Frank Gibbons's homepage
I'm a computational biologist in Fritz Roth's Lab, in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School.
Projects currently underway
I'm currently investigating some novel, interesting, network motifs I've discovered in yeast, using high-throughput datasets.
In other work, BioTrawler (or try the development version) uses web services to discover, integrate, and display biological networks, on the fly.
Published Projects
Gibbons FD, M Proft, K Struhl, and FP Roth
Chipper: discovering transcription-factor targets from chromatin
immunoprecipitation microarrays using variance stabilization
Genome Biology, 6(11):R96 (2005)
PDF
Software
On the one-year anniversary of its publication (1 November 2006), this paper
had been accessed almost 4000 times (2400 of those within the first ten weeks).
Rual JF, K Venkatesan, T Hao, T Hirozane-Kishikawa, A Dricot, N Li, GF Berriz, FD Gibbons, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437 (7062):1173-8 (2005) PDF
Proft M, FD Gibbons, M Copeland, FP Roth, and K Struhl Genome Wide Identification of Sko1 Target Promoters Reveals a Regulatory Network Operated Upon Osmotic Stress in Yeast. Eukaryotic Cell, 4(8):1343-1352 (2005) PDF
FD Gibbons, JE Elias, SP Gygi, and FP Roth. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. J. Am. Soc. Mass Spectrom., 15, 910-912 (2004). PDF Software
JE Elias, FD Gibbons, OD King, FP Roth, and SP Gygi. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotech., 22(2):214-219 (2004). PDF Software
S Asthana, OD King, FD Gibbons, and FP Roth. Predicting protein complex membership using probabilistic network reliability. Genome Res., 14, 1170-1175 (2004) PDF Software
FD Gibbons and FP Roth. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res., 12(10): 1574-1581 (2002). PDF Software
Perl, Python, SWIG, R & friends
PDL allows you to get decent performance when using Perl for serious number-crunching. Here's an index I generated to the documentation, which used to be pretty hard to find your way around. In Perlish fashion, a lot of the function names are non-intuitive. Here are some notes I kept as I was learning to use it, in the form of a PDL FAQ. Supposedly, PDL can talk to R, using this PDL::R module. I don't think I've ever used it.
SWIG is a pretty awsome tool for hooking your favourite scripting language (Python, Perl, etc.) up to your favourite "real" programming language (Java, C++, etc.). It's now mentioned in Wikipedia. I used to host an index here, but it's too out of date to be of any use.
Tempted to leave your Perlish ways behind? Want to become a pythonista? This phrasebook will help you on your way.
I translated Ugo Taddei's VisAD Java examples into Jython here. Apparently, a lot of people come here just for that. I don't use VisAD - I think it was the wrong tool for what I was trying to do. The Python Imaging Library and R (along with rpy, the R/Python interface) have given me much more satisfactory results.