James Lindsay
Computational Biologist
- Location
- Hartford, Connecticut Area
- Industry
- Biotechnology
As a LinkedIn member, you'll join 150 million other professionals who are sharing connections, ideas, and opportunities. And it's free! You'll also be able to:
- See who you and James Lindsay know in common
- Get introduced to James Lindsay
- Contact James Lindsay directly
Summary
I am a student and research assistant pursuing my PhD at the University of Connecticut funded by the Graduate Assistantship for Areas of National Need.
I have assembled the genome of the tammar wallaby for publication in Genome Biology and currently working on the de novo assembly of other organisms using multiple sequencing platforms.
During my research I have analyzed and published small RNA and repeatative sequences of the tammar genome. I developed a pipeline to effeciently distinguish small RNA from backround in RNA-seq experiements.
Currently I am preparing to publish a novel scaffolding algorithm that allows scientists to improve large draft genomes using paired sequening data. The algorithm utilizes powerful graph decomposition techniques and Integer Linear Programming to accuratly order and orient contigs of a draft assembly without heuristics.
Specialties
bioinformatics, de novo assembly, genome assembly, algorithm development, software engineering, parallel algorithms, threaded programming, scalable algorithms
Experience
Research Assistant
University of Connecticut
Educational Institution; 1001-5000 employees; Higher Education industry
June 2007 – Present (4 years 9 months) Hartford, Connecticut Area
Pursuing a PhD in Computer Science by researching and developing high performance tools for computational biology.
Work closely with the Center for Applied Genetic and Technology to assemble genomes for non-model organisms. Sucessfully published an assembly of the tammar wallaby genome. Currently involved in the assembly of several other organisms including the horseshoe crab.
Actively researching scalable scaffolding algorithms for hybrid de novo assemblies of large, repetative genome. The novel algorithm utilizes fast c/c++ and python coding strategies. Expect a publication shortly.
Software Engineer
NEOS & Vgo Software, Inc
Public Company; 11-50 employees; Information Technology and Services industry
June 2005 – July 2007 (2 years 2 months) Manchester, CT
This was a summer internship which continued on a part time bases during the school year.
Contributed to software which automated the generation of data driven web applications. Programming was primarily done in Java, although the output was written in several languages including PHP, JSF, Struts and Javascript.
Helped develop and deploy a large web application for a fortune 500 company. The project involved creating a high performace a web portal and was completed succesfully on a short deadline.
Worked closely with several other programmers and utilized versioning systems and multiple programming languages.
Skills & Expertise
- C
- C++
- Java
- Web Development
- genome assembly
- Bioinformatics
- Computational Biology
- DNA sequencing
- Research
- Software Development
- Software Engineering
- Technical Training
- Server Architecture
- Combinatorial Optimization
- MPI
- Algorithms
- Algorithm Design
- Biomedical Informatics
- LaTeX
- Matlab
- High Performance Computing
- Python
- Machine Learning
Publications
-
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
- Genome Biology
- 2011
Authors: James LindsayWe present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.
-
Enhancing genome assemblies by integrating non-sequence based data
- BMC Proceedings
- 2011
Authors: James LindsayMany genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies.
Education
The University of Connecticut
PhD, Computer Science
2010 – 2014 (expected)
Activities and Societies: bioinformatics
The University of Connecticut
MS, Computer Science
2007 – 2009
The University of Connecticut
BS, Computer Science and Engineering
2003 – 2007
Additional Information
- Websites:
- Interests:
-
bioinformatics, genome assembly, hiking, backpacking, snow shoeing, landscaping, tom foolery.
- Honors and Awards:
-
2011 - Scholarship to attend IPAM workshop in Computational Genomics
2011 - Best poster at 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences
2010 - Recipient of the Graduate Assistance in Areas of National Need fellowship
2008 - Scholarship to attend Summer Institute in Statistical Genetics