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Fen Z. Hu, Ph.D.
Operations Director, Center for Genomic
Sciences
Allegheny-Singer Research Institute
320 East North Avenue
Pittsburgh, PA 15212
Phone: (412) 359-8094
Fax: (412) 359-4377
Email: fhu@wpahs.org
Education
Ph.D. Molecular and Cell Biology and Genetics. Dissertation: The Genetics
of Human Severe Pediatric Gastroesophageal Reflux Disease. Drexel
University College of Medicine, Philadelphia, PA. 2004.
M.S. Molecular and Human Genetics. Thesis : Mapping Of A Gene For Severe
Pediatric Gastroesophageal Reflux To Chromosome 13q14. Masters Thesis,
MCP-Hahnemann School of Medicine, Philadelphia, PA. 1999.
Academic and Professional Appointments
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2007-present
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Assistant Professor of Microbiology and Immunology, Drexel
University College of Medicine, Philadelphia, PA.
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2003-present
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Operations Director, Center for Genomic Sciences,
Allegheny-Singer Research Institute, Pittsburgh, PA.
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1998-2002
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Laboratory Manager, Center for Genomic Sciences,
Allegheny-Singer Research Institute, Pittsburgh, PA.
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1997-1998
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Senior Research Assistant, Center for Genomic Sciences,
Allegheny University of Health Sciences, Pittsburgh, PA.
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1997
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Research Specialist 3, Center for Genomic Sciences, University
of Pittsburgh School of Medicine, Pittsburgh, PA.
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Professional Interests
- Bacterial biofilm
pathogenesis, current projects include:
- Testing the distributed
genome hypothesis
- Identifying and
characterizing chronic virulence genes in Haemophilus influenzae,
Streptococcus pneumoniae, and Pseudomonas aeruginosa
- Assessing the degree of
genomic plasticity among isolates of pathogenic bacterial species
- The genetics of inherited
human diseases, current projects include:
- Pediatric gastroesophageal
reflux disease
- Craniosynostoses
- Dupuytren's contracture
- Ear development
- Development of efficient laboratory
and computational systems
- Design of an integrated high
throughput automated molecular biological laboratory
http://www.centerforgenomicsciences.org/facilities/robotic.html
- Algorithm development for
bioinformatic processes including: genotyping, allele calling, binning,
re-arraying, and array analysis.
Significant Scientific and Computational Accomplishments
Mapping of a gene for severe pediatric gastroesophageal reflux disease
Mapping of a gene for Dupuytren contracture
Cloning of genes associated with scarless wound healing
Design and Development of a Suite of Software Programs for automated handling
of genotypic data
Design and Development of a Suite of Software Programs for interfacing and
integrating multiple
robotic platforms used for gene array development and analyses
Memberships in Scientific Societies
Association for Research in Otolaryngology
American Society for Human Genetics
American Society for Microbiology
Grants
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04/2004 - 03/2009
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NIH-NIDCD 3R01DC02148, Molecular Analysis of Pathogens in
Otitis Media by PCR, $1,458,322 (Co-Investigator)
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07/2000 - 11/2008
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NIH-NIDCD- 2R01DC04173- The Role of Biofilms in the
Pathogenesis of Otorrhea, $3,073,808 (Co-Investigator)
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04/2003 - 08/2008
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NIH/NIDCD R01 DC05659-01 Pneumococcal Biofilms in Otitis
Media, $2,273,595 (Co-Investigator)
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07/2006 - 08/2008
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Genetics of Sleep Deprivation and Fatigue, $800,000
(Co-Investigator)
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10/2005 – 09/2008
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M2006-0070 Gene Expression in Peripheral Blood Mononuclear
Cells from Multiple Sclerosis Patients Undergoing Beta-Interferon Therapy,
$51,471 (Principal Investigator)
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Perspectives and Editorials
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Ehrlich, G.D., Hu, F.Z., Lin, Q., Costerton, J.W., and
Post, J.C. Intelligent implants to battle biofilms. ASM News 70:127-133, 2004.
