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Francis Barany

Research Profile

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Chemicals & Drugs

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Colorectal Neoplasms

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Oligonucleotide Array Sequence Analysis

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Yi-Wen Chen; Udara Dharmasiri; Mateusz L Hupert; Maneesh R Pingle; Hong Wang; Malgorzata A Witek; Francis Barany; Steven A Soper
Modular microfluidic system fabricated in thermoplastics for the strain-specific detection of bacterial pathogens.
Hong Wang; Diana Williams; Francis Barany; Hui-Wen Chen; Pin-Chuan Chen; Proyag Datta; Jost Goettert; Mateusz L Hupert; Michael C Murphy; Tana L Pittman; Steven A Soper
Fully integrated thermoplastic genosensor for the highly sensitive detection and identification of multi-drug-resistant tuberculosis.
Manny Bacolod; Francis Barany
Molecular profiling of colon tumors: the search for clinically relevant biomarkers of progression, prognosis, therapeutics, and predisposition.

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All Publications

2012: Yi-Wen Chen; Udara Dharmasiri; Mateusz L Hupert; Maneesh R Pingle; Hong Wang; Malgorzata A Witek; Francis Barany; Steven A Soper
Modular microfluidic system fabricated in thermoplastics for the strain-specific detection of bacterial pathogens.
Lab on a chip 2012;12(18):3348-55.
2012: Hong Wang; Diana Williams; Francis Barany; Hui-Wen Chen; Pin-Chuan Chen; Proyag Datta; Jost Goettert; Mateusz L Hupert; Michael C Murphy; Tana L Pittman; Steven A Soper
Fully integrated thermoplastic genosensor for the highly sensitive detection and identification of multi-drug-resistant tuberculosis.
Angewandte Chemie (International ed. in English) 2012;51(18):4349-53.
2011: Manny Bacolod; Francis Barany
Molecular profiling of colon tumors: the search for clinically relevant biomarkers of progression, prognosis, therapeutics, and predisposition.
Annals of surgical oncology 2011;18(13):3694-700.
2011: Udara Dharmasiri; Samuel K Njoroge; Malgorzata A Witek; Morayo G Adebiyi; Joyce W Kamande; Mateusz L Hupert; Francis Barany; Steven A Soper
High-throughput selection, enumeration, electrokinetic manipulation, and molecular profiling of low-abundance circulating tumor cells using a microfluidic system.
Analytical chemistry 2011;83(6):2301-9.
2010: Zhiyong Peng; Steven A Soper; Maneesh R Pingle; Francis Barany; Lloyd M Davis
Ligase detection reaction generation of reverse molecular beacons for near real-time analysis of bacterial pathogens using single-pair fluorescence resonance energy transfer and a cyclic olefin copolymer microfluidic chip.
Analytical chemistry 2010;82(23):9727-35.
2010: Iyare Esemuede; Ann Forslund; Sajid A Khan; Li-Xuan Qin; Mark I Gimbel; Garrett M Nash; Zhaoshi Zeng; Shoshana Rosenberg; Jinru Shia; Francis Barany; Philip B Paty
Improved testing for microsatellite instability in colorectal cancer using a simplified 3-marker assay.
Annals of surgical oncology 2010;17(12):3370-8.
2010: Manny Bacolod; Francis Barany
Gene dysregulations driven by somatic copy number aberrations-biological and clinical implications in colon tumors: a paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology.
The Journal of molecular diagnostics : JMD 2010;12(5):552-61.
2010: Yu-Wei Cheng; Kamran Idrees; Richard Shattock; Sajid A Khan; Zhaoshi Zeng; Cameron Brennan; Philip B Paty; Francis Barany
Loss of imprinting and marked gene elevation are 2 forms of aberrant IGF2 expression in colorectal cancer.
International journal of cancer. Journal international du cancer 2010;127(3):568-77.
2010: Garrett M Nash; Mark I Gimbel; Alfred M Cohen; Zhaoshi Zeng; Mackevin I Ndubuisi; Daniel R Nathanson; Jurg Ott; Francis Barany; Philip B Paty
