Sarah J. Aerni
E-mail: sarah@computationalbio.com
Website: http://www.computationalbio.com
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Objective |
A PhD that involves research in computational and possibly experimental investigation into the
molecular basis of human disease, biological sequences and cellular processes, allowing me to
apply and expand upon the knowledge I have obtained in the field of Computational Biology
and Bioinformatics. My current research interest is in single-cell expression profiling of organisms using image analysis and machine learning techinques. | |
Education |
In Progress, Fall 2006 | Stanford University | Palo Alto, CA |
Ph.D. Biomedical Informatics |
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♦ Primary Advisor Serafim Batzoglou
♦ Co-Advisor Stuart Kim ♦ William R. Hewlett Fellow (Stanford Graduate Fellowships) ♦ National Science Foundation Graduate Research Fellow ♦ http://bmi.stanford.edu/ |
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| 2001-2005 | University of California, San Diego | La Jolla, CA | |
B. S. Biology with Specialization in Bioinformatics, magna cum laude |
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Minor in French Literature
♦ Cumulative GPA: 3.84 |
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Research Interests |
I am interested in creating novel tools for use in Biological analysis, as well as modification and refinement of current techniques. I am particularly interested in developing and applying such tools for research in gene regulation, systems, population genetics, evolutionary theories and disease such as in cancer, antigen-induced disease, as well as other genetic conditions. |
Awards Received |
Phi Beta Kappa Society Member 2006 Finalist for Computing Research Association's Outstanding Undergraduate Award Program Caledonian Honor Society at Muir College, UCSD Provost’s Honors William R. Hewlett Fellowship (a Stanford Graduate Fellowship) National Science Foundation Graduate Research Fellowship |
Publications, abstracts and posters |
Xiao Liu, Fuhui Long, Hanchuan Peng, Sarah J Aerni, Min Jiang, Adolfo Sanchez-Blanco1, John I. Murray, Robert H. Waterston, Serafim Batzoglou, Eugene W Myers, Stuart K. Kim "Molecular signatures and gene expression at the single cell level in C. elegans", (in preparation for submission)
Sarah J Aerni, Doron Lipson, Stas Volik, Collin C. Collins, Michael Barrett, Zohar Yakhini, Benjamin J. Raphael "Combined Analysis of Copy Number Changes and Structural Rearrangements in Cancer Genomes", (in preparation for submission) B.T Messmer*, B. Raphael*, S.J Aerni, G.F Widhopf, L.Z Rassenti, J.G Gribben, N.E Kay, T.J Kipps"Computational Identification Of CDR3 Sequence Archetypes Among Immunoglobulin Sequences in Chronic Lymphocytic Leukemia" Leukemia Research (In Press) 2008. *co-authors Benjamin J Raphael, Stanislav Volik, Peng Yu, Chunxiao Wu, Guiqing Huang, Elena V Linardopoulou, Barbara J Trask, Frederic M Waldman, Joseph Costello, Kenneth J Pienta, Gordon B Mills, Krystyna Bajsarowicz, Yasuko Kobayashi, Sridharan Shivaranjani, Pamela Paris, Quanzhou Tao, Sarah J Aerni, Raymond P Brown, Ali Bashir, Joe W Gray, Jan-Fang Cheng, Pieter de Jong, Mikhail Nefedov, Thomas Ried, Hesed M Padilla-Nash and Colin C Collins "A sequence based survey of the complex structural organization of tumor genomes", Genome Biology 2008, 9:R59. Acknowledgement: Ali Mortazavi, Evonne Chen Leeper Thompson, Sarah T. Garcia, Richard M. Myers, Barbara Wold1 "Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire" Genome Res. 16:1208-1221, 2006. Sarah J. Aerni, Eleazar Eskin “10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB)”,RECOMB 2006: 546-562 ( electronic edition) Bradley T Messmer, Benjamin J Raphael, Sarah J Aerni , George F Widhopf, Laura Z Rassenti, Traci L Toy, and Thomas J Kipps “A Bioinformatic Approach To CLLIGHV Sequence Analysis Identifies Extensive Ig Sequence Archetypes Among Both Mutated And Unmutated Sequences”, (The 2005 American Society of Hematology Annual Meeting –abstract published in BLOOD (Vol 106, Number 11, Nov16, 2005, pg25a)) Benjamin J Raphael, Sarah J Aerni, George F. Widhopf, Thomas J Kipps, Bradley T Messmer “Advanced Tools For Analysis Of Large CLL IgV Gene Sequence Collections”,(X International Workshop on CLL http://www.iwcll.org/ - abstract published in supplement to Leukemia & Lymphoma (Vol 46, Suppl 1, 2005) ) |
Employment and Internships |
Bioinformatics Intern | ||
| July 2005-present | Wold Lab, California Insititute of Technology | Pasadena, CA | |
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Created 3 Python-based motif finders for Cistematic package,
implementing Greedy, Gibb’s Sampler and Expectation maximization
algorithms including background modeling using Markov models
♦ Used Cistematic package to identify possible motifs in ENCODE region for use in presentations at committee meetings |
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| January 2005-present | Bioinformatics Laboratory, UCSD | La Jolla, CA | |
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Created programs using Perl, Python and C to analyze sequence data
