For the most up-to-date information:

http://www.linkedin.com/in/mgaldzic

Publications

PEER REVIEWED

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert M. Sauro,
and John H. Gennari. (2011) Standard Biological Parts Knowledgebase.
PLoS ONE. 6(2): e17005. doi:10.1371/journal.pone.0017005

Jean Peccoud, J Christopher Anderson, Deepak Chandran, Douglas Densmore,
Michal Galdzicki, Matthew W Lux, Cesar A Rodriguez, Guy-Bart Stan, and Herbert M Sauro.
Essential information for synthetic DNA sequences. (2011) Nature Biotechnology. 29, 22.
doi:10.1038/nbt.1753

John H Gennari, Maxwell L Neal, Michal Galdzicki, and Daniel L Cook.
(2011) Multiple Ontologies in Action: Composite Annotations
for Biosimulation Models. Journal of Biomedical Informatics. 44(1):146-54.
doi:10.1016/j.jbi.2010.06.007

Ze Tian, Nathan Palmer, Patrick Schmid, Hui Yao, Michal Galdzicki, Bonnie Berger,
Erxi Wu, Isaac S. Kohane. (2009) A practical platform for blood biomarker study by using
global gene expression profiling of peripheral whole blood. PLoS ONE. 4(4):e5157.

Erxi Wu, Nathan Palmer, Ze Tian, Annie P. Moseman, Michal Galdzicki,
Xuetao Wang, Bonnie Berger, Hongbing Zhang, and Isaac S. Kohane.(2008)
Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR
genetically defined cells. PLoS ONE. 3(11):e3794.

Jeffrey R. Guyon, Julie Goswami, Susan J. Jun, Marielle Thorne, Melanie
Howell, Timothy Pusack, Genri Kawahara, Leta S. Steffen, Michal Galdzicki
and Louis M. Kunkel (2009) Genetic isolation and characterization of a
splicing mutant of zebrafish dystrophin. Human Molecular Genetics. 18(1):202-11.

Vamsi Veeramachaneni, Michal Galdzicki, Wojciech Makalowski, Raman
Sood, and Izabela Makalowska. (2004) Mammalian Overlapping Genes: The
Comparative Perspective. Genome Research 14:280-286.

Raman Sood, Izabela Makalowska, Michal Galdzicki, Ping Hu, Erica
Eddings, Christiane M. Robbins, Tracy Moses, Jin Namkoong, Suzie Chen,
and Jeffrey M. Trent. (2003) Cloning and characterization of a novel
gene SHPRH encoding a conserved putative protein with SNF2/helicase
and PHD-finger domains from the 6q24 region. Genomics, 82/2:153-161.

BOOK CHAPTERS

Michal Galdzicki, Deepak Chandran, John H. Gennari, Herbert M. Sauro.
(2011) Data Model Standardization for Synthetic Biomolecular Circuits and Systems.
In H. Koeppl, G. Setti, M. di Bernardo, and D. Densmore, (Eds.),
Design and Analysis of Biomolecular Circuits. (pp. 281-293). New York: Springer.
doi:10.1007/978-1-4419-6766-4_13

INVITED TALKS

Michal Galdzicki
Synthetic Biology Open Language (SBOL) and CAD Tools - information exchange and design.
US Army Engineer Research and Development Center Synthetic Biology and the Environment Workshop,
Creekside Inn, Palo Alto CA, 2011.

Michal Galdzicki
Synthetic Biology Open Language (SBOL) a new information sharing framework
to encourage re-use of DNA components for biological engineering.
Combi Seminar, University of Washington, 2011.

Michal Galdzicki, Daniel L. Cook, Benjamin L. Zaitlen, Ryan Roper,
Herbert M. Sauro, and John H. Gennari
Building the Cell Behavior Ontology (CBO): An Illustrated Guide.
Cell Behavior Ontology Workshop 2, Biocomplexity X, 2009.

Michal Galdzicki
Organizing Biological Parts: A semantic model of synthetic biology designs
NLM Informatics Training Conference, 2009

Michal Galdzicki. Building Ontologies and Standards in the Systems
Biology Community. NIGMS Cell Behavior Ontology Workshop, 2009.

