Hi, I’m Katherine and I’m currently Bioinformatics Manager at the Natural History Museum in London. In November, I will be moving to Northumbia University as Vice Chancellors Fellow in Bioinformatics. My research focuses on the analysis and systematic integration of largescale omics data and the development of approaches for the analysis of next generation sequencing data, with a focus on evolutionary genetics.
I originally studied Molecular Biology as an undergraduate at Newcastle but, due to a lack of jobs in the area at the time and following a disappointing third year project, I spent the next few years outside of science: managing a pub and restaurant (great fun, poor pay), and then working as an administrator for the Civil Service (better pay, mind-numbingly boring).
Eventually my love of biology and computing science led me back to Newcastle to the, then relatively new, MRes Bioinformatics course. I subsequently stayed to do a PhD in Computing Science (during which I was lucky enough to be one of the first Computing Science PhDs in the UK to do laboratory work during my project). As a Post-Doc I worked on a diverse range of project; from data analysis to software and algorithm development, and involving yeast, human and bacterial data, before moving to London to join the NHM.
My current research is very different from the classic “model-organism“-oriented work earlier in my career, and I often refer to it as “I’m a bioinformatician, get me out of here!” If it has DNA, then we want to sequence it; I work with sharks, whales, scallops, tapeworms and a whole host of other invertebrate species. This week I’m looking forward to talking about the changes in bioinformatics over the last few years, and the challenges ahead as we apply bioinformatics algorithms to more diverse species.
I’m a PhD candidate in Integrative Biology at the University of Guelph in Guelph, Ontario. My PhD research is interdisciplinary and spans microbiology, bioinformatics (analyzing biological data, for e.g. DNA sequences, using computer science), ecology and chemistry – where I often work collaboratively with chemists. My specialty lies in how plants, fungi and insects interact with one another in tropical ecosystems. I ask questions like; how does plant chemistry affect other organisms in the community? And, what variables are important for determining which fungi colonize the interior of leaves (termed fungal endophytes)? More recently, I’m working on a project that looks at whether digestion of seeds by bats influence fungi the colonize seeds and improve seed germination. This fall, I’ll be going to Brazil to work with a chemist on how these fungal endophytes contribute to the chemistry in plants. You might be wondering, why are these questions important? My work aims to contribute to our understanding of how species interact with one another in a highly diverse and complex ecosystem. This is especially important because of the decline in species diversity in the tropics, due to factors such as deforestation and climate change. There are also potential applications for agriculture, through how plants may defend themselves against enemies and pharmacy by discovering new compounds which may have properties to combat human diseases.
Part of the fun of being a tropical ecologist, is getting to travel to different sites and comparing the answers to our research questions. During my PhD, I’ve conducted research in the lowland rainforests of Costa Rica and the cloud forests of the Andes in Ecuador. These research trips can last anywhere between 1 week to 4 months. I enjoy exploring new places, learning new languages, eating tasty food and drinking the local beers and wines. So, this type of work agrees with me. However, when in Guelph, you can find me tending to my balcony garden, meeting with the Guelph chapter of a women in STEM organization and running in the trails. I hope you enjoy my week on @biotweeps.
Find out more about me and my work here:
Luis Pedro Coelho is a Young Principal Investigator at Fudan University. He works on the analysis of microbial communities in different environments, such as the marine environment or the human gut using computational methods, namely metagenomic analysis and fluorescence microscopy analysis.
In particular, he is interested in comparing and contrasting the microbial communities in different environments such as the guts of different mammals and assessing how much they share in terms of genes and species and how exactly they differ. Luis also works on computational method development (bioinformatics) with a focus on enabling reproducible research and best practices with minimal user intervention. In this facet of his work, he is the lead on several scientific software projects for image analysis, metagenomics, and data science.
Before moving to Fudan in 2018, he was a postdoctoral researcher in Peer Bork’s group at the European Molecular Biology Laboratory (EMBL). He has a PhD from Carnegie Mellon University where he worked under the supervision of Prof. Bob Murphy and a MSc from Instituto Superior Técnico in Lisbon.
Meaghan L. Pimsler is a Postdoctoral Fellow at the University of Alabama working with Dr. Jeff Lozier to integrate physiological, morphological, population genetic, and transcriptomic approaches to study the factors shaping adaptation in native pollinators. She earned her PhD from in the Department of Entomology at Texas A&M University, where she used de novo transcriptomics to investigate sexual dimorphism and behavioral ecology in an invasive blow fly with a unique and poorly understood sex determination mechanism. She received her BS in entomology from Cornell University in 2007, and subsequently spent three years in Okinawa, Japan working at two high schools as an English teacher.