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Publications
1. Forbes
ML, Horsey E, Hiller NL, Buchinsky FJ, Hayes JD, Compliment JM, Hillman T,
Ezzo S, Shen K, Keefe R, Barbadora K, Post JC, Hu FZ, Ehrlich
GD. Strain-specific virulence
phenotypes of Streptococcus pneumoniae assessed using the Chinchilla laniger model of
otitis media. PLoS One 3;4:e1969, 2008.
2. Hu FZ, Ehrlich GD.
Population-level virulence factors amongst pathogenic bacteria: Relation to infectious outcome. Future Microbiol 3(1):31-42, 2008.
3. Hogg JS, Hu FZ, Janto
B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD. Characterization and modeling of the Haemophilus influenzae core and
supra-genome supragenome based on the complete genomic sequences of Rd and 12
clinical nontypeable strains.
Genome Biology 8(6):R103, 2007.
4. Buchinsky
FJ, Forbes M, Hayes J, Hu FZ, Greenberg P, Post JC, Ehrlich GD. Phenotypic plurality among clinical
strains of nontypeable Haemophilus influenzae determined by symptom
severity in the chinchilla model of otitis media. BMC Microbiology 7:56, 2007.
5. Mußmann
M, Hu
FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Glöckner
FO, Amann R, Koopman WJH, Janto B, Hogg JS, Boissy R, Lasken RS, Stoodley P,
Ehrlich GD. Insights into the
genome of large sulphur bacteria revealed by analysis of single
filaments. PLoS Biology 5(9):e230, 2007.
6. Hiller NL,
Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K,
Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley
SD, Post JC, Ehrlich GD, Hu FZ.
Comparative genomic analyses of seventeen Streptococcus
pneumoniae strains:
Insights into the pneumococcal supragenome 2. J Bacteriol 189;22:8186-8195, 2007.
7. Singh MK, Scott TF,
LaFramboise WA, Hu FZ, Post JC, Ehrlich GD. Gene expression changes in peripheral blood mononuclear
cells from multiple sclerosis patients undergoing $-interferon
therapy. J Neurol Sci 258L52-59, 2007.
8. Erdos G, Sayeed S, Hu
FZ, Antalis PT, Shen K, Hayes JD, Ahmed AI, Johnson SL, Post JC, Ehrlich
GD. Construction and
characterization of a highly redundant Pseudomonas aeruginosa genomic
library prepared from 12 clinical isolates: Application to studies of gene distribution among populations. Int J Pediatr Otorhinolaryngol 70:1891-1900,
2006.
9. Shen K, Sayeed S,
Antalis P, Gladitz J, Ahmed A, Dice B, Janto B, Dopico R, Keefe R, Hayes J,
Johnson S, Yu S, Ehrlich N, Jocz J, Kropp L, Wong R, Wadowsky RM, Slifkin M,
Preston RA, Erdos G, Post JC, Ehrlich GD, Hu FZ. Infect Immun 74(9):5272-5283, 2006.
10. Donfack J, Buchinsky
FJ, Derkay CS, Steinberg BM, Choi SS, Conley SF, Meyer CM, 3rd,
McClay JE, Campisi P, Hu FZ, Preston RA, Abramson AL, Ehrlich GD, Post
JC. Four mutations in
epidermodysplasia verruciformis 1 (EVER1) gene are not contributors to
susceptibility in RRP. Int J
Pediatr Otorhinolaryngol
70:1235-1240, 2006.
11. Kathju S, Satish L,
Rabik C, Rupert T, Oswald D, Johnson S, Hu FZ, Post JC, Ehrlich
GD. Identification of
differentially expressed genes in scarless wound healing utilizing PCR
suppression subtractive hybridization.
Wound Rep Reg
14:413-420, 2006.
