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Nik Brown |
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My research focus is on computational skepticism and collective intelligence. This research involves knowledge aggregation, machine learning, statistics, data mining, text mining, distributed algorithms, and web search. The tools (robots, data analysis and data visualization) for my research are built using python (Matplotlib, NLTK, Twisted, regular expressions, etc.), C++ (Boost, Qt), Django, Objective-C, Java and the Android Java SDK.
Gathering, analyzing and interpreting data relevant to a particular biological question is a difficult and fundamental task. This dissertation is about the development of approaches to exploit collective intelligence to improve the acquisition, analysis and interpretation of biological data. Collective Intelligence is the integration of machine learning techniques with distributed human interaction to develop algorithms that exploit the computers ability to processes large datasets with humans' abilities to find patterns and meaning in data. Some examples of collective intelligence include: Google's PageRank, Wikipedia, IBM's Many Eyes project (http://manyeyes.alphaworks.ibm.com/manyeyes/page/About.html), SETI@home (http://setiathome.berkeley.edu/), Social Networks, Folksonomies, and many others. Some links the Nik Brown's websites: thyroids.info - thyroid modelling, dnachips.org - code sharing for dnachip and microarray data analysis, brainmapping.net - code sharing for brainmapping and fMRI data analysis, chipseq.net - a grassroots think tank for chipseq data, computationallinguistics.net - computational linguistics,diseasome.org - aggregating knowledge for human disease, folksonomies.net - folksonomies, rnaseq.net - code sharing for rnaseq data analysis, tagedelic.org - a folksonomy for biomedical search, abacadaba.com - Tools for website maintenance, performance and seo, capoeirista.net - a grassroots think tank for capoeiristas, clipartist.net - aggregating, annotating and enhancing public domain and creative commons clip art, abacadaba.com - Tools for website maintenance, performance and seo, colouringbook.org - coloring books created from public domain clip art, fatweasel.com - internet tools for machine learning, data mining, visualisation, applied mathematics, statistics and collective intelligence, folksonomies.net - folksonomies, geeklish.net - learn to speak geek :: computer science, programming, linux and networking, lynky.net - a grassroots think tank for link analysis, mutantgenetics.com - open source tools for computational biology and bioinformatics, peacesymbol.org - a tribute to the peace symbol and the peace sign (aka CND logo), tagedelic.net - a grassroots think-tank for tag and keyword analysis. |
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Christina Kim |
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Lost Amongst Work
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| Robyn Javier neurobyn[AT]ucla.edu |
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Robyn is a third-year Cybernetics major, with an emphasis in neurosystems. She hopes to take part in an upcoming project involving math modeling of neurofibromatosis. You can usually find her in the lab, either working, or jamming with the other department Jazz musicians. |
| Jason Lee jasontlee[AT]ucla.edu |
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Jason is pursuing a B.S. degree in Electrical Engineering (with a Biomedical Engineering option). He began in the lab as a work study student in Spring 2003, maintaining this website and the network of computers in the lab. At one point or another he supposedly was modeling the kinetics of Angiostatin with the goal of understanding its low efficacy in human in antiangiogenesis cancer therapy. Currently, Jason is working on VISION-BIOMODBASE, an on-line interactive project for mathematical models. Jason spends infinitely many hours as an avid badminton player (playing competitively since 1997) and was President of UCLA Badminton during its revamping era from 2003-05; he currently serves as its Executive Advisor. Watch his team battle for the Southern California Collegiate Badminton League championship and at Collegiate Nationals, and bring (more) fame to UCLA! |
| Kai-Jye Lou tiamat06[AT]ucla.edu |
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Kai-Jye is a fourth-year cybernetics major pursuing the neurosystems concentration. He is currently working on a project pertaining to identifiability analysis in linear systems. Someday, he hopes to work on projects that lead to the development of neuroprostheses that restore motor or sensory functionality in injured patients, but he will be perfectly happy working to develop more comprehensive neural network models. For the little free time that he has, most of it is squandered at the racquetball courts or in producing original creations (and disasters) in the kitchen. |
| Pep Charusanti pep[AT]chem.ucla.edu |
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Pep is a Ph.D. student in the Department of Chemistry,
working on math models of drug effects in chronic myeloid leukemia.
