Scott Carlson

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<font size='6'>Scott Carlson</font>
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[[image:Scott_Carlson.png|220px|right]]
[[image:Scott_Carlson.png|220px|right]]
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I'm a first year PhD student in MIT's department of Bioengineering.  This content is questionable at best since I'm still figuring out the whole Wiki thing.  For now you can download my [http://web.mit.edu/scottmc/www/Scott_Carlson_CV.pdf CV].  Feel free to read whatever happens to be here.
 
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Skip to the [[Scott_Carlson#Bio|Bio]] if you'd rather read my life story than my research.
 
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=Research=
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I'm a 5th-year graduate student in Biological Engineering at the Massachusetts Institute of Technology.  I work with Professor Forest White on phosphoproteomics applied to diabetes and cancer.
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==Proteomics==
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=Research Interests=
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==Biostatistics==
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==Graduate Research==
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==Bioengineering==
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=== MAP kinases in cancer and diabetes ===
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The mitogen-activated protein kinases (MAPKs) are involved in signal transduction downstream of stress and growth factors.  Activation of JNK in a critical event in development of type II diabetes, and activation of ERK is involved in both diabetes and cancer.  I am combining mass spectrometry a chemical genetics strategy, developed by Kevan Shokat, to identify substrates of these kinases.
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=Curriculum Vitae=
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=== Mechanisms of oncogenesis by KRAS mutation ===
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Activating mutations in KRAS occur in about 60% of all cancers.  The KRAS oncogene signals through several major pathways, including the Raf/MEK/ERK cascade.  This cascade is a major target for pharmaceutical research because of its importance in KRAS signaling and because it is targeted by other important oncogenes.  My goal is to understand how KRAS activation leads to cancer development by activating this and other pathways.
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=Other Interests=
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=== Regulation of alternative splicing ===
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Regulation of mRNA splicing is implicated in development of cancer, and especially in the progression to metastasis.  The splicing factor FOX2 is a global splicing regulator particularly important in development and frequently up-regulated in poorly differentiated cancers.  In collaboration with the Sharp Lab at MIT I am trying to understand how mitogenic and oncogenic signaling affects FOX2 activity.
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'''Politics'''
 
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'''Martial Arts'''
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==Undergraduate Research==
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'''Europe'''
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===Clinical Proteomics===
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Using the combination of informatics and high-throughput experiments to identify clinically relevant diagnostics.  I worked with Dr. Harvey Cohen at Stanford to identify blood biomarkers for Kasawaki disease, monitor juvenile arthritis, and identify premature infants at risk for common disorders.
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'''Computer Programming'''
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===Biostatistics===
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High-throughput experiments in proteomics and genomics have required a range of new statistical methods.  Protein measurements are often strongly correlated, and correlated variables interfere with most of the statistical analyses.  I applied clustering methods as a form of data-reduction to reduce problems introduced by correlated proteins.
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===Computational Genetics===
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I worked with Dr. Leonid Kruglyak and Dr. Elaine Ostrander on study of genetic variability among pure-breed dogs.  This work was published in Science (see the CV).
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=iGEM=
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=Comments?=
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I'm a graduate student adviser for MIT's undergraduate team for the International Genetically Engineered Machines competition.  See the [http://2008.igem.org iGEM] website or our [[IGEM:MIT/2008|team wiki ]] for more information.
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What's the point of a Wiki homepage if people don't make changes?  Add anything here.
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=Curriculum Vitae=
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Download my CV [http://web.mit.edu/scottmc/www/Scott_Carlson_CV.pdf here].
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</wikionly>
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=Bio=
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''Go back to [[Scott_Carlson#Research|Research]] if you got here by mistake and don't really want to read my life story.''
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'''High School'''
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I'm from Seattle WA, in the Pacific Northwest. Early on I planned to be a computer programmer, and I taught myself several programming languages. That plan lasted exactly one week after I got my first programming job.  If you've ever worked in a grey cubicle in corporate America then you understand why I got out.  Otherwise just be grateful that you don't understand that particular type of pain.  After a string of random events I ended up doing genetics and computational biology with Leonid Kruglyak at the Fred Hutchinson Cancer Research Center.  I spent three summers there working on all sorts of computational genetics (genetic linkage analysis, haplotype inference, phylogeny).  Since then, all my research has focused on that stuff.
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'''College'''
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Looking at colleges it was a close call between Stanford and MIT.  Taking it right to the deadline, Stanford won out because of more attractive undergrads and better weather. Turned out to be a good choice because here I am at grad school, and now I've been at both places. (don't be stupid, if weather or hot students actually mattered I'd be at UCSD right now.  I chose Stanford for academic reasons)  I majored in Chemistry with a minor in Bio.  Prof. Richard Zare was my academic advisor but I never even looked at doing research in pure chemistry.
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Along the way I spent a quarter in Oxford reading History of Science ("reading" is British for taking classes, as much as Oxford teaches classes).  The "big picture" experience was a lot of fun, and it was great traveling around Europe.
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In my sophomore year I got involved in biostatistics in medical research with Dr. Harvey Cohen in the Dept. of Pediatrics at the Stanford med school.  All the details are in the [[Scott_Carlson#Research|Research]]. The experience completely reshaped my perspective on science, especially working with data from premature infants.  ''The big picture hits you fast and hard when half the children in your dataset did not survive.''
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So that's how I ended up moving from Chemistry to Biostatistics to Bioengineering.  Going into my Senior year at Stanford I applied for PhD programs in bioengineering.  MIT felt like a great fit, and I deferred my spot here until 2006.  At the same time I applied for the Master of Philosophy in Computational Biology at Cambridge University.  I was fortunate enough to get a scholarship from the Gates Cambridge Trust that covered tuition and expenses.
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'''Interlude: England'''
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'''MIT'''
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Current revision

