The Genomics Lab

In today's episode I spoke again to Dr Christopher Todd from the Babraham institute. Chris is a postdoctoral researcher in Wolf Reiks lab who talked to me about transposable elements and epigenetic priming of enhancers with human embryonic development. Chris gave a great talk at GREECS 2022 where he discussed his research and I absolutely loved his talk, so immediately messaged him to join me on the podcast! If like me, you feel unclear on what exactly are transposable elements, the details of their function & classification and want to learn more about enhancer priming, stay tuned to learn lots! Even if you do know these things, I guarantee you will still learn so much from Chris! Hope you all enjoy! Chris' twitter: https://twitter.com/C_D_Todd Reik lab twitter: https://twitter.com/ReikLab Chris profile on Babraham website: https://www.babraham.ac.uk/people/member/746 Google scholar: https://scholar.google.com/citations?user=WPqJa6QAAAAJ&hl=en

TGL made it to 2022! On todays episode, I spoke to Dr Benjamin Rein, a neuroscientist all the way from Stanford. We speak all about Bens experience of science communication on social media, Ben uses Tik Tok & instagram to make awesome short videos on scientific papers and topics and has gained a following of +600,000 on tik tok! He also talks all about his passion for neuroscience, his PhD research and then we talked a lot about stuff we dont know a lot about! Hope you enjoy this conversation & be sure to check Ben out on social media using the links below! Bens tik tok - https://www.tiktok.com/@dr.brein?lang=en Bens instagram - https://www.instagram.com/doctor.brein/?hl=en Bens website - https://www.benrein.com

In today's episode I spoke again to Dr Patrick CN Martin from the Biotech research and innovation centre at the University of Copenhagen, about spatial transcriptomics. Patrick is a post doctoral researcher who has been working on ST and more specifically, this pre print which we also took a deep dive into, on todays episode! Patricks new tool, named Vesalius (stay tuned to find out why) is able to decipher tissue anatomy from ST data by converting transcriptomic information into a color code for image segmentation. The tool is able to successfully detect tissue architecture in mouse embryo and brain from high resolution ST data by incorporating image processing algorithms. Vesalius is a tool to perform high-resolution in silico anatomization and molecular characterization from ST data. If like me, you feel unclear on what exactly is ST and how it works, stay tuned to learn lots! Even if you do know what ST is, don't worry! once Patrick taught me all about ST, we took a deep dive into the pre print, and discussed so many interesting topics. Patricks twitter: https://twitter.com/pcnmartin The pre print: https://www.biorxiv.org/content/10.1101/2021.08.13.456235v2 GREECS registration : https://whova.com/portal/registration/early_202201/

This week I spoke to Alka Gupta. Alka has just finished up her PhD and begun her postdoctoral position at UCSC in the Sharma Lab where she is now working on epigenetic inheritance. Today we spoke about her PhD research in which she was looking at the role of microRNAs in male infertility. We learnt about Sertoli cells, spermatogenesis and shrinking testis! Tune in to find out more! Contact Alka here: https://twitter.com/alka_gupta__ GREECS registration link: https://whova.com/portal/registration/early_202201/

Today I speak to Dr Paul Okunieff , founder and consultant of Diacarta. DiaCarta is a leading translational genomics and personalized diagnostics company based in California. DiaCarta provides highly sensitive and advanced technologies aiming to change the landscape of precision medicine and molecular diagnostics by impacting healthcare treatment plans and the well-being of individuals around the world. Today me and Paul chat about the use of biomarkers in genomics, we touch on his recent coauthored papers in nature scientific reports here . We also discuss some ethical issues behind biomarkers and how events like 9/11 led Paul to pursue his career in this field. Please visit Diacartas website here to find out more about them and connect with them on LinkedIn here .

On todays episode, I speak to Sudarshan Pinglay, a PhD student from NYU medical center. Sudarshan is involved in the dark matter project- we talk about the dark matter of the genome, where introns, repetitive and regulatory elements reside. Sudarshan works specifically on the HOXA locus. The Hox family of genes pattern the head to tail axis in the developing embryo. In mammals, there are are four separate clusters (HoxA,B,C and D). Both space and time of Hox gene expression is colinear to their sequence in the genome. Loss of this leads to serious defects. Sudarshan talks about his wet lab and dry lab work, where he has been using the HoxA cluster as a model to understand how the expression of Hox genes is regulated in order to pattern the developing nervous system. He tells us about his work aiming to build the HoxA cluster from the ground up so that he could manipulate the various players that have been implicated in Hox gene regulation and understand the pattern of Hox gene expression and embryonic development. This is the pre print we discussed in todays episode, and more on the dark matter genome project can be found here. Sudarshan can be found on twitter here !

In todays episode, I speak to Dr Hamish King, a Sir Henry Wellcome Fellow affiliated with the Blizard Institute at Queen Mary University of London. Hamish is interested in how errors in gene regulation lead to changes in the behaviour and function of B cells, an important cell type in our immune system that makes antibodies to fight and remember infections. Hamish talks about how he uses wet lab and bioinformatic techniques to answer these questions. Dr King is also due to become a laboratory head at WEHI in early 2022, where his lab will focus on answering a range of questions including: How immune-specific chromatin-based mechanisms regulate gene expression Whether autoimmune-associated genetic risk loci disrupt regulatory function of enhancers If disease-specific epigenomic networks exist in autoimmunity We talk also in the episode, about Hamish's recent paper which is accessible here , you can also find Hamish on twitter here where he is happy to be contacted further about his research and upcoming vacancies in his brand new lab.

