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Publications |
Refereed
Publications (SELECTED)
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G. Alterovitz, M. Xiang, J. Liu, A. Chang, and M. F.
Ramoni, "Discovering Biofluid Biomarkers Using an
Information Theoretic Proteomics Framework,"
Proceedings of the Pacific Symposium on Biocomputing,
2008 (In press).
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G. Alterovitz, M. Xiang, I. S. Kohane, and M. F. Ramoni,
"Mass Similarity Shapes Protein Interaction Networks
and Is Conserved Across Evolution," PLoS ONE,
2007 (In Press).
- J. L. Maron, K. L. Johnson, D. Slonim, C. Q. Lai, M.
Ramoni, et al., "Gene expression analysis in pregnant
women and their infants identifies unique fetal
biomarkers that circulate in maternal blood," J
Clin Invest, vol. 117, pp. 3007-3019, Oct 1 2007.
- G. Alterovitz, T. Muso, P. Malalur, and M. F. Ramoni, "A
Systematic Approach to Quantifying Evolutionary
Functional Trends Across the Universal Tree of Life,"
Proceedings of the IEEE 7th International Symposium
on Bioinformatics and Bioengineering (BIBE), 2007.
- G. Alterovitz, E. Lyashenko, M. Xiang, and M. F.
Ramoni, "Linking Protein Mass with Function via
Organismal Massome Networks," Proceedings of the
IEEE 7th International Symposium on Bioinformatics and
Bioengineering (BIBE), 2007.
- G. Alterovitz, J. Liu, E. Afkhami, and M. F. Ramoni,
"Bayesian methods for proteomics," Proteomics,
Jul 24 2007.
- G. Alterovitz and M. F. Ramoni, "Bioinformatics
and Proteomics: An Engineering-Based Problem Solving
Approach," IEEE Transactions on Education,
vol. 50, pp. 49-54, 2007.
- G. Alterovitz, M. Xiang, M. Mohan, and M. F. Ramoni,
"GO PaD: The Gene Ontology Partition Database,"
Nucleic Acids Res, 2007.
- M. Aivado, D. Spentzos, U. Germing, G. Alterovitz,
X. Y. Meng, et al., "From the cover: Serum proteome
profiling detects myelodysplastic syndromes and
identifies CXC chemokine ligands 4 and 7 as markers for
advanced disease," Proc Natl Acad Sci U S A,
vol. 104, pp. 1307-12, Jan 23 2007.
- G. Alterovitz, V. Muralidhar, and M. F. Ramoni, "Gene
Lethality Detection and Characterization via Topological
Analysis of Regulatory Networks," IEEE
Transactions on Circuits and Systems I, vol. 53,
2006.
- G. Alterovitz and M. F. Ramoni, "Discovering
Biological Guilds through Topological Abstraction,"
AMIA Annu Symp Proc, pp. 1-5,
2006.
(Winner, Epstein award. First
place, AMIA student paper competition)
- G. Alterovitz and M. F.
Ramoni, "Biological Network Epitomes via Topological
Compression," Proceedings of IEEE Genomic Signal
Processing and Statistics (GENSIPS), 2006.
[PDF
Download]
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G. Alterovitz, V.
Muralidhar, and M. F. Ramoni, "Gene Lethality
Detection Across Biological Network Domains: Hubs Versus
Stochastic Global Topological Analysis," Proceedings of IEEE Genomic Signal Processing and
Statistics (GENSIPS), 2006.
[PDF
Download]
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G. Alterovitz, J. Liu, J.
Chow, and M. F. Ramoni, "Automation, parallelism, and
robotics for proteomics," Proteomics, Jun 19
2006.
[Summary/Web Link]
[PDF
Download]
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G. Alterovitz, E. Afkhami,
J. Barillari, and M. Ramoni, "Proteomics," in
Encyclopedia of Biomedical Engineering, M. Akay, Ed.
New York: John Wiley & Sons, 2006.
[Summary/Web Link]
[PDF
Download]
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G. Alterovitz, D. Patek,
I. S. Kohane, and M. Ramoni, "Human Protein
Meta-Interaction Database (HPMD) Potentiates Integration
for Meta-Analysis," Proceedings of IEEE Genomic
Signal Processing and Statistics (GENSIPS), 2005.
[PDF
Download]
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G. Alterovitz, I. S.
Kohane, and M. Ramoni, "Characterizing Human Protein
Mass Density Distributions," Proceedings of IEEE
Genomic Signal Processing and Statistics (GENSIPS), 2005.