12. Allegrucci M, Hu FZ,
Shen K, Hayes J, Ehrlich GD, Post JC, Sauer K. Phenotypic characterization of Streptococcus pneumonia
biofilm development. J
Bacteriol 188;7:2325-2335, 2006.
13. Shen K, Gladitz J,
Antalis P, Dice B, Janto B, Keefe R, Hayes J, Ahmed A, Dopico R, Ehrlich N,
Jocz J, Kropp L, Yu S, Nistico L, Greenberg DP, Barbadora K, Preston RA, Post
JC, Ehrlich GD, Hu FZ.
Characterization, distribution and expression of novel genes among
eight clinical isolates of Streptococcus pneumoniae. Infect Immun 74;1:321-330, 2006.
14. Braxton E, Ehrlich G,
Stoodley P, Hall-Stoodley L, Veeh R, Hu F, Fux C, Quigley M, Post
JC. The role of biofilms in
neurosurgical device-related infections. Neurosurg Rev 28;4:249-255, 2005.
15. Hu FZ, Nystrom A, Ahmed A,
Palmquist M, Dopico R, Mossberg I, Gladitz J, Rayner M, Post JC, Ehrlich GD,
Preston RA. Mapping of an
autosomal dominant gene for Dupuytren’s contracture to
chromosome 16q in a Swedish family.
Clin Genet 68:424-429, 2005.
16. Ehrlich GD, Stoodley P,
Kathju S, Zhao Y, Mcleod BR, Baliban N, Hu FZ, Sotereanos N, Costerton
JW, Stewart PS, Post JC, Lin Q.
Engineering approaches for the detection and control of orthopaedic
biofilm infections. Clin
Orthop 437:59-66, 2005.
17. Ehrlich GD, Hu FZ,
Shen K, Stoodley P, Post JC.
Bacterial plurality as a general mechanism driving persistence in
chronic infections. Clin
Orthop 437;20-24, 2005.
18. Stoodley P, Kathju S, Hu
FZ, Erdos G, Levenson JE, Mehta N, Dice B, Johnson S, Hall-Stoodley L,
Nistico L, Sotereanos N, Sewecke J, Post JC, Ehrlich GD. Molecular and imaging techniques for
bacterial biofilms in joint arthroplasty infections. Clin Orthop 437:31-40, 2005.
19. Shen K, Antalis P,
Gladitz J, Sayeed S, Ahmed A, Yu S, Hayes J, Johnson S, Dice B, Dopico R,
Keefe R, Janto B, Chong W, Goodwin J, Wadowsky RM, Erdos G, Post JC, Ehrlich
GD, Hu FZ.
Identification, distribution, and expression of novel (nonRd) genes in
ten clinical isolates of nontypeable Haemophilus influenzae. Infect Immun 73;6:3479-3491,
2005.
20. Gladitz J, Shen K,
Antalis P, Hu FZ, Post JC, Ehrlich GD. Codon usage comparison of novel genes in clinical isolates
of Haemophilus influenzae.
Nucleic Acids Res 33;11:3644-3658, 2005.
21. Hu FZ, Donfack J, Ahmed A,
Dopico RJ, Johnson S, Post JC, Ehrlich GD, Preston RA. Fine mapping a gene for pediatric
gastroesophageal reflux on human chromosome 13q14. Hum Genet
114;6:562-572, 2004.
22. Jiang S, Gitlin J, Deng
FM, Liang FX, Lee A, Atala A, Bauer SB, Ehrlich GD, Feather SA, Goldberg JD,
Goodship JA, Goodship TH, Hermanns M, Hu FZ, Jones KE, Malcolm S,
Mendelsohn C, Preston RA, Retik AB, Schneck FX, Wright V, Ye XY, Woolf AS, Wu
XR, Ostrer H, Shapiro E, Yu J, Sun TT. Lack of major involvement of human uroplakin genes in
vesicoureteral reflux:
Implications for disease heterogeneity. Kidney Int 66;1:10-19, 2004.
