Our Mission
The Informatics and Scientific Applications group is a small group working in the cramped space between faculty, core facilities and high performance computing. We have a number of core responsibilities including first pass analysis for the sequencing core and software/analysis support for the proteomics mass-spectrometry core. We also support the infrastructure for instrument scheduling and invoicing across many FAS facilities.
A large part of our remit is to smooth the path of scientific discovery by working with faculty, post-docs and grad students to design and analyze sequencing experiments for the most efficient bang for the buck. Our group is currently small (two bioinformaticians and two web developers) so we have limited resources to fulfill this area but we are aiming to grow and expand our services.
Services
The Informatics group provides bioinformatics analysis support for all users of the Core Sequencing facility and to FAS faculty groups regardless of the origin of their data. In addition we have the responsibility for sample submission, tracking, scheduling and billing services for many of the core instrument facilities across FAS.
We are small in number and try to cover the needs of as many people across campus as possible. This means, however, that we can’t provide in-depth or long-term analysis services for single groups. In these cases we encourage PIs to budget for a bioinformatics post-doc in their grant applications. We are very happy to provide letters of support and text detailing our expertise, and outlining possible analyses in grant applications.
Team
Tim Sackton
Director of Bioinformatics
Aaron Kitzmiller
Director of Software Operations
Adam Freedman
Data Scientist maintaining pipeline for Illumina sequencer data processing, also working on methods for analysis of RNA-seq (and other omics) data.
Nathan Weeks
Research Application Developer, adapting and optimizing informatics applications for FAS High Performance Computing infrastructure. His professional background includes software engineering and research IT system administration. He is a Computer Science PhD candidate through Iowa State University, where his (almost-finished) research focused on parallel computing and HPC fault tolerance.
Danielle Khost
Computational biologist specializing in third generation sequencing and genome assembly. She completed her PhD at the University of Rochester on repetitive element biology in 2019.
Gregg Thomas
Computational biologist specializing in comparative genomics and phylogenetics.
Rawan Olayan
Computational biologist specializing in single cell RNA-seq.
David D'Antonio
Research Application Developer designing and building applications to support the Cores. He's been doing web design development since the days of the Standards Wars.
Subir Shakya
Postdoctoral Fellow co-advised by Tim Sackton and Scott Edwards working on the evolution of enhancer elements in birds.
Alumni
Meghan Correa
Senior Software Engineer BA in Biochemistry and Molecular Biology, Boston University, MA in Information Technology Systems Management, Harvard University Extension School. Careers previous to software include: Molecular Biologist, Peace Corps Volunteer.
Alexandria D'Souza
Bioinformatician working on proteomics analysis, in particular to support quantitative and computational work with the Woo Lab in the Chemistry and Chemical Biology department.
Michele Clamp
Former Director of Informatics and Scientific Applications Yes those are aggressive filters on the photo – what of it?
Allison Shultz
Former Bioinformatics Scientist working on analyses of genomic data, specializing on population genomics. Currently Curator of Birds, LA County Museum. Learn more about her research on her website.
John Gaspar
Bioinformatics Scientist, specializing in data processing and genomic enrichment assays.
Yasin Kaymaz
Bioinformatics Scientist working in collaborative projects with Boehringer Ingelheim on brain circuitry underlying symptom domains of relevance to the central nervous system. These projects involve various types of single cell Next generation sequencing data analysis, integration, and interpretation. He gained his B.Sc. in Biochemistry (Ege University), and M.Sc. in Bioinformatics from Boston University. He graduated from University of Massachusetts Medical school with a PhD degree in Bioinformatics and Computational Biology.
Tommy Tang
Bioinformatics scientist working closely with Catherine Dulac's lab to catalog and understand the diversity and function of cell types in the mouse brain using single-cell RNA-seq and other cutting-edge techniques. He gained his PhD in Genetics and Genomics at the University of Florida and did a postdoc in computational biology at MD Anderson Cancer Center. He cares about reproducible research and open science. You can visit his personal website here
Brian Arnold
Bioinformatics scientist working on population genetics across a diverse taxonomic range including bacteria, plants, and animals.
Juerg Straubhaar
Bioinformatics scientist working closely with Doug Melton's lab on single-cell RNA-seq and other methods. Also does proteomics.
Andy Bryant
Software Developer, building applications that support research throughout the Faculty of Arts and Sciences. Prior to joining the Informatics team, he worked as a developer, filmmaker, and educator.
Scott Van Buren
Bioinformatics Scientist working with Dr. Catherinc Dulac’s lab to help catalog and understand the diversity and function of cell types in the mouse brain."