[PDF
Download]
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M. Aivado, D. Spentzos,
G. Alterovitz, H. H. Otu, F. Grall, et al., "Optimization
and evaluation of surface-enhanced laser desorption/ionization
time-of-flight mass spectrometry (SELDI-TOF MS) with
reversed-phase protein arrays for protein profiling,"
Clin Chem Lab Med, vol. 43, pp. 133-40, 2005.
[Summary/Web Link]
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Alterovitz G, Aivado M, Spentzos D, Libermann T, Ramoni
M, and Kohane I, "Analysis and Robot Pipelined
Automation for SELDI-TOF Mass Spectrometry,"
Proceedings of the International Conference of IEEE
Engineering in Medicine and Biology, San Francisco, CA,
USA, 2004.
[Summary/Web Link]
[PDF
Download]
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Alterovitz
G. "Electrical Engineering and
Nontechnical Design Variables of Multiple Inductive Loop
Systems for Auditoriums," J. Deaf Stud. Deaf Educ.,
9: 202-209, 2004. [PDF
Download]
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Alterovitz G, Staelin DH, Philip JH.
"Temporal patient state characterization using
iterative order and noise (ION) estimation: applications to
anesthesia patient monitoring, Journal of Clinical
Monitoring and Computing, 17:351-359, 2002.
[PDF Download]
Books (Academic)
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G. Alterovitz, M. F.
Ramoni, and eds., "Systems Bioinformatics: An
Engineering-Based Problem Solving Approach," Artech
House, 2007.
[Amazon]
[Book Site]
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G. Alterovitz, L.
Armstrong, P. DasGupta, D. Eaves, F. Grant, et al.
delegates, A New Magnetic North: How Canada Can
Attract and Retain Young Talent. Toronto:
Canada25, 2000.
[PDF
Download]
Conferences
and Publications (Not
mentioned above)
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G. Alterovitz, T. Muso, P. Malalur, and M. F. Ramoni, "Functional
protein information across space and time,"
Proceedings of the IEEE Information Theory Workshop,
Lake Tahoe, CA, 2007 (Invited).
- G. Alterovitz, E. Lyashenko, M. Xiang, and M. F.
Ramoni, "Functional Enrichment Across Organism
Massomes," in RECOMB, Oakland, CA, 2007.
- G. Alterovitz, "Information
Theory Applications in Bioinformatics,"
Proceedings of the Information Theory Applications
Workshop, San Diego, CA, 2007 (Invited talk).
- C. Wood and G. Alterovitz, "Fundamentals of
Design for Synthetic Biology," in Systems
Bioinformatics: An Engineering Case-Based Approach,
G. Alterovitz and M. F. Ramoni, Eds. New York: Artech
House, 2007.
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V. Muralidhar, G. Szabo, and G. Alterovitz, "Topological
Analysis of Biomolecular Networks," in Systems
Bioinformatics: An Engineering Case-Based Approach,
G. Alterovitz and M. F. Ramoni, Eds. New York: Artech
House, 2007.
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G. Alterovitz, E. Afkhami, and M. Ramoni, "Robotics,
Automation, and Statistical Learning for Proteomics," in New Developments in
Robotics Research, J. X. Liu, Ed. New York: Nova
Science Publishers, Inc., 2005.
[Summary/Web Link]
[PDF
Download]
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G. Alterovitz, M. Xiang,
M. F. Ramoni, and I. S. Kohane, "Protein Network
Topology Metric Conservation: From Yeast to Human,"
in RECOMB, Cambridge, MA, 2005
(Invited).
[PDF
Download]
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G. Alterovitz, D. Patek,
M. F. Ramoni, and I. S. Kohane, "The Human Massome of
Protein Interactions: A New Mass Spectrometry-Based
Perspective," in RECOMB, Cambridge, MA, 2005.
[PDF
Download]
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M. Aivado, D. Spentzos,
F. Grall, H. H. Otu, G. Alterovitz, et al., "Optimization
and standardization of SELDI-TOF MS-derived protein
profiles from hydrophobic ProteinChip arrays," in
German, Austrian, and Swiss Societies of Hematology and
Oncology (DGHO), Innsbruck, Oct 2004.
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Alterovitz G, Aivado M, Libermann T, Ramoni M, and
Kohane I, "Machine Learning Techniques for Proteomic
Classification and Marker Selection Using Sample
Fractionation with SELDI-TOF MS," International
Conference on Analysis of Genomic Data, Boston, MA,
2004.