Michal Galdzicki, Heather Peters, Alal Eran, Iris Eisenberg-Loebl,
Kayla Vatalaro, Rae Graham, David Pinedo, Paul Lavoie, Mei Han, Rachel
Hundley, Ellen Hanson, Alvin Kho, Charles Nelson, Leonard Rappaport,
Stephanie Brewster, Ingrid Holm, Louis Kunkel, Isaac Kohane.
Clustering of Genome Wide Expression Profiles in Autism Spectrum
Disorder. Boston Autism Consortium, 2006.

OTHER PUBLICATIONS

Jeff Johnson, Michal Galdzicki, Herbert Sauro (2010)
Standard for the Electronic Distribution of SBOLv Diagrams. BBF RFC #68. doi: 1721.1/60086

Michal Galdzicki, Deepak Chandran, Alec Nielsen, Jason Morrison,
Mackenzie Cowell, Raik Grunberg, Sean Sleight, Herbert Sauro (2009)
Provisional BioBrick Language (PoBoL). BBF RFC #31. doi: 1721.1/45537

Michal Galdzicki and Sung Lee. Bio-Central Semantic Knowledgebase
of Biomolecular Interaction Data. W3C Workshop on Semantic Web for
Life Sciences, 2004.

Michal Galdzicki, Izabela Makalowska, Tyra G Wolfsberg. (2000)
Pattern formation and developmental mechanisms [Web alert], Current
Opinion in Genetics & Development, 10:345-346. doi:10.1016/S0959-437X(00)00093-9

Tyra G Wolfsberg, Michal Galdzicki, Izabela Makalowska. (2000)
Genetics of disease [Web alert], Current Opinion in Genetics &
Development, 10:245-246. doi:10.1016/S0959-437X(00)00089-7

Izabela Makalowska, Tyra G Wolfsberg, Michal Galdzicki. (2000)
Chromosomes and expression mechanisms [Web alert] Current Opinion in
Genetics & Development, 10:139-140. doi:10.1016/S0959-437X(00)00073-3

CONFERENCE ABSTRACTS (presented by author)

Michal Galdzicki, Laura Adam, J. Christopher Anderson, Deepak Chandran, Douglas Densmore, Drew
Endy, John H Gennari, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay Maheshwari, Barry Moore,
Chris J. Myers, Jean Peccoud, Cesar A. Rodriguez, Nicholas Roehner, Guy-Bart Stan, Mandy Wilson,
Herbert M. Sauro. Synthetic Biology Open Language: A standardized information exchange framework
for synthetic biologists. The 5th International Meeting on Synthetic Biology, Stanford University,
Stanford, CA, June 15-17, 2011.

Michal Galdzicki, Cesar Rodriguez, Herbert Sauro, Laura Adam, J. Christopher Anderson, Deepak Chandran,
Douglas Densmore, Drew Endy, John H. Gennari, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay
Maheshwari, Barry Moore, Chris J. Myers, Jean Peccoud, Nicholas Roehner, Guy-Bart Stan, Mandy Wilson,
Herbert M. Sauro. (2011) Evolution of SBOL. design information exchange standard, International Workshop
on Bio-Design and Automation 2011, San Diego Convention Center, San Diego, CA, June 6-7, 2011.

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, John Gennari and Herbert Sauro
A Semantic Knowledge Base of Standard Biological Parts
International Workshop on Bio-Design and Automation 2010, Anaheim, CA

Michal Galdzicki, Deepak Chandran, Herbert Sauro, Daniel Cook, and John Gennari. (2009)
Bridging Synthetic Biology Models and Experiments using PoBoL.
International Workshop on Bio-Design and Automation 2009, San Francisco, CA (poster)

Deepak Chandran, Michal Galdzicki, and Alec Nielsen. (2009)
Bridging Synthetic Biology Design and Experiments using PoBoL.
International Workshop on Bio-Design and Automation 2009, San Francisco, CA (talk)

Michal Galdzicki, Heather Peters, Alal Eran, Iris Eisenberg-Loebl,
Kayla Vatalaro, Rae Graham, David Pinedo, Paul Lavoie, Mei Han, Rachel
Hundley, Ellen Hanson, Alvin Kho, Charles Nelson, Leonard Rappaport,
Stephanie Brewster, Ingrid Holm, Isaac Kohane, Louis Kunkel. Large
Scale Microarray Study of Autism Spectrum Disorders in Pediatric
Cohorts. Boston Autism Consortium, 2006.