23. Erdos G, Sayeed S,
Antalis P, Hu FZ, Hayes J, Goodwin J, Dopico R, Post JC, Ehrlich GD.
Development and characterization of a pooled Haemophilus influenzae
genomic library for the evaluation of gene expression changes associated with
mucosal biofilm formation in otitis media. Int J Ped Oto 67;7:749-755,
2003.
24. Ehrlich GD, Veeh R,
Wang X, Costerton JW, Hayes JD, Hu FZ, Daigle BJ, Ehrlich GD, Post
JC. Mucosal biofilm formation on
middle-ear mucosa in the chinchilla model of otitis media. JAMA
287:1710-1715, 2002.
25. Heike C, Seto M,
Ehrlich GD, Preston RA, Hu FZ, Hing A, Jackson C, Palidin A,
Cunningham M. Century of
Jackson-Weiss syndrome: Further
definition of clinical and radiographic findings in “lost” descendants of the
original kindred. Am J Med
Genetics 100:315-324, 2001.
26. Dry GM, Yasinskaya YI,
Williams JK, Ehrlich GD, Preston RA, Hu FZ, Gruss JS, Ellenbogen
R, Cunningham ML. Inhibition of apoptosis: A potential mechanism for syndromic
craniosynostosis. Plast Reconstr Surg 107:425-32, 2001.
27. Ehrlich GD, Hu FZ,
Preston RA, Post JC. The
spectrum of pediatric gastroesophageal reflux. (letter) JAMA. Dec 27;284(24):3125, 2000.
28. Hu FZ, Post JC, Johnson S,
Ehrlich GD, Preston RA.
Reduction of the GER gene region on 13q 14 and exclusion of the 5-HT2A
receptor gene as cause of hereditary severe pediatric gastroesophageal
reflux. Hum Genet. 107:519-525, 2000.
29. Hu FZ, Preston RA, Post JC,
White JG, Kikuchi L, Wang X, Self TW, Allen G, Stiffler RS, McGraw C,
Pulsifer-Anderson EA, Ehrlich GD.
Mapping of a gene for pediatric gastroesophageal reflux to chromosome
13q: A collaboration with a
family self-help group. JAMA 284:325-334, 2000.
30. Darden DL, Hu F Z,
Gorry MC, Dressman D, Li HS, Whitcomb DC, Dohar J, Ehrlich GD. RNA differential display of scarless
wound healing in fetal rabbit indicates downregulation of a CCT chaperonin
subunit and upregulation of a glycophorin-like gene transcript. J Pediatr Surg 35:406-419, 2000.
31. Ehrlich GD, Hoffman HJ,
Zielke HR, White GJ, Hu FZ,
Vigorito R, Dingman JR, Libert T,
Smialek JE, Post JC.
Molecular epidemiological studies of common bacterial and viral
respiratory pathogens in sudden infant death syndrome (SIDS). Proceedings
of the 7th International Symposium on Recent Advances in Otitis Media.
32. Hu FZ, Liu J. Management of intractable ulcer in
diabetic patients with topical antibiotics, West China Medical Journal 2:113, 1996.
33. Hu FZ, Liu J, Fan X. Bacterial milieu in intractable
wounds. West China Medical Journal 4:313, 1995.
34. Wang X, Wu Y, Fan X, Hu
FZ, et al. Reducing
the titer of intestinal bifidobacteria caused by digestive diseases. Chin J Microecology, 7(3):59, 1995.
Book Chapters
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Ehrlich GD, Hu FZ, Post JC. Role for Biofilms in Infectious Disease. In Microbial Biofilms, ASM Press,
pp. 332-358, 2004.
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Presentations
1. Hu, F.Z., Darden, D.L., Gorry, M.C.,
Dressman, D., Li, H., Whitcomb, D.C., Dohar, J., and Ehrlich, G.D.
