The Cape Town wing of The Big Issue just published one of my articles in their April edition. Here's the leader...

Many are the prophets of the Information Age. They preach the wonders of technology, of “information at your fingertips.” Soon, we are told, the Internet will usher in a new era of global connectivity and human understanding. Soon, computers will cure our diseases and do our dishes. But 'soon' means different things in different countries.

Wizzy Digital Courier provides offline Internet to African schools. Using a camera provided by bridges.org, I spent the past few days making a short video documentary of the project. If you have RealPlayer installed, you can view the documentary (a series of five 90-second clips), at

http://tv.oneworld.net/tapestry?story=920

More information on the initiative can be found in the this article, or at the Wizzy Digital Courier website. The trip to Khayelitsha is described in my journal entry site b.

submitted to the watson foundation 10/29/03

“What is the point of the Watson Fellowship?”

I hate that question. Everyone asks; everyone gets a different answer. The truth is, I don’t think a good answer exists. No answer is the right combination of informative and vague. Yes, I am here to learn – but what about? About the digital divide, about other cultures, about adversity and ingenuity, or just “about myself”? All of the above, I know. However, in deciding how to spend my time, all of the above do not always point in the same direction. So far, my biggest “progress, difficulties and triumphs” have been in deciding what to do with myself, and in deciding what I want to get out of the fellowship.

The team at Microsoft, with whom I worked last summer, just published a paper on the work we did, and were kind enough to include me as a co-author. The full citation is:

Gemmell, Jim, Lueder, Roger, Blumenstock, Joshua, Solomon, Evan and Bell, Gordon. Telephone, Television and Radio in the Home of the Future Internet and Multimedia Systems and Applications (IMSA) 2003, August 13-15, 2003, Honolulu, Hawaii, USA.

Abstract

The home of the future will have an all-digital network for all media, backed by multi-terabyte storage. Users will be able keep an entire lifetime of personal media, and vast collections of media that may be of interest for future viewing, reading, or listening. MyLifeBits is a personal store for a digital life, designed to support efficient organization, search, browsing, annotation, and viewing. This paper describes the telephone, television, and radio components of the MyLifeBits system.

You can download the paper here: Word (2.5MB)  PDF (1.7MB)

Gavin J. Gordon, Roderick V. Jensen, Li-Li Hsiao, Steven R. Gullans, Joshua E. Blumenstock, William G. Richards, Michael T. Jaklitsch, David J. Sugarbaker, and Raphael Bueno. Using Gene Expression Ratios to Predict Outcome Among Patients With Mesothelioma Journal of the National Cancer Institute 95:8 (Apr. 2003): 598-605

Abstract

We have recently demonstrated that simple ratios of the expression levels of selected genes in tumor samples can be used to distinguish among types of thoracic malignancies. We examined whether this technique could predict treatment-related outcome for patients with mesothelioma. Methods: We used gene expression profiling data previously collected from 17 mesothelioma patients with different overall survival times to define two outcome-related groups of patients and to train an expression ratio-based outcome predictor model. A Student’s t test was used to identify genes among the two outcome groups that had statistically significant, inversely correlated expression levels; those genes were used to form prognostic expression ratios. We used a combination of several highly accurate expression ratios and cross-validation techniques to assess the internal consistency of this predictor model, quantitative reverse transcription–polymerase chain reaction of tumor RNA to confirm the microarray data, and Kaplan–Meier survival analysis to validate the model among an independent set of 29 mesothelioma tumors. All statistical tests were two-sided. Results: We developed an expression ratio-based test capable of identifying 100% (17/17) of the samples used to train the model. This test remained highly accurate (88%, 15/17) after cross-validation. A four-gene expression ratio test statistically significantly (P = .0035) predicted treatment-related patient outcome in mesothelioma independent of the histologic subtype of the tumor. Conclusions: Gene expression ratio-based analysis accurately predicts treatment-related outcome in mesothelioma samples. This technique could impact the clinical treatment of mesothelioma by allowing the preoperative identification of patients with widely divergent prognoses.

