Computational Technology Development Lead, Genomics Platform, Broad Institute
PhD, Harvard University, 2011
Dr. Carneiro leads the computational technology development team at the Broad Institute of MIT and Harvard. He has contributed to major advances in DNA sequencing analysis with compression algorithms, statistical methods, heterogeneous compute optimizations and a systematic approach to the institute's computational development, distribution and support. His team is also responsible for the evaluation of new sequencing technologies and has provided several methods and tools to handle new data types in the world of next generation sequencing through the Genome Analysis Toolkit (GATK).
Dr. Carneiro joined the Broad Institute in December 2010 after completing a Ph.D. in computational biology from Harvard University. He holds two championships in the International Collegiate Programming Contest organized by the Association for Computing Machinery (ACM) in 2002 and 2003, respectively, and a Programming Excellence Award from the ACM Upsilon Pi Epsilon Society in 2003.
In his previous life, he was a video game developer and has led the development of the world's first massive online location based multiplayer game: Alien Revolt.
Professor, Bioinformatics, National University of Ireland Galway
PhD, Trinity College Dublin
After completing an undergraduate degree in Theoretical Physics, I changed direction to study towards a PhD in the Smurfit Institute of Genetics, Trinity College Dublin. In retrospect, this turned out to be a good move: those were heady days in molecular biology. The genome of the first eukaryote had just been sequenced and there were opportunities for people with a mathematical bent and experience of programming computers to get involved in discovering the subset of life’s secretes that were offered up by the availability of whole genome sequences. After the PhD and a brief period as a postdoctoral researcher in the Royal College of Surgeons in Dublin, I moved to South Africa, working at first as a consultant to the MRC and the government and Director of Training for the South African National Bioinformatics Institute, and then as an Associate Professor at the University of Cape Town. In 2009 I returned to Ireland, taking up a position as Stokes Professor of Bioinformatics at the National University of Ireland Galway.
CHIMUSA, Emile Rugamika
Bx, BioStatistician, CPGR/H3Bionet, Centre for Proteomic and Genomic Research
PhD, University of Cape Town, 2013
BioProfil: Emile received his Bsc in Applied Mathematics at University of Kinshasa. Later on he joined the independent electoral commission (IEC) for United Nations mission in Democratic Republic of Congo (DRC), as software developer and database administrator. He joined the African Institute for Mathematical Sciences in 2007 and obtained his post-graduate diploma in Mathematical sciences at the University of Western Cape, South Africa. He completed his PhD from University of Cape Town, South Africa in Bioinformatics and Computational Biology. During his last year of PhD (2012) Emile later joined African institute for Mathematical Sciences as IT and teaching assistant.
Emile is a mathematical population geneticist whose main focus of research is ”Medical Population Genetics and Computational Statistics methods for mapping complex diseases”. Emile’s interest focuses are in computational and statistical methods for understanding both the genetics and environment architecture of genetic diseases. He is interesting in investigating methodologies of improvement the analysis of large scale genomic studies such as genome-wide association studies or fine-mapping studies and analysing genome wide patterns of variation within and between species to address fundamental questions in biology, anthropology, and medicine. Emile is currently investigating on statistical and computational approach for estimating the heritability of the traits (diseases) using the DNA sequence data of both parents and children particularly new born-babies (family-based) (1) to understand the fraction of phenotypic (traits or diseases) explained by DNA sequence (2) to predict genetic architecture of complex traits (such TB and HIV), and variation in drug/treatment responses at early stage in children (3) to optimal prescription and usage of medicines to effectively manage and treat infectious and non-communicable diseases in Sub Saharan African populations. The long term of his research is to conduct a cohort study in sequencing South African's parents within children or baby-born with tuberculosis and HIV and apply the developed approach in both tuberculosis and HIV public sequence data of children or baby-born.
Emile's project will develop important skills, further job opportunities and tools required for medical population genetic research in Sub-Sahara and South Africa. A wide variety of fields stand to benefit from this research. These fields include the pharmaceutical, biotechnology, computational biology, biostatistics and diagnostic areas. Significant findings milestones achieved are to be disseminated in the form of publications in high-impact international journals and presented at both local and international conferences.
Emile has trained, supervised and co-supervised several AIMS students and masters students (all former AIMS students). He is one of the first recipients of the AASRG. This grant a great start for his early scientific career. The AASRG will help Emile in supporting other AIMS students through supervision
Emile's advise to youths is: (1) Never fail having a dream. Once you have a dream, give it a go ahead and tries. (2) Understanding your mistakes and failures is a starting point to overcome and getting into the track of your success.