KRAS mutation and microsatellite instability: two genetic markers of early tumor development that influence the prognosis of colorectal cancer.
Annals of surgical oncology 2010;17(2):416-24.
2010: Maneesh Pingle; Mark Rundell; Sanchita Das; Linnie M Golightly; Francis Barany
PCR/LDR/universal array platforms for the diagnosis of infectious disease.
Methods in molecular biology (Clifton, N.J.) 2010;632():141-57.
2010: K Granger; M S Rundell; Maneesh R Pingle; R Shatsky; Davise H Larone; Linnie M Golightly; Francis Barany; E D Spitzer
Multiplex PCR-ligation detection reaction assay for simultaneous detection of drug resistance and toxin genes from Staphylococcus aureus, Enterococcus faecalis, and Enterococcus faecium.
Journal of clinical microbiology 2010;48(1):277-80.
2009: Michal Sheffer; Manny Bacolod; Or Zuk; Sarah F Giardina; Hanna Pincas; Francis Barany; Philip B Paty; William L Gerald; Daniel A Notterman; Eytan Domany
Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(17):7131-6.
2009: Manny Bacolod; Gunter S Schemmann; Sarah F Giardina; Philip B Paty; Daniel A Notterman; Francis Barany
Emerging paradigms in cancer genetics: some important findings from high-density single nucleotide polymorphism array studies.
Cancer research 2009;69(3):723-7.
2008: Rondedrick Sinville; Jennifer Coyne; Robert J Meagher; Yu-Wei Cheng; Francis Barany; Annelise Barron; Steven A Soper
Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device.
Electrophoresis 2008;29(23):4751-60.
2008: Zhaoshi Zeng; Martin R Weiser; Eleanor Kuntz; Chin-Tung Chen; Sajid A Khan; Ann Forslund; Garrett M Nash; Mark Gimbel; Yuka Yamaguchi; Alfred T Culliford; Matthew D'Alessio; Francis Barany; Philip B Paty
c-Met gene amplification is associated with advanced stage colorectal cancer and liver metastases.
Cancer letters 2008;265(2):258-69.
2008: Sajid A Khan; Kamran Idrees; Ann Forslund; Zhaoshi Zeng; Shoshana Rosenberg; Hanna Pincas; Francis Barany; Kenneth Offit; Michael P LaQuaglia; Philip B Paty
Genetic variants in germline TP53 and MDM2 SNP309 are not associated with early onset colorectal cancer.
Journal of surgical oncology 2008;97(7):621-5.
2008: Manny Bacolod; Gunter S Schemmann; Shuang Wang; Richard Shattock; Sarah F Giardina; Zhaoshi Zeng; Jinru Shia; Robert F Stengel; Norman Gerry; Josephine Hoh; Tomas Kirchhoff; Bert Gold; Michael F Christman; Kenneth Offit; William L Gerald; Daniel A Notterman; Jurg Ott; Philip B Paty; Francis Barany
The signatures of autozygosity among patients with colorectal cancer.
Cancer research 2008;68(8):2610-21.
2008: Ann Forslund; Zhaoshi Zeng; Li-Xuan Qin; Shoshana Rosenberg; MacKevin Ndubuisi; Hanna Pincas; William Gerald; Daniel A Notterman; Francis Barany; Philip B Paty
MDM2 gene amplification is correlated to tumor progression but not to the presence of SNP309 or TP53 mutational status in primary colorectal cancers.
Molecular cancer research : MCR 2008;6(2):205-11.
2007: Masahiko Hashimoto; Francis Barany; Feng Xu; Steven A Soper
Serial processing of biological reactions using flow-through microfluidic devices: coupled PCR/LDR for the detection of low-abundant DNA point mutations.
The Analyst 2007;132(9):913-21.
2007: Nancy Gavert; Michal Sheffer; Shani Raveh; Simone Spaderna; Michael Shtutman; Thomas Brabletz; Francis Barany; Philip B Paty; Daniel A Notterman; Eytan Domany; Avri Ben-Ze'ev
Expression of L1-CAM and ADAM10 in human colon cancer cells induces metastasis.
Cancer research 2007;67(16):7703-12.
2007: Maneesh R Pingle; Kathleen Granger; Philip Feinberg; Rebecca Shatsky; Bram Sterling; Mark Rundell; Eric Spitzer; Davise Larone; Linnie Golightly; Francis Barany
Multiplexed identification of blood-borne bacterial pathogens by use of a novel 16S rRNA gene PCR-ligase detection reaction-capillary electrophoresis assay.
Journal of clinical microbiology 2007;45(6):1927-35.