E. Coli causes diarrhea, and may fight cancer as well

MANY a stalwart man trembles at the mention of the word “colonoscopy.” Odysseus braved Hades and defied the dreaded Scylla, but never did he confront the neighborhood proctologist. Yet colorectal cancer, the fourth leading cause of cancer worldwide, claims tens of thousands of lives each year, and is not a disease easily wiped aside. Maybe, suggests Dr. GianMario Pitari of Thomas Jefferson University, we can flush it out.

Sailing in seizures of laughter, crawling out from under the heel of love, tearing down a dirt road away from Salvador, the bus shakes and I can't sleep. I'm exhausted, just want to drift away, but as my head bounces against the window all I can think is Paul Simon. Paul Simon, Stevie Wonder, Al Green, they fill my aches with words and sighs with song. Here, on the bus, the lyrics seem out of place. But so am I, and why censor? Paul was right: some stories are magical, meant to be sung. This is what filled my head then and now; this is the story of how I begin to remember...

I like to think my dad is flawless. He's a doctor, but he's also a handyman and a mechanic, a ski patrolman and a sailor - a modern-day renaissance guy with more practical sense than anyone else I've met. He has more letters after his name than I can remember, and though I'm a physics major and he only took the required pre-med classes, he understands the principles much better than I do. But when it comes to computers, he's pretty hopeless. As a computer science student and general techno-geek, I like showing my friends how to do stuff on computers. But with my dad it's different. I get annoyed when he asks for help using spreadsheets, short-tempered when he wanted advice buying a laptop, and unnervingly frustrated when he had trouble with email attachments. I've spent weeks training my grandfather to use AOL, but can't spend more than five minutes tutoring my dad.

I've added a little map of my (tentative) itinerary, as well as links to my proposal and personal statement. Thanks again to everyone who helped me put the project together.

This histogram tool (VBA) is an Excel macro that creates histograms of Affymetrix microarray data, and is useful in finding genome chips that had oversaturation problems. The methodology is described in our Biotechniques article, Correcting for signal errors in the analysis of microarray data [abstract] The code is available from Gullans' lab's website; follow this link.

This clustering software (VC++) implement the clustering algorithms described in Tamayo et al's 1999 PNAS paper. The idea was to build a framework that would enable the user to specify all relevant clustering parameters at run-time. This is basically the shell for the program we used to cluster financial data in Fall '00, with the back-end algorithms removed. The real version was designed for imported datasets, but in this version you can just click around, placing nodes and points wherever you want.

I developed this tool while working at Harvard Institutes of Medicine, in order to visualize the expression leves of genes on DNA microarrays. It is an MS Excel macro that takes a table of numbers and turns it into a colored heatmap, where the brightness/hue is proportional to the size of the number. For example:

The .bas file can be downloaded free of charge by clicking here.

Gavin J. Gordon, Roderick V. Jensen, Li-Li Hsiao, Steven R. Gullans, Joshua E. Blumenstock, Sridhar Ramaswamy, William G. Richards, David J. Sugarbaker and Raphael Bueno. Translation of Microarray Data Into Clinically Relevant Cancer Diagnostic Tests Using Gene Expression Ratios in Lung Cancer and Mesothelioma. Cancer Research 62:17 (Sep. 2002): 4963-4967

Abstract

The pathological distinction between malignant pleural mesothelioma (MPM)and adenocarcinoma (ADCA) of the lung can be cumbersome using established methods. We propose that a simple technique, based on the expression levels of a small number of genes, can be useful in the early and accurate diagnosis of MPM and lung cancer. This method is designed to accurately distinguish between genetically disparate tissues using gene expression ratios and rationally chosen thresholds. Here we have tested the fidelity of ratio-based diagnosis in differentiating between MPM and lung cancer in 181 tissue samples (31 MPM and 150 ADCA). A training set of 32 samples (16 MPM and 16 ADCA) was used to identify pairs of genes with highly significant, inversely correlated expression levels to form a total of 15 diagnostic ratios using expression profiling data. Any single ratio of the 15 examined was at least 90% accurate in predicting diagnosis for the remaining 149 samples (e.g., test set). We then examined (in the test set) the accuracy of multiple ratios combined to form a simple diagnostic tool. Using two and three expression ratios, we found that the differential diagnoses of MPM and lung ADCA were 95% and 99% accurate, respectively. We propose that using gene expression ratios is an accurate and inexpensive technique with direct clinical applicability for distinguishing between MPM and lung cancer. Furthermore, we provide evidence suggesting that this technique can be equally accurate in other clinical scenarios.

