Recently, Bram van Haastrecht, a MSc student from the Free University of Amsterdam (Vrije Universiteit Amsterdam) joined us for an internship! He will be working with our group and Mariana Gomez-Schiavon‘s here at LIIGH-UNAM on mathematical modelling of the MAP Kinase pathway, an important growth mechanism in acral melanoma and other cancers. We are excited to welcome him and we hope he has a great stay!
It’s been a few busy weeks at the CGBioLab! We started with our 4th Summer School, where students from the 1st and 2nd semester of undergrad will join us for the following eight weeks. They come from different schools (Excellence School at Jalpan de Serra, Qro., Tec de Monterrey and LIIGH-UNAM in Querétaro City) and they will be learning different wet lab and bioinformatic skills. We really hope they enjoy and learn loads! This school has been possible thanks to our star senior technician Christian Molina and the generous support from PASPCR and Colgate-Palmolive. Thanks a lot!
Students attending the summer school!
We are also preparing to teach two summer courses, one for the EMBL Cancer Genomics and Transciptomics course, coming up next week, and another one on Ensembl for the SMBE Annual meeting coming up in July. Our PhD students Patricia Basurto, Kenya Contreras and Estef Vazquez will be participating and teachers as well!
Thanks to the generous support of the Melanoma Research Alliance (USA), we are looking for a postdoctoral fellow to join our team to develop a project on identifying mediators of metastatic spread in acral lentiginous melanoma tumours! If you:
Then please see our our official recruitment ad! Please contact Daniela directly if you want to discuss this position. We will be receiving applications until June 30!
There have been some exciting news in the last few months in our lab, even though we have kept working from home! Some of these are:
Times are still challenging, and we are proceeding a bit more slowly with our research given the restrictions still in place. However, we are hopeful that we will be able to pick up the pace soon! Keep an eye open for future job postings, preprints and talks!
Screenshot from our last lab meeting, yesterday!
We are still working from home! It seems likely that we won’t be able to return to in-campus activities until next year, so we have adapted to work through Zoom and Slack! We have attended the 2020 AACR virtual Annual Meeting, participated in the 2020 virtual Genetics of Melanoma Consortium (GenoMEL) meeting, with Caro giving a talk on her PhD project, Daniela participating as guest in the new Your Digital Mentor podcast, and Christian and Daniela giving talks on their work for the BioScience App conference program. We are also meeting weekly and advancing our projects as much as possible.
Our PhD student Irving Simonin is also teaching a Bayesian statistics summer course to the wider LIIGH community, and we have been learning about conjugate models, Markov chain Monte Carlo and statistical software. We have also welcomed a new student, Rodolfo Arriaga, to do a virtual internship in our lab this semester.
We hope everyone is keeping safe to the extent of what’s possible during these difficult months, and hope that soon it becomes possible to meet our collaborators and friends in person again.
Caro Castañeda finishing her talk at the 2020 international GenoMEL meeting
Christian starting his talk at the 2020 BioScience App seminar series
CGBio lab members looking very focused during virtual lab meeting….
Hello everyone, an update from our lab during these difficult times…. We have had to interrupt all of our wet lab work (as the vast majority of labs in affected places have had to do!), but we are still trying to work remotely (when time permits, as of course new challenges have emerged with the lockdown situation). However, some good news: we are happy that a review we worked on for a very long time is now out on Pigment Cell and Melanoma Research! Click here to read “Acral lentiginous melanoma: Basic facts, biological characteristics and research perspectives of an understudied disease“, by Basurto-Lozada et al., it’s open access!
We have also found that a social session twice a week where we can play online games (those by Jackbox.tv are amazing!) and chat about non-work stuff goes a long way. Hopefully the situation will improve soon but for now, please take care and enforce social distancing rules whenever possible, and take care of your mental health!
Christian Molina (far right) with members of Patricia Possik’s group (third from right to left) in Rio de Janeiro, Brazil
We have been active during this month! Postdoc Christian Molina is undergoing an internship at Patricia Possik’s research group, based at the Brazilian National Cancer Institute in Rio de Janeiro, where he is learning the details and protocols for the establishment of PDX models. These are animal models of human tumours that allow us to follow their evolution in vivo, and to test potential therapeutics – in our opinion, very important work for Latin American patients suffering from acral lentiginous melanoma. This is in the context of a collaboration enabled by our Medical Research Council grant, to whom we are very thankful for providing these learning opportunities.