Sara Wuitchik
Bioinformatics postdoc, co-advised by Mike Sorenson (BU Biology), researching the comparative genomics of obligate brood parasitism in birds. She earned her B.Sc. in Marine Biology & Oceanography from the University of Victoria and her Ph.D. in Ecology & Evolutionary Biology from the University of Calgary."
Alejandro Llanos Garrido
Postdoc funded by Real Colegio Complutense at Harvard, working on population genetics to understand the role of genetic diversity in shaping the distributional patterns of different species."
Where to find us
Informatics and Scientific Applications is located on the second basement floor of 52 Oxford Street, Cambridge, MA 02138 aka the Northwest Labs building. Click here for an interactive map and click here for a Google map.
Use the main entrance the building (marked in the map below), which is unlocked during regular business hours. Use the elevator or go down the stairs to the second basement floor. Our office area is through the right set of double doors and then take a right. If you see the Bauer Core, turn around.
If you are planning to drive, please be advised that on-street parking is very limited and University-owned lots require a pre-paid day permit. We strongly urge using public transportation.
Directions
By Public Transportation Take the Red Line to the Harvard Square stop, and choose the “Church Street” exit. Exit through the turnstiles and up the stairway on your left, which leads to Harvard Yard. Walk through the gate into Harvard Yard and proceed straight ahead to the statue of John Harvard. From here take the path to your left, exit the Yard, and veer slightly to the right. The Science Center (a large, concrete structure with a rock formation in front) will be on your left, and Memorial Hall (a large, ornate red brick building with a tall steeple) on your right. This path will take you to the intersection of Kirkland and Oxford Streets. Cross the street, and proceed left down Oxford Street. You will see the Harvard Museum of Natural History on your right. Take the first path on the right after the Museum and follow it to the main entrance of the Northwest Building.
From the North Take I-93 or Route 1 south toward Boston. Take the exit for “Storrow Drive-Cambridge.” Follow Storrow Drive west for approximately 4 miles. After approximately 2 miles Storrow Drive becomes Soldiers Field road. You will not notice any change. Stay in the right hand lane in order to avoid the many left hand exits off Storrow Drive until you reach the exit marked “Harvard Square/Cambridge.” Take the exit and go over the Charles River to the set of lights at Memorial Drive. Go straight ahead through the lights. You will now be on JFK Street. After you pass the intersection of JFK and Mt. Auburn Street, you will come to another set of lights where Nini’s Corner and The Coop are on the left, and Out of Town News and the subway “T” stop will be on your right. Go straight (veering slightly to the right) through these lights, passing Out of Town News. You will then approach another fork in the road — stay to the left of the fork and then immediately get into the right hand lane. This will take you onto Massachusetts Avenue, headed north. Go approximately 0.2 tenths of a mile past the Harvard Law School to Everett Street on your right. Turn right onto Everett Street and go to the next set of lights at Oxford Street. The building directly in front of you and beyond the lights is the Northwest Building.
From the South Take I-93/Route 3 (South East Expressway) north and follow the above directions for Storrow Drive West.
From the West Take I-90 (Massachusetts Turnpike) east. Get off the Cambridge/Allston exit (#18) and follow signs for Cambridge bearing to the right. As you come off the Turnpike exit, a 10-story hotel is on your right. Begin to move to the left lane as you pass the hotel. There is a traffic light at the corner of the hotel. Go through this light, but be prepared to make a left, before the bridge (do not cross over the bridge). You will now be on an entrance ramp leading onto Storrow Drive with very rapid traffic. Follow Storrow Drive approximately 1/2 mile. Stay in the right lane, which will become the “Harvard Square/Cambridge” exit on your right. Follow the directions given above for coming from the north starting with “. . . Take the exit and go over the Charles River . . .”
PARKING
On-street metered parking There are limited 2-hour metered spaces available on Oxford and Kirkland Streets (these meters only accept US quarters).
Commercial Garages There are also commercial parking garages in Harvard Square, however the Division cannot validate parking for those businesses.
University Day-Permit Parking Limited parking is available for department visitors in nearby University-operated parking garages. Day permits can be purchased up to 2 weeks in advance, which is highly recommended as the lots fill-up quickly, in person (at the Harvard Parking Office at 3 Bow Street) or online. Daily permits are $14.00. All major credit cards are accepted, and all sales are final (no refunds or exchanges). If you wish to purchase a permit online, we recommend requesting a permit for the 52 Oxford Street Garage (Monday-Friday, 7:00am-11:30pm) or 10 Everett Street (Monday-Friday, 7:15am-11:00pm).