Welcome to Episode 29 of The Genomics Lab! On today's episode we talk to Alexandria Andrayas who is a PhD candidate in the Soc-B Centre for doctoral training which is a new and unique programme in biosocial research. The programme is funded by the Economic and Social Research Council and the Biotechnology & Biological Sciences Research Council. It combines the strengths of the University of Essex, Manchester and UCL. The impact of smoking on health can be mediated through several biological pathways and it is well documented that smoking can be linked to large differences in DNA methylation as Alex discusses today. We also discuss the need and importance of giving consideration to the role that society may play in studies such as these. Stay tuned to find out more about epigenetics, DNA methylation and biosocial research. Contact alex here: https://www.iser.essex.ac.uk/people/aandra My preprint: https://www.biorxiv.org/content/10.1101/2021.09.02.458717v1

Welcome to Episode 28 of The Genomics Lab! On today's episode we talk to Dr.Patrick CN Martin who is a postdoctoral researcher at the University of Copenhagen. He completed his PhD in Dr Radu Zabets lab in 2020 where he investigated the binding mechanisms of transcription factors to DNA. His research involved development of an R package, ChIPAnalyser. A user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of transcription factors to DNA. His research focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). Aside from his research, Patrick enjoys coding, astrophysics and is now working in the exciting field of spatial transcriptomics! We also discuss the use of clinical data in genomics research, learning to code and bioinformatics. Hope you all enjoy! (See below for links) Patrick's twitter: https://twitter.com/pcnmartin Patrick's paper: https://www.sciencedirect.com/science/article/pii/S2001037020304736?via%3Dihub ChIPAnalyser Bioconductor package: https://www.bioconductor.org/packages/release/bioc/html/ChIPanalyser.html

This week we are honoured to host Professor Wendy Bickmore, the Director of the MRC Human Genetics unit at the University of Edinburgh. Wendys research laboratory focuses on trying to better understand the 3D organisation of the genome, and how this controls how the genome functions during normal development. They are further interested in how this may be perturbed into disease. Wendy talks to us about some of her recent work which has been extremely important for better understanding enhancer function and also, some of the challenges and questions which remain to be answered in the field. She also provides some great insight into the experiments and methods ongoing in her lab now. Find Wendy on twitter here : https://twitter.com/wendy_bickmore Find out more about Wendys laboratory here: https://www.ed.ac.uk/mrc-human-genetics-unit/research/bickmore-group

Welcome back! Today we are talking to Kathleen Ivey, a PhD student from the University of Texas at Arlington in the Castoe Lab. Kat talks to us all about her journey to her PhD, with a background in vet tech & herpetology. Kat now focuses on population genomics, with a particular interest in Rattlesnakes. She tells us all about being out in the field collecting the species right through to the laboratory investigation of gene expression! Find links to Kats socials below! Kats twitter: https://twitter.com/KatIvey2 Kats publications : https://scholar.google.com/citations?user=wVZuQykAAAAJ&hl=en Kats instagram: https://www.instagram.com/blondetravelingcircus/?hl=en

Welcome back for another episode! This week we chat to Dr Peter Sarkies from Imperial College London / MRC LMS! Peter is a senior lecturer running his own laboratory which aims to make connections between epigenetic gene regulation and evolution. Peter talks to us all about his research involving investigation of a wide range of epigenetic pathways including small RNA's such as Piwi interacting RNAs (piRNAs), DNA methylation and histone modification. Talking about RNAs is a first for us on the podcast, so we really enjoyed listening to everything Peter had to say! Publication relevant to todays discussion: https://www.nature.com/articles/s41559-020-01293-z?proof=t Blog post relevant to todays discussion: https://lms.mrc.ac.uk/epigenetics-evolution-in-the-fast-lane/ Lab website: https://psarkies.wixsite.com/epievo Contact Peter on twitter here: https://twitter.com/PSarkies

On todays episode, we talk to Dr Sarah Marzi from Imperial College London all about her work into the epigenetic regulation in neurodegenerative diseases like Alzheimers and Parkinsons. Sarah tells us about her journey into this field and describes what exactly neurodegenerative diseases are?! She also talks to us about her contributions to the field so far, including her work on epigenetic modifications, more specifically histone acetylation differences in people with and without Alzheimers and what these histone modifications mean for gene regulation. She also tells us all about the current and future plans for her research and her lab, which sounds very promising and exciting. Contact Sarah on twitter here: https://twitter.com/sj_marzi Read the paper in nature neuroscience here: https://www.nature.com/articles/s41593-018-0253-7?WT.feed_name=subjects_dementia

