The Genomics Lab

Transposons and epigenetic priming of enhancers within early human embryo development with Dr Christopher Todd Apr 13, 2022

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

Neuroscience meets epigenetics - Doctor Ben Rein Feb 18, 2022

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

Spatial transcriptomics with Dr Patrick CN Martin Dec 08, 2021

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/

Epigenetics & fertility with Alka Gupta Nov 17, 2021

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/

Biomarkers in genomics with Dr Paul Okunieff Oct 27, 2021

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.

The dark matter of the genome with Sudarshan Pinglay Oct 06, 2021

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!

The immune system: B cells and Epigenetics with Dr Hamish King Sep 22, 2021

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.

Epigenetic biomarkers of exposure to tobacco smoke : A biosocial approach with Alexandria Andrayas Sep 08, 2021

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

Dissecting the binding mechanisms of Transcription Factors to DNA with Dr Patrick CN Martin Aug 25, 2021

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

Remote control of gene expression: enhancers and the 4D genome with Professor Wendy Bickmore Aug 11, 2021

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

Rattlesnakes and Population Genomics with Kat Ivey Jul 28, 2021

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

Making connections between epigenetics and evolution with Dr Peter Sarkies Jul 14, 2021

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

Epigenetic regulation in neurodegenerative diseases with Dr Sarah Marzi Jun 30, 2021

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

DNA nanotechnology with Dr Andrew J Lee Jun 16, 2021

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

Non-CG Methylation and its Role in Development with Dr Ozren Bogdanovic Jun 09, 2021

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.

The association between socioeconomic factors, the methylome and heart failure with Dr Mark Pepin and Dr Adam Wende May 19, 2021

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

Extrachromosomal circular DNA, chromosome evolution & circular DNA in human disease with the Regenberg Lab (Dr Birgitte Regenberg and Dr Sam Keating) May 12, 2021

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/

Single Cell Technology Development and Spatial Omics with Dr Cátia Moutinho May 05, 2021

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

The importance of DNA damage in all areas of disease and the potential for personally tailored oncological treatments based on the analysis of DNA damage using machine learning, with Dr Anna Poetsch Apr 28, 2021

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

Cancer epigenetics & the role of Ybx1 in fine tuning PRC2 activity to control embryonic brain development with Dr Myron Evans Apr 21, 2021

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

The role of Yq-linked genes in fertility and offspring sex ratio with Dr Peter Ellis Apr 14, 2021

We're back after the Easter Break with an extremely interesting episode with Dr Peter Ellis from the School of Biosciences at the University of Kent! Dr.Ellis is a Lecturer in Molecular Genetics and Reproduction at the University of Kent. His research thus far has involved the identification of novel genes on the mouse Y chromosome that affect sperm head shape and fertility; the discovery of a genomic conflict between the mice sex chromosomes as they compete to influence offspring sex ratio. Also the identification of mechanisms regulating meiotic and post-meiotic transcriptional silencing of the sex chromosomes. His lab investigates the molecular biology of reproduction, the conflicting roles played by sex-linked genes in regulating this process, and the relationship between DNA damage repair mechanisms and the checkpoints governing meiotic progression.

Find Peters profile here where you can access his publications

Connect with Peter on twitter here

DNA methylation & epigenetic reprogramming during development with Dr Maxim Greenberg Mar 31, 2021

Join us today as we speak to Dr Maxim Greenberg, located at the Institut Jacques Monod in the heart of Paris. IJM is one of the premier institutes for fundamental research in the life sciences in France. Maxim's lab aims to better understand the epigenetic consequences of DNA methylation during a specific window of development which occurs in the first week of embryogenesis but ripples throughout life. Another aim of the Greenberg lab is to better understand what DNAme is doing when it is not at promoters? And its corollary: how do promoters stay DNA methylation free?

Today we discuss several of Maxims publications (linked below), the function of DNA methylation and the process of DNA methylation deposition and removal. Maxim also gives us an interesting insight into the details of how his lab aim to better understand epigenetic reprogramming in development.

Connect with Maxim on twitter

Maxims Lab website

Publications discussed in todays episode are linked below:

Greenberg M.V.C. (2021) Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Frontiers in Cell and Developmental Biology

The diverse roles of DNA methylation in mammalian development and disease.

The Role of Mitochondrial Quality Control Pathways in Familial and Non-Familial Variants of Disease, with David Tumbarello Mar 24, 2021

Join us today as we speak to Dr David Tumbarello, from the University of Southampton, as he talks to us about his dynamic and varied academic career that has taken him from New York, to Southampton, stopping off at a number of places in between!! David's lab currently focuses on understanding the cellular mechanisms and molecular machinery required for subcellular trafficking of membrane associated and cytosolic cargo via endocytosis and autophagy. Knowledge of these mechanisms is critical for understanding the molecular mechanisms of cancer and neurodegenerative diseases , which stem from defects in various membrane trafficking and cell signalling pathways.