from tumor genomes and determine areas of interest based on
results
♦ Creating software for VDJ analysis of CLL patients ♦ Annotation of VDJ junction analysis of leukemia patients using Perl and Java ♦ Analysis of sequence homology of antibody using blast tools and clustering |
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| September 2003 - December 2005 | Computer Science and Engineering Department, UCSD | La Jolla, CA | |
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Selected by professors to be a member of team of tutors for
specific courses
♦ Assisted students in introductory Java and Fluency in Information Technologies courses ♦ Grading/critique of assignments and tests, proctoring exams, led lab section |
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| June 2003 - January 2005 | Scripps Institute of Oceanography | La Jolla, CA | |
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Harvested, managed and compiled data of Scripps scientific cruises
for SIO Explorer website (SIO Cruise archives) part of the
National Science Digital Library
nsdl.sdsc.edu
♦ Programming in Perl, C-shell, and Awk in the Unix environment |
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Activities |
Student Representative, Biomedical Informatics Training Program Executive Committee, Stanford |
| Stanford Association for Multi-Disciplinary Medicine and Science (S.A.M.M.S.) Signatory Member, Biomedical Informatics program representative | |
| Science Bus (Stanford University) an after-school science curriculum for grade school children at the East Palo Alto Charter School-Participant as a student tutor | |
| Stanford-South Africa Student Seminar Series student coordinator | |
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10th annual International Conference on Research in Computational
Biology (RECOMB 2006) - Serving on the anniversary committee |
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Southern California Bioinformatics Summer Institute – NIH/NSF
funded program providing an education and mentored research
program to undergraduate and graduate students interested in
pursing a career in Bioinformatics.
instructional1.calstatela.edu/jmomand2/ |
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10th annual International Conference on Research in Computational
Biology (RECOMB 2006) - Serving on the anniversary committee |
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Enduring Resources for Earth Science Education Teacher Workshop –
member of GDC Team. |
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Scripps Institute of Oceanography’s Geological Data Center Open
House– Presenter |
Memberships |
Golden Key International Honour Society International Society for Computational Biology |
PowerPoint Presentations |
Michal Linial "10 Years of RECOMB", Research in Computational Molecular Biology, Cinema Palace,
Venice Lido, IT, 03 April 2006.
(Presentation of 10 Years of the International Conference on Research in Computational Molecular
Biology (RECOMB)
http://www.iscb.org/newsletter9-1/ppt/recomb-10-years-final-short.ppt
Sarah Aerni "RNA Secondary Structure Prediction: Dynamic Programming Approaches", RNA chapter presentation for the textbook Neil C. Jones, Pavel A. Pevzner. "An Introduction to Bioinformatics Algorithms". MIT Press, 2000 (available at http://www.bioalgorithms.info/slides.htm#Ch6 - RNA) Sarah Aerni "cisGreedy Motif Finder for Cistematic", 2006 Southern California Bioinformatics Summer Institute Final Presentations, Los Angeles, CA, August, 2006. (available at http://instructional1.calstatela.edu/jmomand2/2006_website/presentations2006 ) Sarah Aerni "cisGreedy Motif Finder for Cistematic", 2005 Southern California Bioinformatics Summer Institute Final Presentations, Los Angeles, CA, August, 2005. (available at http://instructional1.calstatela.edu/jmomand2/3rd_Year/finalPPT/index.htm ) |
Volunteer experience |
Mental Health Assistant Intern (Psychiatric Ward) |
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| 2000-2001 | Century City Hospital | Century City, CA | |
Ski Instructor |
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| Winter 1998-2000 | Turnverein Lauchringen | Schwarzwald, Germany | |
Tutor |
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| 1998-1999 | Maple Center | Beverly Hills, CA | |
Tennis Assistant |
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| Summer 1997-1999 | Marymount Tennis Team | Los Angeles, CA | |
Homework Helper |
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| 1997-1998 | Beverly Hills Public Library | Beverly Hills, CA | |
References |
Upon request, please email sarah@computationalbio.com |
Skills and Qualifications |
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Current and previous computer programming experience in Java, ANSI C, C++, Python, Perl, csh/awk, bash, Scheme, R and Matlab) ♦ Unix, Windows and Mac OS X Environments ♦ Photoshop, Microsoft Word, Excel, PowerPoint ♦ Biochemical and Molecular Biology laboratory experience |
Languages |
Fluency in English, German and a Swiss dialect, competence in French |