Identification of genes differentially expressed in a scarless model of wound
healing. Allegheny University of the Health Sciences Second Annual Research
Conference, October 8-9, 1997, King of Prussia, Pennsylvania. (Poster
Presentation)
2. Hu, F.Z., Darden, D.L., Gorry,
M.C., Dressman, D., Li, H., Whitcomb, D.C., Dohar, J., and Ehrlich, G.D.
Identification of genes differentially expressed in a scarless model of wound
healing. ARO Midwinter Meeting, St. Petersburg Beach, Florida, February
15-19, 1998. (Poster Presentation)
3. Hu, F.Z., Preston, R.A., White,
G.J., Kikuchi, L., Allen, G., Neiswanger ,K., Stiffler, R., Self, T., PAGER,
Ehrlich, G.D., and Post, J.C. Gene mapping of severe pediatric
gastroesophageal reflux. Annual Mid-winter Meeting of the Association for
Research in Otolaryngology, St. Petersburg Beach, Florida, February 14, 1998.
(Slide Presentation)
4. Hu, F.Z., Preston, R.A.,
White, G.J., Kikuchi, L., Allen, G., Neiswanger ,K., Stiffler, R., Self, T.,
PAGER, Ehrlich, G.D., and Post,
J.C. Gene mapping of severe pediatric gastroesophageal reflux. Annual
Mid-winter Meeting of the Association for Research in Otolaryngology, St.
Petersburg Beach, Florida, February 14, 1999.
5. Ehrlich, G.D., Hoffman,
H., Zilkie, R., White, G., Hu, F.Z., Vigarido, R., Post, J.C.
Molecular Epidemiological Studies Of Common Bacterial And Viral Respiratory
Pathogens In SIDS. 7th International Symposium on Recent Advances in Otitis
Media. Ft. Lauderdale, FL, June 1999.
6. Schneck, F.X., Preston,
R. A., Hu, F.Z., Herz, D., Barmada, M., Aston, C., Post, J.C., and
Ehrlich, G.D. Putative Mapping of a Gene for Vesicoureteral Reflux to
Chromosome 11. American Academy of Pediatrics Annual Meeting - Urology
Section. Chicago, IL October 31, 2000.
7. Ehrlich, G.D., Hayes,
J., Veeh, R., Hu, F.Z., Wang, X. and Costerton, J.W. Direct
Electronmicrographic Imaging of Biofilms on the Middle-ear Mucosa. Annual Mid-winter Meeting of the
Association for Research in Otolaryngology, St. Petersburg Beach, Florida,
February 6, 2001.
8. Kathju, S., Rabik, C.,
Wang, X., Hayes, J., White, G.J., Johnson, S., Hu, F.Z., Post,
J.C., and Ehrlich, G.D. Molecular Analysis of Scarless Fetal Wound
Healing. Annual Mid-winter
Meeting of the Association for Research in Otolaryngology, St. Petersburg
Beach, Florida, February 6, 2001.
9. Hu, F.Z., Preston, R.A.,
Johnson, S., Ahmed, A., Gladitz, J., Post, J.C., and Ehrlich, G.D.
Post-Genomic Strategy for the Positional Cloning of the Gene for Severe
Pediatric GERD. American College of Gastroenterology, Las Vegas, Nevada,
October 20-24, 2001.
10. Hu, F.Z., A. Nyström, A. Ahmed,
R. Dopico, I. Mossberg, M. Palmquist, J. Gladitz, M. Rayner, J.C. Post, R.A.
Preston, and G.D. Ehrlich.
Mapping a Gene for Dupuytren Contracture in Two Swedish Families.
American Society for Human Genetics Annual Meeting, Baltimore, MD, October
15-19, 2002.
11. Erdos, G., Sayeed, S.,
Shen, K., Antalis, P., Hayes, J, Goodwin, J., Hu, F., Post, J.C., and
Ehrlich, G.D. Genomic Plasticity
and Shifting Gene Expression Patterns in Biofilm Forming Pseudomonas
aeruginosa, a Pathogen of Otorrhea.