Today we discuss one of David's lab's recent papers, published June 2020, which looks at multiple mitochondrial quality control pathways that exist to maintain the health of mitochondria, the mitochondrial stress response and identify the interaction of molecules associated with this response with E3 ubiquitin ligase Parkin - involved in Parkinson's disease.

Read the paper here: https://eprints.soton.ac.uk/438725/

Find David on Twitter here: @DavidTumbarello

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

Evolutionary genomics- exploring the genomic basis of biological adaptations and transitions with Dr Jordi Paps Montserrat Mar 17, 2021

In today's episode, we speak to Dr Jordi Paps-Montserrat, lecturer in the School of Biological Sciences at the University of Bristol. Jordi did his PhD at the University of Barcelona, before completing his post-doc at the University of Oxford. We talk with Jordi today about his work on evolutionary genomics, and how we can elucidate biological adaptations and the origins on animals and plants throughout evolution by looking at the genomic and molecular pathways underlying these evolutionary shifts.

Contact Jordi here: jordi.paps@bristol.ac.uk

Jordi's Twitter: @JordiPaps

View Alex's paper, which Jordi discusses, here: https://linkinghub.elsevier.com/retrieve/pii/S0960982219315957

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

Genomic analysis of the Ashanti Dwarf pig of Ghana and Sustainable agricultural production utilising genomic tools with Sethlina Naa Dodua Aryee Mar 10, 2021

Join us today as we speak to an inspirational Woman in STEM, Sethlina Naa Dodua Aryee, raised in Ghana, who moved to the University of Cambridge to complete her PhD in sustainable food production through the use of genomic and bioinformatic tools - a global issue that she has been passionate about for her whole life. Sethlina speaks to us today about her research into the genomics of the indigenous Ashanti Dwarf pig, following cross-breeding of the indigenous species with some overseas species, as well as the differences between studying in Ghana and the UK. The indigenous Ashanti dwarf pig is hugely disease-resistant, so it is of great importance to harness this trait for sustainable food security.

Email Sethlina here: snda2@cam.ac.uk

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

Celebrating Women in STEM for International Women's Day, with Dr Louise Beard and Dr Michelle Taylor: Bonus Ep2 Mar 08, 2021

In order to celebrate International Women's Day 2021, we have picked two inspirational role models at our University and invited them to speak to us about their experiences of being a woman in science. We learn about their varied and exciting careers, and then we discuss all of our personal experiences of being a woman in science - from how we were inspired into the field, what we feel are the biggest barriers and how to overcome them, as well as some really great advice from both Dr Louise Beard and Dr Michelle Taylor on all stages of the academic journey. We are very lucky at the University of Essex to be working within a hugely inclusive and supportive environment, but it is important to recognise not all women are this lucky. We discuss the Athena Swan charter, an initiative in academia and the workplace to increase equality for all people, in all roles, and how some of the specific action plans within the charter have directly impacted the University of Essex in order to make it a more inclusive workplace.

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

CTCF binding, nucleosome positioning and 3D chromatin organization with Dr Christopher Clarkson Mar 03, 2021

In today's episode, we are excited to be talking to Dr Christopher Clarkson, currently based at UCL, where he has just started a post-doctoral research position.

In 2020, Dr. Clarkson completed his PhD at the University of Essex where he investigated changes of nucleosome positioning and 3D chromatin organization! In today's episode, we discuss how CTCF binding strength correlates with nucleosome repeat length and what the implications are of this on gene regulation. We further discuss how regions in the genome where CTCF is able to bind are extremely important for cellular differentiation and boundary formation within the genome.

Email: c.clarkson@ucl.ac.uk

Chris' Nucleic Acid Research article: CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Twitter: find Chris on twitter here.

Check out Biobox Analytics here, the ideal platform for working with NGS data, running and designing bioinformatic pipelines and generating the perfect plots: https://biobox.io/

Designer Babies, Disseminating Science, and Dinosaurs with Professor Darren Griffin Feb 24, 2021

In today's episode, we are privileged to be speaking to Professor Darren Griffin, who is currently based at the University of Kent, where he is the director of the Centre for Interdisciplinary Studies of Reproduction, and Professor of Genetics.
Darren is President of the International Chromosome and Genome Society, and is a world leader in the field of cytogenetics, performing the first successful cytogenetic preimplantation genetic diagnosis, as well as playing a large role in the development of a universal test for genetic disease in IVF, known as karyomapping. Darren also sits on the faculty of CoGen (controversies in genetics), so we were able to have some really interesting discussions with him, not only on the scientific side of his work but also on the ethical implications.

In addition to talking to us about his hugely exciting research, we also hear from Darren about his experience in science communications. Darren is passionate about making scientific research publicly accessible, and has authored a book (available: https://www.amazon.co.uk/Preimplantation-Genetic-Testing-Advances-Reproductive/dp/1138333301), as well as taking part in 2 documentaries. Darren also has some very exciting other endeavours on the horizon, and we speak to him about his upcoming 6-part documentary series for young adults, as well as a course he is involved with that is taking some of this pioneering IVF research over to Dubai, to teach students there.