Contents

I'm a 5th-year graduate student in Biological Engineering at the Massachusetts Institute of Technology. I work with Professor Forest White on phosphoproteomics applied to diabetes and cancer.

Research Interests

Graduate Research

MAP kinases in cancer and diabetes

The mitogen-activated protein kinases (MAPKs) are involved in signal transduction downstream of stress and growth factors. Activation of JNK in a critical event in development of type II diabetes, and activation of ERK is involved in both diabetes and cancer. I am combining mass spectrometry a chemical genetics strategy, developed by Kevan Shokat, to identify substrates of these kinases.

Mechanisms of oncogenesis by KRAS mutation

Activating mutations in KRAS occur in about 60% of all cancers. The KRAS oncogene signals through several major pathways, including the Raf/MEK/ERK cascade. This cascade is a major target for pharmaceutical research because of its importance in KRAS signaling and because it is targeted by other important oncogenes. My goal is to understand how KRAS activation leads to cancer development by activating this and other pathways.

Regulation of alternative splicing

Regulation of mRNA splicing is implicated in development of cancer, and especially in the progression to metastasis. The splicing factor FOX2 is a global splicing regulator particularly important in development and frequently up-regulated in poorly differentiated cancers. In collaboration with the Sharp Lab at MIT I am trying to understand how mitogenic and oncogenic signaling affects FOX2 activity.


Undergraduate Research

Clinical Proteomics

Using the combination of informatics and high-throughput experiments to identify clinically relevant diagnostics. I worked with Dr. Harvey Cohen at Stanford to identify blood biomarkers for Kasawaki disease, monitor juvenile arthritis, and identify premature infants at risk for common disorders.

Biostatistics

High-throughput experiments in proteomics and genomics have required a range of new statistical methods. Protein measurements are often strongly correlated, and correlated variables interfere with most of the statistical analyses. I applied clustering methods as a form of data-reduction to reduce problems introduced by correlated proteins.

Computational Genetics

I worked with Dr. Leonid Kruglyak and Dr. Elaine Ostrander on study of genetic variability among pure-breed dogs. This work was published in Science (see the CV).

iGEM

I'm a graduate student adviser for MIT's undergraduate team for the International Genetically Engineered Machines competition. See the iGEM website or our team wiki for more information.

Curriculum Vitae

Download my CV here.

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