ARO Midwinter Meeting, Daytona Beach Florida, February 22-27, 2003.
12. Ehrlich, G.D., Weedn,
V., Kathju, S., Peterson, J., Balaban, N., Shirtliff, M., Post, C., Lin, Q.,
Leduc, P., Hu, F.Z., Kaiser, T., Becker, J., Sotereanos, N.,
Costerton, W. Development of
Intelligent Implants for Biofilm Prevention in Orthopedic Prostheses. ASM Conference on Bio-, Micro-, and
Nanosystems, New York, New York July 7-10, 2003.
13. Donfack J., Hu F.Z.,
Amed A., Dopico R., Post J.C., Ehrlich G.D., Preston R.A. Fine Mapping a Gene For Severe
Pediatric Gastroesophageal Reflux On Human Chromosome 13q14. 53rd Annual
Meeting of the American Society of Human Genetics, Los Angeles, California,
November 4 - 8, 2003. (Poster Presentation)
14. Antalis, P., Gladitz,
J., Shen, K., Hu, F.Z., Sayeed, S., Hayes, J., Ahmed, A., Johnson, S.,
Dopico, R., Chong, W., Goodwim , J., Singh, M., Post, J.C., Ehrlich, G.D.,
and Erdos, G. Demonstration of Extensive Genomic Plasticity Among Clinical
Isolates of Haemophilus influenzae and Evidence for a Population-Based
Supra-Genome. ASM Biofilms 2003
Victoria Island, BC CANADA, Oct 31-Nov 2, 2003.
15. Hu, F.Z. Introduction of Human
Genetic Science, CGS Faculty Retreat, Pittsburgh, PA, March 2, 2004.
16. Singh, M. K.,
LaFramboise, W.A., Hu, F.Z., Scott, T.F., Post, J.C., Ehrlich, G.D.
Gene Expression changes in peripheral blood mononuclear cells from Multiple
Sclerosis Patients Undergoing ß-interferon. 56th Annual Meeting of
the American Academy of Neurology, April 2004.
Invited Presentations
1. Hu, F.Z. TDT and Case-Control
Association Studies to Fine Map the GERD 1 Gene on Chromosome 13q14, Shantou
University, Shantou China, October 9, 2003.
2. Hu, F.Z. Genetics of Severe
Pediatric Gastroesophageal Reflux. Department of Gastroenterology, Baylor
College of Medicine, July 2, 2001.
3. Hu, F.Z. A Post-Genomics
Approach to Positionally Cloning the Pediatric GERD Gene at Chromosome 13q14,
AstraZeneca, Molndal, Sweden, October 31, 2000.
4. Hu, F.Z. Mapping a Gene for
Severe Pediatric Gastroesophageal Reflux, West China University of the
Medical Sciences, Chengdu, Sichuan, CHINA, October 12, 1999.
Computer Programs Designed
GetSizes - Visual BASIC program designed to make allele calls and
zygosity determinations from ABI-generated genotyping data. This program is
over 98% accurate and compares very favorably with commercial software
products costing tens of thousands of dollars.
GetCalls - Visual BASIC program designed to sort the alleles for a
given marker by size, perform a rounding function, and then check and verify
inheritance within the family, such that an inspection is performed to ensure
that the children's alleles correspond to the parents bin allelic data, and
convert data to a format read for LINKAGE.
CheckInherit - Visual BASIC program designed to test families for
allowable alleles based upon parentage - to be used before submitting
genotypic data to LINKAGE.
MakeLink - Visual BASIC program to convert genotyping data into
correct file format for submission to LINKAGE.
GetLods - Visual BASIC program designed to interface with LINKAGE and
extract lod scores into a tabular form and highlight scores differentially
depending on significance.
QbotRearray - Visual BASIC program to automatically take normalization
data from hybridization films and use it to re-program the arraying robot to
rearray cDNA libraries leaving out the highly expressed clones.
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