Email: D.K.Griffin@kent.ac.uk

Website: http://www.kent.ac.uk/bio/griffin/

Twitter: @darrenkgriffin

Instagram: @profdazzy

Running a genomics core facility and discussing careers in genomics - Nicky Hales Feb 17, 2021

Don't miss today's episode, as we are joined by Nicky Hales, who runs a Genomics Core Facility in Texas! This episode is a little different to usual, as we are focusing more on a genomics based career path, and excitingly, it's a career path we did not know much about - so it was a real learning curve to talk to Nicky. Nicky explains to us how she found herself in this position, what a Core Facility is (we had no idea before chatting to Nicky!), the significance of core facilities, and what a typical day looks like for Nicky. We discuss some of the techniques that Nicky runs at her facility, how she learnt all about how to perform each technique, and her favourite techniques (as well as the ones she doesn't enjoy quite so much..!).

If you have any further questions, don't hesitate to contact Nicky:

Google Scholar: Nicole Hales

Twitter: @nicky_rosemarie

IG: @nicky.rosemarie

Email: nicole.hales@unths

Social media in academia and networking as a PhD student - Joseph Festa and Brad Richardson (Bonus Ep1) Feb 10, 2021

Something a little different - our first BONUS episode. Today we talk to Brad and Joe about our experience of using social media as a networking an science communications tool. Brad and Joe briefly introduce their research (for once, not genomics......) and we then discuss the pros and cons of a number of social media platforms, as well as the power of social media as a networking and opportunities tool. We had so much fun filming this episode, so we hope you enjoy listening to something a little more relaxed than the usual hardcore science!

Contact Joe: Twitter @festafitness or Instagram @festa.science or listen to his podcast The Research Lounge!

Contact Brad: @Twitter B_D_Richardson or Instagram @the.neuro.scientist

Epigenetic biomarkers of exposure to tobacco smoke : A biosocial approach - Alexandria Andrayas Feb 03, 2021

Welcome to Episode 6 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

Using explainable AI to understand the enhancer histone modification code - Jareth Wolfe Feb 03, 2021

Welcome to Episode 5 of The Genomics Lab! On today's episode we talk to Jareth Wolfe who is a final year PhD student at the University of Essex. We talk to Jareth today about his work on using explainable artificial intelligence models in order to identify enhancers in DNA. Jareth explores the link between histone modifications and enhancers, explains the importance of enhancers, and gives us an insight into how his model was developed and trained to identify these enhancers. We also discuss with Jareth what benefit his model brings over other methods of identifying enhancers. Contact Jareth: jw18713@essex.ac.uk Twitter: @jareth_wolfe

How neuroepigenetics can help us to better understand spinal cord injury -Jess Chadwick Jan 20, 2021

Welcome to Episode 1 of The Genomics Lab! On today's episode we talk to Jess Chadwick who is a third year PhD researcher at Imperial College London. She is doing her PhD in molecular neuroscience, investigating the molecular mechanisms of axonal regeneration after spinal cord injury. Jess talks to us about how axonal injury in the spinal cord usually results in no regeneration, but how in the peripheral nervous system, neurons can re-grow and regenerate to a certain extent. Jess explains how her research aims to study the regenerative mechanisms in peripheral neurons, and identifying which molecular targets need to be activated to achieve regenerative effects, which become promising targets for boosting spinal cord regeneration. We also discuss the role that epigenetics plays in this neurological research. Jess predominantly works in the mouse nervous system, and she discusses with us some of the limitations, ethical considerations and benefits of a mouse model for this line of research. Jess will welcome any questions or feedback so we have provided her contact information below. Hope you all enjoy our first episode! (See below for links)

Jess's twitter: https://twitter.com/J ess_Chadwick

Jess's email: j.chadwick17@imperial.ac.uk

Jess's academic Instagram: https://www.instagram.com/neuro.genomics.jess/

Identifying genetic variants for inherited retinal disease - Laura Whelan Jan 20, 2021

Welcome to Episode 3 of The Genomics Lab! On today's episode we talk to Laura Whelan, who is a PhD researcher at the School of Genetics & Microbiology at the Trinity College Dublin. Laura is part of the Target 5000 programme; the first large-scale study to apply next generation sequencing to the Irish inherited retinal diseases (IRD) patient population. Laura discusses with us some of the causes of IRDs, the different types of IRD, the kind of inheritance involved in these diseases, and how her lab and the Target 5000 initiative use sequencing techniques to both discover novel genetic variants, and validate previous findings of genetic variants involved in the cause of IRDs. Laura discusses the impact of IRD on quality of life, the scale of the problem and the future of this work in terms of improving the diagnostics of IRDs.

Laura's twitter: https://twitter.com/PhD_With_LauraLaura's research paper: https://www.mdpi.com/2073-4425/11/1/105/htmLaura's Instagram: https://www.instagram.com/phd_with_laura/

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