After recuperating sufficiently from the rigors of her undergraduate education, she began her postgraduate journey with Dr. Jeffery K. Tomberlin and Dr. Aaron M. Tarone in 2010. Meaghan has had a deep and abiding love of arthropods her entire life, and determined at the age of four that she would be an entomologist. She helped found entomology clubs in both high school and college, and has helped organize many entomology themed outreach and enrichment events, including working with the Smithsonian Museum of Natural History on their BugFest, and with Cornell University’s Entomology Department on their Open House.
Meaghan is particularly experienced in the field of forensic entomology, and this has led to a certification in Crime Scene Investigation with Texas Engineering and Extension Services; teaching at workshops for federal, state, and local law enforcement groups; several national and international trips to give invited seminar talks; the opportunity to coordinate symposia at the 2013 and 2014 Entomological Society of America annual meetings as well as the 2016 International Congress of Entomology; and her election to Treasurer of the North American Forensic Entomology Association. Meaghan’s current passion, outside of her research, is science policy. After joining the organizing committee for the March for Science- Birmingham, AL, she was selected as an Entomological Society of America Science Policy Fellow in the Class of 2017. She looks forward to talking with you about entomology, bumble bees, bioinformatics, statistics, science policy, and anything else you might be interested in.
Megan recently finished her PhD with Jay T. Lennon at Indiana University where she specialized in microbial ecology and evolution. Her dissertation focused on how cyanobacteria-phage interactions within microbial communities evolve in response to nutrient limiting conditions. She’s now returned to her home state of Nebraska (USA) and is applying her technical expertise in microbial ecology and informatics to studying cyanobacterial blooms at the University of Nebraska Water Sciences Laboratory.
Megan is an advocate for undergraduate STEM education and community outreach. While at Indiana University, she was greatly involved with engaging underrepresented students in the Women In STIM (Science, Technology, Informatics, and Mathematics) Living Learning Center and designed seminar courses for undergraduate professional development.
When she’s not sciencing, Megan is likely out and about on her bicycle roaming the old railroads turned trails in Lincoln or hiking with her dogs, Nala (lab retriever) and Sarah (St. Bernard).
This week on biotweeps, she’ll be focusing on skills she’s picked up during graduate school, new analytical chemistry skills she’s learning at the Water Sciences Laboratory, discussion about harmful algal blooms in the news, informatics, and work-life balance.
You can follow Megan after Biotweeps on twitter (@meganllarsen) or on her website (http://meganllarsen.wordpress.com).
I’m a Post-Doctoral bioinformatician working with the Centre for Bacterial Cell Biology (CBCB) and the Interdisciplinary Computing and Complex bioSystems (ICOS) research group at Newcastle University. My research focuses on the large-scale integration of biological data in order to generate novel, testable hypotheses.
I originally studied Molecular Biology as an undergraduate at Newcastle but, due to a lack of jobs in the area at the time I graduated, I spent the next few years initially managing a pub and restaurant (great fun, poor pay), and then working as an administrator for the Civil Service (better pay, mind-numbingly boring).
Eventually my love of biology and computing science led me back to Newcastle to the, then relatively new, MRes Bioinformatics course. I subsequently stayed to do a PhD in Computing Science (during which I was lucky enough to be one of the first Computing Science PhDs in the UK to do laboratory work during my project).
As a Post-Doc I have worked on a diverse range of project; from data analysis to software and algorithm development, and involving yeast, human and bacterial data. During my week on Biotweeps I primarily hope to describe how varied, interesting and novel bioinformatics research can be, but also discuss some of the practicalities of computational research, and the process of becoming an independent researcher (which I am currently in the initial stages of).
I’m a Research Fellow at Monash University in Melbourne, Australia, and a molecular biologist by training. The goal of my PhD project was to identify the chromosome breakpoints in leukemia patients (back before the Human Genome Project made that an afternoon’s work), and I’ve been working in various leukemia genetics projects ever since. I’m currently working on a translational project, trying to bring a molecular discovery (the inappropriate expression of a certain protein in leukemia) made 20 years ago through to a useful clinical application. It’s my first time in a lab with a real biochemistry focus rather than a genetics or cellular biology focus, which is… challenging?
More generally, I’m interested in leukemia stem cells, the cells that are responsible for relapse after chemotherapy, and how they manage to survive and regenerate the leukemia all by themselves. Through my work I aim to understand the genetic mutations and epigenetic events that drive gene expression patterns which control this behaviour. Things I am interested in and wish I was more adept at include bioinformatics and understanding how genome organisation works; good luck with that. Outside of work, I am a keen if slow runner, a keen if mad baseball fan, and a keen if misguided semi-colon user. I have a blog I last updated about two years ago.