[Summary/Web Link]
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Aivado M, Alterovitz G, Spentzos D, Grall F, Otu H, Cho
J, Ramoni M, and Libermann T, "Reliable and
reproducible SELDI-TOF MS-derived serum peptide and
protein profiles for the diagnosis of Myelodysplastic
Syndromes," ProteinChip Technology Users' Group
Meeting, San Diego, 2004.
[Summary/Web
Link]
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Alterovitz G, Aivado M, Libermann T, and Ramoni
M, "Noise
Characterization in Biological and Technical Replicates
for Surface-Enhanced Laser Desorption/Ionization
Time-of-Flight Mass Spectrometry," 6th Annual
Conference on Computational Genomics, Boston, MA, 2003.
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Alterovitz G, Armstrong L, Grant F, Sinha S, Konopek
M. "Health Care," A New Magnetic North,
Toronto: Canada25, 2000.
[PDF Download]
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Alterovitz
G and Hogue C. "Comparing Secondary
Structure Prediction with Genomic Structure Datasets
from Methanococcus jannaschii and Aquifex aeolicus,
Journal of Microbial and Comparative Genomics,
Vol. 3, No. 4, C-21, 1998
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Feldman H, Alterovitz G, Plaskos
N, and Hogue C. "A
Potential to Predict Protein Thermostability Derived
from the Genome of Methanococcus jannaschii,
Journal of Microbial and Comparative Genomics,
Vol. 3, No. 4, C-27, 1998.
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Mouchawar G, Street A, Alterovitz G, Tchou C, Badelt
S. "Sural Nerve Sensory Thresholds of Defibrillation
Waveforms, Journal of the American College of
Cardiology, Vol 31/2A,
373A, Feb. 98.
Invited Talks (ACADEMIC, Not mentioned above)
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G. Alterovitz, "Bayesian
Methods in Proteomics," in Bayes Boot Camp,
Boston, MA, 2006.
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Alterovitz
G. "Clinical Monitoring Using Temporal
Patient State Characterization," Whitehead
Institute, July 23, 2003. (Invited by Dr. Eric Lander,
Director of Whitehead Institute and Co-founder of Human
Genome Project)
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Alterovitz
G. and Morley M., "US-Canadian Medical
Research and Health Care Policies: Perspectives from
Recent Fulbright Scholars, March 8, 2000, MIT.
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Alterovitz
G. (USA speaker). "A Look at US/Canadian
Differences, Sundial Inn, Rotary Club (Orillia,
Canada Chapter), Feb. 20, 1999.
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Alterovitz G. "The Fulbright Program Experience: A
Fulbrighter's Perspective. In commemoration of 50 years
of Fulbright Scholarships (1948-49/1998-99)," International Student Center, Feb. 3, 1999.
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Alterovitz
G. "1997 Patterson Prize Acceptance Talk,
Pittsburgh Athletic Center, May 1997.
THESES
and other WORK (ACADEMIC)
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G. Alterovitz, "A
Bayesian Framework for Statistical Signal Processing and
Knowledge Discovery in Proteomic Engineering," in
Electrical and Biomedical Engineering Cambridge:
Massachusetts Institute of Technology, PhD Thesis, 2005.
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G. Alterovitz, "Temporal
Characterization of Patient State with Applications to
Prediction of Tachycardia in Anesthesia via Induction of
Inhaled Desflurane," in S.M. Thesis, Electrical
Engineering and Computer Science Cambridge, MA:
Massachusetts Institute of Technology, 2001.
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G. Alterovitz, M. Kellis,
and M. F. Ramoni, "6.092: Bioinformatics and
Proteomics: An Engineering-Based Problem Solving
Approach," Retrieved September 20, 2005, from MIT
OpenCourseWare site: http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-092January--IAP--2005/CourseHome/index.htm,
April 22, 2005 2005 (Electronic Media).
publications (Professional)
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Asher, D. ed.
Graduate Admissions Essays: Write
Your Way into the Graduate School of Your Choice,
(My essays were bought and appear in this book).
[Summary/Web Link]
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Alterovitz
G. (Front Cover Story). "From Windows to
Supercomputing," Cross Platform Strategies,
Winter 1995. Alterovitz G. "Northern Reflections,"
Attachι,
Vol. 2, No. 1, 2000.
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Alterovitz
G. "Life Sciences Workbench Data Analysis
Toolbox for Excel," HMS Beagle, Issue 36,
Aug. 1998.
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Alterovitz
G. "ISIS/Draw,"
HMS Beagle,
Issue 18, Oct. 1997.
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Alterovitz
G. "The Internet Revolution and its
Affect on the Medical Profession, MacNet,
Feb. 1996.
50+ articles in city-based and/or AP-affiliated
newspapers.
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