Associate Professor, Dept. of Animal Breeding and Genetics, SLU, Uppsala, Sweden
Professor, Uppsala, Sweden, 1995
Erik Bongcam-Rudloff received his doctorate in medical sciences from Uppsala University, Sweden. He is now the Director of the SLU Global Bioinformatics Centre (SGBC) at the Swedish University of Agricultural Sciences. Erik was the chairman of EMBnet (2003-2010) (www.embnet.org), a science-based group of worldwide collaborating bioinformatics nodes. Bongcam-Rudloff is today Chair of SeqAhead (www.seqahead.eu), a Biomedical European COST Action: "Next Generation Sequencing Data Analysis Network" and Coordinator of ALLBIO, a FP7 project: "Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science" (www.allbioinformatics.eu). He is also the founder of eBioinformatics.org the creators of eBiotools, eBioX and eBioKit (www.ebioinformatics.org).
His main research deals with development of bioinformatics solutions and teaching for the Life Sciences community.
Developer, Bioinformatics, CPGR
Masters Degree, University of Cape Town, 2010
I was awarded my bachelors degree in Systems engineering in 2002 at the Universidad del Valle in Colombia, and for over 10 years I have taken part of multiple software projects for both academia and private companies. I have developed software as a Freelancer for companies in Colombia, USA, South Africa and the UK. I moved to South Africa in 2007 as a member of the central node at National Bioinformatics Network located in Cape Town. I started my MSc in Computer Science in 2008 and finished in 2010, the topic of this research was about collaborative annotations for biological data. The collaborations held during this time allowed me to visit the European Bioinformatics Institute and worked there as an intern at the proteomics Services team. I started a PhD in Bioinformatics under the supervision of Dr. Nicola Mulder at the end of 2010, the current focus of this research is on the visualization of protein-protein interactions using recent web technologies such as HTML5. I am part of the CPGR team since January 2014.
Project Manager Ebola and Lassa virus fever, Organismic and Evolutionary Biology, Harvard University
PhD, Harvard University, 2013
Population geneticist and scientific project manager with experience in the population genetics, diagnostic and next-generation sequencing technologies, human genotyping, and GWAS.
Le Cao, Kim-Anh
Senior Research Officer, Diamantina Institute, University of Queesnsland
PhD, Université de Toulouse, 2008
Dr Kim-Anh Lê Cao was awarded her Ph.D in 2008 in Université de Toulouse,France. She was awarded the "Marie-Jeanne Laurent-Duhamel" prize 2009 of the Société Française de Statistique (French Statistical Society) for her Ph.D thesis.
She has been working in the University of Queesnsland for the last 5 years, first as a postdoc and then as a researcher in the Queensland Facility for Advanced Bioinformatics. She is now appointed the Diamantina Institute in cancer research, UQ. She has been teaching Statistics at the undergraduate and Master level for 4 years and has been running 3 days workshops entitled ‘An Introduction to Statistics for Biologists, with programming in R’.
Her research interests are multidisciplinary as they focus on mathematical statistics to characterize molecular biological systems. She is interested in developing sound statistical methods to address biological questions arising from frontier molecular technologies, ranging from biomarker selection, omics data integration and analysis of longitudinal or time course high throughput data. She is one of the main developers of the mixOmics R package dedicated to the integrative analysis of `omics' data (see http://www.math.univ-toulouse.fr/~biostat/mixOmics and its associated interface http://mixomics.qfab.org/).
Project Leader, Plant and Animal Genomes, The Genomic Analysis Centre
PhD, University of Manchester
Manuel manages and participates in projects for the annotation and analysis of transcriptomes and epigenomes of various plant and animal genome species.
Since joining TGAC, he has worked on the annotation and analysis of the oilseed castor bean genome which produces Ricinoleic acid, a raw material with industrial applications in automotive engines. Other species of interest include Tomato, Arabidopsis and Chicken. Manuel holds a Ph.D. in Computer Science from the University of Manchester, UK, where he worked on the application of machine learning techniques to protein sequence family classification in Professor Terri Attwood’s group. He continued his post-doctoral research in clinical genomics at the Wellcome Trust Sanger Institute, Cambridge, developing the DECIPHER database and accessory tools for visualization of personal genomics data. He also received an M.Sc. in Bioinformatics from the University of Manchester, and a B.Sc. in Biology from the University of Navarra, Spaiin.
Postdoctoral Researcher, Metapopulation Research Group, University of Helsinki
PhD, Helsinki University of Technology, 2000
My background is in signal processing, pattern recognition, and machine learning. Before moving into bioinformatics, I was working with automatic speech recognition and neural networks at Neural Networks Research Centre, Helsinki University of Technology supervised by Academian Teuvo Kohonen. 2005 I moved to DNA Sequencing and Genomics Lab at Viikki campus of University of Helsinki. During 2005- 2010 I did microarray data analysis including detection, gene expression, and array comparative genomic hybridization. Majority of that work was related to non-model organisms using custom arrays. Besides data analysis, I was also responsible for probe design. 2010 I joined Metapopulation Research Group at Helsinki University to participate in a butterﬂy sequencing project. Its ﬁrst step, ﬁnished 2012, was to make a draft assembly of Melitaea cinxia genome. Related to this project, I was also working with RNA-Seq data to characterize different butterﬂy populations.
My general research interests are in computational methods and machine learning. Being involved in biological projects, I am also interested in understanding biology better. Both of these topics are never-ending odysseys for me.