His goal is to understand how drug resistance emerges in this disease
and affects dynamics and both the cellular and molecular level. Outside
of research you can find him hiking wherever there's a nice trail (or
no trail at all sometimes), going back and forth, back and forth, back
and forth between the two walls of the campus swimming pool, or his
favorite, traveling abroad and speaking different languages. One of
these days people will call him professor Pep, but for now a simple
"Yo man, how's it going?" will get his attention.
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| Pamela Douglas pamelita[AT]ucla.edu |
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Pamela is a second-year Neuroengineering student. Her
interests focus on modeling manganese toxicity and understanding the
Parkinsonian symptoms associated with it. Outside of biomedical engineering,
Pamela enjoys running, baking, playing guitar, dodgeball, and art.
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Marisa Eisenberg |
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Marisa is a second-year graduate student in the Biomedical
Engineering Interdepartmental Program, working on a math model of
the hypothalamus-pituitary-thyroid regulatory system, with a focus
on the pituitary. She received a B.S. in Cybernetics at UCLA in 2003.
When not lost in the winding labyrinth that is the lab, she also plays
keyboards with her rock band, Radar Radar, or spends time upstairs watching the universe
go by with the UCLA telescopes. Marisa's other interests include but
are not limited to: video games :), sketching/art/graphic design,
kung-fu, music (jazz, rock, and lots of other random stuff), philosophical
and otherwise interesting discussions, reading, sci-fi, sushi, star
trek and her two cute pet rats, 12 and 21.
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| Sharon Hori seiko24[AT]ucla.edu |
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Sharon is a Ph.D. student who graduated from UCLA with
B.S. degrees in Cybernetics and Applied Math, and an M.S. degree in Biomedical
Engineering. She's developed a mathematical model of insulin receptor
trafficking to elucidate the role of receptor endocytosis and recycling
in the development of insulin resistance and Type II diabetes. Currently,
she's developing a model of drug efflux across the blood-brain barrier
to assist in the development of codrugs for various brain diseases. Outside
the lab, Sharon tutors calculus and plays the piano, but not at the same
time, of course. She can also bake 30-minute brownies in only 20 minutes!
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Daniel Song |
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Daniel is currently a Ph.D. student in the Dept. of Computer
Science. He is studying the effect of Pegasys Peginterferon a-2a (PegIFN)
and ribavirin treatment on heptatitis C viral kinetics in infected patients.
Currently he is collaborating with Dr. Vincent Agnello from Lahey Clinic
(MA), who is performing extensive studies of HCV infection in chimpanzees.
In his spare time, he enjoys playing the violin and watching sporting
events. He is also an active member of his local church.
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| Levan Atanelov levani[AT]ucla.edu |
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Levan graduated from UCLA with a B.S. in Cybernetics,
and has since published a cancer paper, taught as a professor of chemistry
at a community college and interviewed for medical schools. He is currently
in his second year studying at Yeshiva University in New York.
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| Fiona Chandra se_lain[AT]eudoramail.com |
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Fiona graduated from the UCLA Cybernetics IDP in Fall
2005. She is currently running around interviewing for graduate school
and working in multiple labs. She recently got the chance to catch
up on her reading hobby on the plane.