This week we took a slight detour away from our normal topic of conversation (Genomics) and immersed ourselves into the world of DNA nanotechnology with Dr Andrew J Lee, the centre manager of the Bragg Centre for materials research. Andy is a weaver of DNA and nanoscale filmaker in the Bioelectronics group. He develops nanostructures that are self assembled from DNA molecules to template, control and study a variety of single biological entities and inorganic processes. We spoke about Andrews academic background, what DNA nanotechnology is, its methods AND its applications. This episode was so fascinating and Andy explains a very complex topic in a very simple and accessible way! If you're keen to hear more about DNA origami and smiley face emojis made out of DNA, then stay tuned! You can contact Andy via twitter here : https://twitter.com/AndrewJLee90

Our second guest from the Garvan Institute of Medical Research in Sydney, is DrOzren Bogdanovic. We are so privileged to talk today to Ozren about his work in developmental epigenetics which covers how DNA methylation participates in diverse developmental processes, and how deposition and removal of the methylation mark impacts upon embryonic and germline integrity. We discuss his recent publication on non-CG methylation at satellite DNA repeats - something a little different this week! Widespread non-CG methylation occurs in mammalian embryonic stem cells and in the brain. In mammals, it is found at CAC trinucleotides in the nervous system, and is associated with transcriptional repression. It is found at CAG trinucleotides in embryonic stem cells, and CAC methylation is a known conserved feature of adult vertebrate brains. However, in his recent work, Ozren describes how, as opposed to any of these established methylation signatures, a novel form of non-CG methylation occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, and is critical for development. Ozren also discusses enzymes responsible for this observed novel methylation mark. We hope you enjoy listening as much as we enjoyed talking to Ozren. Ozren's recent publication we discuss can be found here . If you want to find out more, contact Ozren on Twitter or via ">email .

On todays episode we speak to Dr Adam Wende and Dr Mark Pepin! We discuss their recent publication which has been all over twitter recently! During the research, they identified an association between socioeconomic factors, the methylome, & heart failure. We discuss all of the motivations, methodological techniques and interesting findings from the study! Adam and Mark previously worked together, with Adam being Marks doctoral supervisor, but they tell us about their common interest for running & the future plans for their research and careers. Stay tuned to find out more. Find the publication here: https://journals.physiology.org/doi/full/10.1152/ajpheart.00036.2021 Contact Adam here: adamwende@uabmc.edu or https://twitter.com/AdamWende Contact Mark here: pepinme@gmail.com or https://twitter.com/MarkEPepin

In today's episode we speak to Dr Birgitte Regenberg and Dr Sam Keating from the Regenberg Lab, University of Copenhagen, about extrachromosomal circular DNA and it's significance in human disease. Circular DNA originates from chromosomes but differs from linear chromosomes as they mostly don’t have centromeres - so if a gene is trapped on a circle, it can amplify its copy number to much above the normal 2 copies in a few cell cycles. If the gene is expressed, this means that much more protein is produced than it should be. The Regenberg lab aims to understand how circular DNA is formed, maintained and how it affects the biology of the cell - thereby looking at eccDNA growth advantages or disadvantages in things such as aging and cancer. Contact the lab here https://twitter.com/regenberg_lab Find the labs website here https://www.regenberglab.net/

We've reached episode 20!!! In celebration of our twentieth episode, we are speaking today to Dr Cátia Moutinho about single cell sequencing and spatial omics - two up and coming techniques that everyone seems to be talking about at the moment. Cátia is Group Leader of the Single Cell Technology Development in the Garvan Institute in Sydney, Australia. The aim of Cátia's lab is to perform and optimise single-cell-related experiments, to develop the latest methods and approaches in molecular cellular genomics. We talk today about the importance of the development of these techniques, how her lab works, and why these techniques are so 'in demand' at the moment. Contact Cátia here Cátia's Twitter Cátia's LinkedIn https://www.catiamoutinho.com/ Listen to Ellie's 3-Minute-Thesis here Listen to Liv's 3-Minute-Thesis here

This week we speak to Anna Postsch. Anna is a group leader at the biotechnology center at the University Dresden! Her group employs computational techniques and machine learning approaches to assess and model DNA damage and repair processes, mutagenesis and genome editing to develop clinical applications. We also had some interesting conversations about taking machine learning methods into medicine and the security and trust surrounding machine learning. Dr Poetsch also discusses her diverse background and interesting career journey to her current position!! Listen along to find out all about her academic background, her research and insight into applying ML in the biomedical world. Anna's Biotechnology centre website can be found here Anna's research group Anna's published article on the novel coronavirus variant can be found here

On this weeks episode we are discussing Cancer and developmental biology in genomics with Dr Myron Evans! Myron is currently a post doctoral research fellow at St Judes Childrens research hospital in Memphis, Tennesse! Myron discusses with us his journey into cancer biology and shares a unique perspective of life working at a research hospital. He tells us all about his work into Ybx1 and how it fine tunes Polycomb repressive complex 2 activity to direct embryonic brain development. Additionally, Myron fills us in on all the cool techniques and methods he has used during his research! Access Dr.Evans Nature communications paper here: https://www.nature.com/articles/s41467-020-17878-y Connect with Myron on twitter here: https://twitter.com/myron_evansPhD