Fryer RM., Randall J., Yoshida T., Hsiao LL., Blumenstock J., Jensen KE., Dimofte T., Jensen RV., Gullans SR. Global Analysis of Gene Expression: Methods, Interpretation, and Pitfalls  Experimental Nephrology 10:2 (2002): 64-74

Abstract

Over the past 15 years, global analysis of mRNA expression has emerged as a powerful strategy for biological discovery. Using the power of parallel processing, robotics, and computer-based informatics, a number of high-throughput methods have been devised. These include DNA microarrays, serial analysis of gene expression, quantitative RT-PCR, differential-display RT-PCR, and massively parallel signature sequencing. Each of these methods has inherent advantages and disadvantages, often related to expense, technical difficulty, specificity, and reliability. Further, the ability to generate large data sets of gene expression has led to new challenges in bioinformatics. Nonetheless, this technological revolution is transforming disease classification, gene discovery, and our understanding of regulatory gene networks.

LL Hsiao, RV Jensen, T Yoshida, KE Clark, JE Blumenstock, SR Gullans. Correcting for signal errors in the analysis of microarray data Biotechniques 32:2 (Feb. 2002): 330-337

Abstract

A variety of technical errors have risen in data analysis when using cDNA or oligonucleotide microarrays. One of the most insidious problems is saturation of hybridization signal of high abundant transcripts. This problem arises due to the truncation of laser fluorescence signal. When the hybridization signal on the microarray is very strong, this truncation has resulted in serious consequences that may not be readily apparent to the user. As an illustration of this problem, two subclasses of normal human tissue samples (six liver and six lung) were analyzed with Affymetrix GeneChip® probe arrays to evaluate patterns of expression for ~7000 human genes. Five of these datasets were found to suffer from signal truncation. This caused several tissues to be incorrectly classified using hierarchical clustering. To rectify this problem so that the gene expression data could be properly compared and clustered, we developed a "filtering" procedure that identifies a subset of genes least affected by the signal saturation (The filtering procedure can be obtained at www.hugeindex.org).

DNA Sequence Visualization Tool (VC++) - Visualize sequence similarities in a long strand of DNA. The program will draw arc that connect matching sequences greater than a lenth specified by the user. not yet uploaded

Small Java application designed to track desktop work patterns. The application uses JDBC to query and store data in databases. not yet uploaded

Can anything be more than the sum of its parts? The abundance of theories of 'emergence' seems to suggest that it can. Each theory of 'emergence', in its own particular way, asserts that novel properties 'emerge' as a system grows more and more complex. 'Emergence' has been attributed to all sorts of phenomena: consciousness 'emerges' from the brain; macroeconomic patterns 'emerge' from spending patterns; highway traffic 'emerges' from driving mentalities, etc. The concept is very powerful and all-encompassing, and has fascinated me since I first hear about it. In this highfalutin paper, which I just finished writing for a philosophy class, I conclude that 'emergence' is, essentially, a sham. Here's the link to the Inefficacy of 'Emergence'

I took a non-academic leave of absence from Wesleyan during the academic year that started in the Fall of 2000. Specifically, I had developed a package of simple agent-based clustering algorithms under the guidance of my advisor, Rick Jensen. Starting in the Summer of 1999 I began thinking about the situations in which this general class of algorithms could be effectively implemented. Over the course of that academic year I read up on the literature, and eventually went to an ICCS conference on Complex Systems and an IEEE conference on robotics.