Michal Galdzicki, Alal Eran, Iris Eisenberg-Loebl, Alvin Kho,
Heather Peters, Kaitlin Graham, Stephanie Brewster, Rachel Hundley,
Ellen Hanson, Janice Ware, Leonard Rappaport, Ingrid Holm, Louis
Kunkel, Isaac Kohane. Expression profiling of blood in Autism. ASHG,
2006.

Michal Galdzicki, Alal Eran, Alvin Kho, Iris Eisenberg-Loebl,
Heather Peters, Stephanie Brewster, Rachel Hundley, Ellen Hanson,
Janice Ware, Leonard Rappaport, Ingrid Holm, Louis Kunkel & Isaac
Kohane. Expression Profiling Of White Blood Cells In Autism. IMFAR,
2006.

Michal Galdzicki, Mezbah U. Faruque, Ping Hu, Erica Eddings, Pamela
Pollock, Izabela Makalowska, Christiane Robbins, Tracy Moses,
Elizabeth Gillanders, Joan-Bailey-Wilson, Raman Sood, Jeffrey M.
Trent. A43: Detailed Genomic Characterization and Candidate Gene
Analysis of 1p22 Region in Search of a Melanoma Susceptibility Gene.
NHGRI Annual Scientific Retreat, 2002.

OTHER CONFERENCE ABSTRACT

Cesar Rodriguez and Michal Galdzicki. (2011) Design, Implementation,
and Deployment of Electronic Datasheets. International Workshop on
Bio-Design and Automation 2011.

Alec Nielsen, Deepak Chandran, Michal Galdzicki, Sean Sleight, Herbert Sauro,
Daniel Cook, and John Gennari. (2009) PoBoL in the Lab: Structured Organization
of Biological Samples for Laboratory Management and Automation.
International Workshop on Bio-Design and Automation 2009.

Casey L. Overby, Michal Galdzicki, John H. Gennari. (2008) Analysis of
simulation environments utilized in biomedical research.
AMIA Annual Symposium Proceedings. 6:1077.

Casey L. Overby, Michal Galdzicki, John Gennari. Features of
Simulation Environments Utilized in Biomedical Research. National
Library of Medicine Annual Biomedical Informatics Trainee Meeting,
2008.

Alal Eran, Iris Eisenberg, David Pinedo, Kaitlin Graham, Michal
Galdzicki, Ingrid A Holm, Isaac S Kohane, Louis M Kunkel, Mutation
Analysis of the Retinoic Acid Receptor Alpha Gene (RARA) in Autism.
ASHG, 2006.

Alal Eran, Alvin Kho, Iris Eisenberg, Michal Galdzicki, Kamila
Naxerova, Marco Ramoni, Louis Kunkel, Isaac Kohane. Meta Prediction
of Human microRNA Targets. ISMB, 2006. (Best Poster Prize)

Eisenberg-Loebl Iris, Michal Galdzicki, Alal Eran, Holm Ingrid,
Isaac Kohane and Louis Kunkel. Peripheral Blood Mononuclear Cell
Collection and RNA Extraction Methodology from ASD Affected Children
and Normal Controls. IMFAR, 2006.

Alal Eran, Stephanie Jo Brewster, Michal Galdzicki, Eisenberg-Loebl
Iris, Heather Peters, Louis Kunkel, Isaac Kohane, and Holm Ingrid.
Diagnostic Markers and Ethical Dilemmas: Byproducts of the Children's
Hospital Boston Autism Study. IMFAR, 2006.

Sung Lee, Michal Galdzicki, Ryusuke Masuoka, Yannis Labrou, and Jon
Agre. "MED-STEER: Enabling Composition and Execution of Semantically
Described Medical Informatics Services for Mobile Caregivers,"
Biomedical Informatics for Clinical Decision Support, BECON/BISTIC
Symposium, 2004.

Kevin M. Brown, Raman Sood, Elizabeth M. Gillanders, Michal
Galdzicki, Pamela M. Pollock, Graham J. Mann, Nicholas K. Hayward,
Jeffrey M. Trent. An integrative technological approach to identify a
novel melanoma susceptibility gene on chromosome 1 (1p22). 24.3453.
Cellular, Molecular, and Tumor Biology. AACR 2004.