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| Greg Ferl gzferl[AT]ucla.edu |
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Greg received his Ph.D. in Biomedical Engineering in
2005. His dissertation includes a description of mathematical models
used to describe and predict the biodistribution of anti-CEA monoclonal
antibodies as well as a section on microarray data analysis. He is currently
working as a post-doc in the Dept of Molecular and Medical Pharmacology
at UCLA, where his research focuses on mathematical modeling of cancer
treatment using PET and microPET data.
http://www.crump.ucla.edu/public/somi/gferl.html |
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Tova Fuller |
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Tova graduated from UCLA with a B.S. in Cybernetics (Spring 2002) and an M.S. in Biomedical Engineering (Summer 2004). Her Masters thesis focused on mathematical modeling and simulation of the hypothalamo-pituitary-thyroid axis to address thyroid hormone treatment bioavailability measures in humans. Tova entered the Medical Scientist Training Program (MSTP) at UCLA in Fall 2004. |
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Brian Gurbaxani |
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Brian received his Ph.D. in Molecular Biology at UCLA. He is now a senior scientist at the Centers for Disease Control and Prevention in Atlanta, GA, in the Viral Exanthems and Herpes Virus Branch. He is active in writing data mining algorithms for large datasets related to human papiloma virus (HPV), cervical cancer, and chronic fatigue syndrome (CFS). He is interested in datamining, visualization, and modeling techniques for high dimensional biological datasets. Brian is also an adjunct assistant professor of electrical and computer engineering at Georgia Tech, where he supervises graduate students doing research for the CDC as part of their thesis, mostly in the area of signal processing and algorithm development for ‘omics technologies. |
| Charles Harless charles[AT]harless.net |
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Charles left UCLA at the end of 2005 to explore and pursue opportunities outside of academia/research. Prior to this, he worked as a Programmer Analyst in the Division of General Internal Medicine in the UCLA David Geffen School of Medicine. He finished a MS in Computer Science in Spring 2005. In Dec 2005, he was offered a chance he could not pass up. He has left academics and even healthcare and is working for the Walt Disney Internet Group as a Software Engineer. Having been a Disney fan his whole life, he is having fun in his cool new digs. He specifically is part of the Walt Disney Parks and Resorts Online which provides the online websites for the Disney themeparks such as Disneyland, Walt Disney World, etc. Plus, his work is only 5 minutes from where he lives which makes the commute enjoyable for LA! He tries to return to UCLA when possible and is always interested in hearing from fellow Biocybers. |
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Jane Lin |
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Jane graduated from UCLA in 2003 as a Departmental
Scholar in Biomedical Engineering, with a B.S. in Cybernetics (and
concentration in Bioinformatics) and an M.S. in Biomedical Engineering.
She is currently a Ph.D. student in the Dept. of Biomedical Engineering
at Boston University, researching the effects of transcriptional
regulation on predicting phenotype from genotype, using the bidirectional
promoter as a model system. When Jane is not breaking her back solving
differential equations, she can be found rock climbing, playing
the guitar, or watching obscure independent movies.
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Yuliya Mulina |
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Lost Amongst Work
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Jenna Rickus |
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Jenna Rickus finished her Ph.D. in Neuroscience
and Neuroengineering in 2003. She is now an assistant professor
in Agricultural and Biological Engineering and Biomedical Engineering
at Purdue University. Her research interests include the dynamics
of structured protein networks, how temporal patterns of neurotransmitter
production and release contribute to neurological disorders, modeling
biomolecular function for biosensor design, and creating continuous
biosensors for taking time-resolved measurements of biological
signals. Her free time is spent hanging out with her son, George.
You can visit her lab at http://pasture.ecn.purdue.edu/~rickus/.
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Solomon Russell |
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Lost Amongst Work
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Karin Sinavsky |
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lost amongst work
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| James Skrinska james[AT]networkapplications.net |
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James recently finished his Masters thesis and resides now in north San Diego. His current work involves the integration of compartmental analysis with the abstract measurements collected through web activity. In the short, he is looking to drive business sales through identifying well defined customer profiles which can be used for target marketing campaigns and impulse shopping. When he isn't rigidly exhausting his left brain, he gives the righty a chance. He is currently building a collection of art pieces (watercolor, oil, charcoal, pastel) for a showing, and is always working to improve on classical piano and popular guitar. And if he isn't doing any of the above, he is most likely surfing (with lots sunscreen nowadays) or training for some triathalon. |