Open position: Bioinformatics scientist

Michele Clamp is building up Harvard’s bioinformatics teamĀ on the college (Cambridge) campus, and she’s got an open position in collaboration with Susan Mango’s group:

The Mango Lab in the Harvard Department of Molecular and Cellular Biology in collaboration with the FAS Informatics Group seek a bioinformatician for genomics analysis. The successful candidate will primarily focus their work on the Mango lab, while embedded within a cohort of informaticians who develop and apply cutting edge approaches to a range of biological questions. Current projects within the Mango lab use genomics to study transcriptional regulation and chromatin dynamics during development. ChIP-seq, FAIRE-seq, RNA-seq, Oligopaint etc. are used to probe the chromatin landscape as cells transition from pluripotency to cell-fate commitment, and the successful candidate will collaborate with lab members to analyze the datasets. The remaining effort will be used to support groups in the Faculty of Arts and Sciences (FAS) that use genomic approaches such as ATAC-seq, Chip-seq, FAIRE-seq, and related methodologies. This will include consulting with faculty groups, teaching workshops on statistical and informatics approaches for understanding these methods, and developing best practice recommendations and benchmarks.

For more information, or to apply, [see here.]

New positions opening in the group

Construction on the new laboratory here at Harvard is starting to look like it might actually get done. They’re projecting our move-in date to be the first week of November. I’ve been meeting with prospective rotation students and postdoc candidates, even though we still have no place to put anyone or anything. It feels like we have a bunch of planes in the air stacked up in holding patterns, waiting for the bulldozers to finish the runway.

I plan to search for three key staff positions this fall. The first open position is our all-important administrative lab coordinator. I’m already sorely missing our lab coordinators over the years at Janelia, Margaret Jefferies, Patrice Neville, and Sarah Moorehead, and we don’t even have an open lab here yet. An ad is now out in all the fashionable color supplements (here’s the one at Nature Jobs). Help us spread the word, if you know of someone who might be interested in the position!

The other two positions will be two scientific software developers, working on our main codebases in HMMER, Infernal, and Easel. We’re going to make a push on the high performance computing ends of things, including parallelization (SIMD vectorization, threading, and MPI), so I want to find a software engineer with experience in C programming in parallel HPC scientific applications. We’re also going to make a push in the visualization and web development end of things, so I want to find a web developer with experience in data visualization who’d also be interested in being a general guru of much of our front-facing stuff, including our web presence, issue tracking, github, and software distribution. I don’t have ads out for these positions yet, but will do soon-ish.


Some bugs crept through testing and into the 3.0b1 release of HMMER3. They’re fixed, and the link in the “3.0b1” release post below was quietly updated to the 3.0b2 tarball available for download on our FTP site.

I fixed a bug with the new code that deals with fragment-rich alignments (sometimes hmmbuild was failing, complaining about a failed “trace validation”). I also added the –tblout and –domtblout options to hmmscan, which should’ve been there in the first place.