Also, Daniela has been in Lima, Peru, participating as an invited speaker in the International Symposium on Immunology and Biotchnology, organised by the Peruvian Institute of Health. She discussed methodologies for identifying genes associated to disease, especially our work in melanoma, and you can watch her talk here. Next week, she will attend the Scientific Retreat of the Melanoma Research Alliance, in Washington, DC where she will chair a roundtable discussion and participate in the Melanoma Models Workshop.
Back at home, the other members of the CGBio group have been busy preparing a couple of book chapters and a review. We hope to be able to share them with you soon!
We are super pleased for our first alumnus, Isaac Garcia, who did his BSc thesis in our lab! He got an offer for a very comptetitive, fully-funded PhD position at the Sanger Institute, which he has accepted and will start in October! He is an excellent student and we wish him the very best in his future, and hope to keep in touch 🙂
Another year has passed and it’s the time of the year when we think about what we’ve achieved, where we need to improve and our objectives for the year to come. During 2019:
Our Christmas tree made from wooden boxes and Poinsettias at the entrance of LIIGH!
For 2020, we are hoping to see our first PhD students graduate, and finally see the first projects from our lab develop, after a few years in the making! We are also hoping to expand our new liver cancer research line and form new collaborators in this area.
Here’s to a great 2020. Happy holidays and see you next year! 🙂
It’s been a while since we’ve posted an update, but that’s because the lab has been very busy this first part of the year! Here are some events that have happened:
Profs Julia and Tim and Drs Mark and Daniela with the attendants of the “Statistics for GWAS” course
– In January, Daniela participated as an instructor of the Next Generation Sequencing Bioinformatics course that took place during one week in Santiago de Chile, Chile. Caro Castañeda, a PhD student in the lab, attended as a course participant.
– In March, we hosted Prof. Julia Newton-Bishop, Prof. Tim Bishop and Dr. Mark Iles, from the University of Leeds in the UK, who came for a week to teach a course on Statistics for GWAS as part of our Newton Advanced Fellowship. We had participants from several schools at UNAM, as well as students and postdocs from other entities and states in Mexico.
– In April, our first alumnus, Isaac García, started his MPhil in Genome Sciences at the University of Cambridge (Sanger Institute)! Also, Daniela spoke at the 16th GenoMEL Annual Meeting in Athens, Greece, on the lab’s wet lab project investigating the effect of particular germline variants on melanoma risk.
– In May, Daniela spoke at the 11th European Melanoma Workshop in Otranto, Italy, on the lab’s project investigating acral lentiginous melanoma development in Mexico and Latin America, and in the Liquid Biopsy Symposium organised by INMEGEN, Mexico, on the analytical and bioinformatics challenges for the analysis of liquid biopsy specimens. Also, our guest Dr Heinz Arnheiter, scientist emeritus at NIH, arrived to our lab as a visiting professor. Heinz will stay for 2.5 months giving lectures to our academic community on various biological phenomena and interacting with students and postdocs.
– And finally, during June, our PhD student Caro started her academic internships attending the IARC Summer School on Cancer Epidemiology in Lyon, France. She will then visit our collaborators’ labs at the University of Leeds, UK, and then she will undertake a 2-month internship at Prof Ludmil Alexandrov’s lab at UCSD, part of our UC Mexus award investigating the somatic effects of genetic variants in melanoma patients. Also, Daniela spoke at the Noreen O’Neill Melanoma Research Symposium, which took place at The Wistar Institute in Philadelphia, PA, USA.
Also, the first official publication from our lab was published in Bioinformatics! VCF/Plotein is a web application that allows biologists, clinicians and bioinformaticians to prioritise and filter genetic data in the VCF format by displaying information graphically and interactively! Take a look at the paper and the website! You can also see other work that we have participated in in the Publications section.
We also got notification that CONACyT, Mexico’s Council for Science and Technology, will fund us through two awards: One to investigate the transcriptomic profiles of acral lentiginous melanoma tumours from Mexican patients (from the Health Sectoral Fund), and another one led by postdoc Christian Molina to start a new exciting collaboration with Dr Mauricio Díaz at the Neurobiology Institute at UNAM (from the Basic Scientific Research Sectoral Fund). This exciting grant will allow us to expand the repertoire of cancer types we study to investigate by transcriptomic analysis the effects of caloric restriction on liver cancer, which is the fourth most common cause of death from neoplasia in Mexico. This project is a follow-up of work that Christian did during his PhD (you can read the main paper here).
This may be all for the time being – we will try to update our website more frequently from now on! 🙂
