAccess #OA #Science #Research #Polish #Population #Poland #Europe #Genetics #Analysis #Biology #Anthropology @science @anthropology
People of African ancestry are poorly represented in genetic studies. A new effort would change that.
AP reports: "Scientists are setting out to collect genetic material from 500,000 people of African ancestry to create what they believe will be the world’s largest database of genomic information from the population."
Many people of Jewish ancestry have been extremely concerned during recent years, as an unfolding timeline occurs with striking resemblance to pre-WW2 events in the USA and Europe.
This past weekend, at a rally in #SanFrancisco being held for anti-democratic Palestinian supporters, there were chants calling for genocide against the Jewish people and extremely #antiSemitic graffiti sprayed on two banks. 😔
Hey Mastodon! 👋 Here is our #introduction post: We are the Data Visualization Lab at Khoury College of Computer Sciences at Northeastern University. You can find more about our work here: https://vis.khoury.northeastern.edu/
A research team has said it has identified three genetically distinct populations of the Japanese honeybee through whole genome sequencing. https://www.japantimes.co.jp/news/2023/10/16/japan/science-health/japan-honey-bee-research/?utm_content=buffer8911a&utm_medium=social&utm_source=mastodon&utm_campaign=bffmstdn #japan #sciencehealth #tohokuuniversity #tokyometropolitanuniversity #genetics
23 and me has confirmed an attack on their data. Their product features the ability to find "DNA Relatives" Hackers guessed the weak password of a single user, then used the Feature to scrape Data from other users. They then posted a portion of this data online, claiming it contained the data of over 1-million Ashkenazi Jews & 100,000+ people of Chinese Descent. The group then started selling the data for $10 per account.
#Genetics firm #23andMe says user data stolen in credential stuffing attack
The initial data leak was limited, with the threat actor releasing 1 million lines of data for Ashkenazi people. However, on October 4, the threat actor offered to sell data profiles in bulk for $1-$10 per 23andMe account, depending on how many were purchased. https://www.bleepingcomputer.com/news/security/genetics-firm-23andme-says-user-data-stolen-in-credential-stuffing-attack/
23andMe User Data Stolen in Targeted Attack on Ashkenazi Jews
“The company said its systems were not breached and that attackers gathered the data by guessing the login credentials of a group of users and then scraping more people’s information from a feature known as DNA Relatives. Users opt into sharing their information through DNA Relatives for others to see.”
New review: Ancient DNA is an excellent intellectual history of this fascinating discipline that skillfully combines spicy interviews with serious science study.
The Food and Drug Administration authorized marketing of a genetic test for detecting hundreds of gene variants associated with a higher risk of developing certain cancers.
Caribbean Parrots Are Remnants Of A Millennial Scale Extinction | Florida Museum USFWS #forensics | PNAS
by @GrrlScientist via Forbes Science / Forbes
#SciComm #parrots #ornithology #genetics #paleontology #archaeology #museums #biodiversity https://www.forbes.com/sites/grrlscientist/2023/09/27/caribbean-parrots-are-remnants-of-a-millennial-scale-extinction/
Thomas Hunt Morgan was born #OTD in 1866.
He was an American evolutionary biologist, geneticist, embryologist, and science author who won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity.
During his distinguished career, Morgan wrote 22 books and 370 scientific papers. As a result of his work, "Drosophila" became a major model organism in contemporary genetics. via @wikipedia
☭🇨🇳 Hoard foreign DNA data globally, by "law"... :drake_like:
☭🇨🇳 Ban foreign access to CCP subjects' DNA... :drake_like:
☭🇨🇳 Polite suggestions of rank hypocrisy? :drake_dislike:
🔥 「Chinese law makes clear that any information collected using BGI’s machines can be accessed by the Chinese government. A national intelligence law enacted in 2017 stipulates that Chinese firms and citizens are legally bound to share proprietary information acquired in foreign countries whenever requested.
🔥 Since 2019, China has also overhauled the legal framework governing its own vast genetic resources, redefining them as a strategic national resource and tightly restricting access by foreign entities for reasons including national security. Under current Chinese law, foreign entities are banned from collecting genetic material in the country or moving such resources abroad.」
Also, crossover events between Y chromosome & X resulting in novel recombinations are a fucking thing, as are Barr Bodies & deactivation of chromosomes.
Dr. Ian Malcolm (Jeff Goldblum) Expertly describes [Complex Systems] & the unpredictability of emergent complexity in systems.
How these genetic variables & hormone products interplay w/brain development, self identity, processing of cultural norms, is an example of a highly variable outcome.
Unexpected link between pure mathematics and genetics discovered
"[T]he team of researchers (from Oxford, Harvard, Cambridge, GUST, MIT, Imperial, and the Alan Turing Institute) have discovered a deep connection between the sums-of-digits function from number theory and a key quantity in genetics, the phenotype mutational robustness."
A team of scientists say they've found evidence that early human ancestors went through a "prolonged, severe bottleneck" in which ~1,280 individuals capable of reproducing were able to sustain a population for about 117,000 years.
A global population maintained by only 1280 people? That's the size of a slightly larger-than-average high school. It's mind-boggling that they managed not to die out over 117,000 years.
The US security state is collecting DNA at the border and in the penal system and plundering commercial databases like geneology services people mistakenly assume are private so maybe finding out you're 17% $RACE isn't that important when you're helping to build a eugenics panopticon
FBI Hoovering (ha) Up DNA at a Pace that Rivals China, Holds 21 Million Samplea and Counting
#surveillance #militarization #genetics #police
Özti war nicht weiß.
Der Ivory-Man war eine "Lady".
Bin ja mal gespannt, was sonst noch so für Fehlannahmen über die europäische Vergangenheit ans Licht kommen.
Interesting #research email today. A while ago I took part in a study on visual pattern recognition, and just had a follow up email inviting me to more research.
I scored 100% which apparently puts me in the top 1% of people in the test. I wonder how much of this is #genetics (my eyes and brain) and how much may be influenced by practice. I’ve always been a #designer and have worked with colour, pattern & visual elements for 28 years (including education). #GraphicDesign
The glaciers of the last ice age left their mark on the genetic diversity of species across the globe
I finished my summer internship this week! I spent 4 months working with a team of biologists and statisticians at The Jackson Laboratory, building visualization software for their research needs. The lab I worked with focuses on analyzing genetics, the microbiome, and addiction-related traits. Here's an overview of some of the EDA tools I built for them in #Python ☺️ #genetics #biology #addiction #dataviz #computerscience #research #phd
If you're doing cool work with data vis + bio, lmk!
Our love of nature is highly individual and how we plan our cities and urban green spaces should take this into account, say scientists
Heredity And Early Experiences Are The Reasons People Love Nature | @GoteborgsUni & @_SLU | published in @Trends_Ecol_Evo
by @GrrlScientist via @ForbesScience / @Forbes
Tambets, K., Yunusbayev, B., Hudjashov, G. et al. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 19, 139 (2018). https://doi.org/10.1186/s13059-018-1522-1 #OpenAccess #OA #Article #Science #Demography #History #Language #Languages #Population #Genetics #PopulationGenetics #Genomics #Biology #Geography #Europe #Asia #Academia #Academic #Academics @science @biology
Regeneron Pharmaceuticals, a maker of synthetic biologic treatments, is acquiring Decibel Therapeutics, developer of gene therapies to treat hearing loss and balance disorders.
The Mystery Genes That Are Keeping You Alive - Nobody knows what around a fifth of your genes actually do. It’s hoped they could hold th... - https://www.wired.com/story/unknome-proteins-human-genome/ #science/health #genetics #science
Does anyone know what it was? I don't think I was dreaming!