2006: Yu Wen; Sarah F Giardina; David Hamming; Jennifer Greenman; Emmanuel Zachariah; Manny Bacolod; Hao Liu; Jinru Shia; Peter S Amenta; Francis Barany; Philip B Paty; William Gerald; Daniel A Notterman
GROalpha is highly expressed in adenocarcinoma of the colon and down-regulates fibulin-1.
Clinical cancer research : an official journal of the American Association for Cancer Research 2006;12(20 Pt 1):5951-9.
2006: Masahiko Hashimoto; Francis Barany; Steven A Soper
Polymerase chain reaction/ligase detection reaction/hybridization assays using flow-through microfluidic devices for the detection of low-abundant DNA point mutations.
Biosensors & bioelectronics 2006;21(10):1915-23.
2006: Daniel J Turner; Maneesh R Pingle; Francis Barany
Harnessing asymmetrical substrate recognition by thermostable EndoV to achieve balanced linear amplification in multiplexed SNP typing.
Biochemistry and cell biology = Biochimie et biologie cellulaire 2006;84(2):232-42.
2006: Dafna Tsafrir; Manny Bacolod; Zachariah Selvanayagam; Ilan Tsafrir; Jinru Shia; Zhaoshi Zeng; Hao Liu; Curtis Krier; Robert F Stengel; Francis Barany; William L Gerald; Philip B Paty; Eytan Domany; Daniel A Notterman
Relationship of gene expression and chromosomal abnormalities in colorectal cancer.
Cancer research 2006;66(4):2129-37.
2006: Yu-Wei Cheng; Carrie Shawber; Dan Notterman; Philip B Paty; Francis Barany
Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay.
Genome research 2006;16(2):282-9.
2005: Steven A Soper; Masahiko Hashimoto; Catherine Situma; Michael C Murphy; Robin L McCarley; Yu-Wei Cheng; Francis Barany
Fabrication of DNA microarrays onto polymer substrates using UV modification protocols with integration into microfluidic platforms for the sensing of low-abundant DNA point mutations.
Methods (San Diego, Calif.) 2005;37(1):103-13.
2005: Masahiko Hashimoto; Mateusz L Hupert; Michael C Murphy; Steven A Soper; Yu-Wei Cheng; Francis Barany
Ligase detection reaction/hybridization assays using three-dimensional microfluidic networks for the detection of low-abundant DNA point mutations.
Analytical chemistry 2005;77(10):3243-55.
2005: Daniel J Turner; Monib A Zirvi; Francis Barany; Rosalie Elenitsas; John T Seykora
Detection of the BRAF V600E mutation in melanocytic lesions using the ligase detection reaction.
Journal of cutaneous pathology 2005;32(5):334-9.
2005: Catherine Situma; Yun Wang; Mateusz L Hupert; Francis Barany; Robin L McCarley; Steven A Soper
Fabrication of DNA microarrays onto poly(methyl methacrylate) with ultraviolet patterning and microfluidics for the detection of low-abundant point mutations.
Analytical biochemistry 2005;340(1):123-35.
2005: Catherine M Phelan; Virna Dapic; B Tice; Reyna Favis; Elaine Kwan; Francis Barany; Siranoush Manoukian; Paolo Radice; Rob B van der Luijt; B P M van Nesselrooij; G Chenevix-Trench; Trinidad Caldes; Miguel de la Hoya; S Lindquist; Sean V Tavtigian; David E Goldgar; A Borg; Steven A Narod; Alvaro Monteiro
Classification of BRCA1 missense variants of unknown clinical significance.
Journal of medical genetics 2005;42(2):138-46.
2005: Reyna Favis; Norman P Gerry; Yu-Wei Cheng; Francis Barany
Applications of the universal DNA microarray in molecular medicine.
Methods in molecular medicine 2005;114():25-58.
2004: Reyna Favis; Jianmin Huang; Norman P Gerry; Alfred T Culliford; Philip B Paty; thierry soussi; Francis Barany
Harmonized microarray/mutation scanning analysis of TP53 mutations in undissected colorectal tumors.
Human mutation 2004;24(1):63-75.
2004: Gloria Thomas; Rondedrick Sinville; Shelby Sutton; Hannah Farquar; Robert P Hammer; Steven A Soper; Yu-Wei Cheng; Francis Barany
Capillary and microelectrophoretic separations of ligase detection reaction products produced from low-abundant point mutations in genomic DNA.
Electrophoresis 2004;25(10-11):1668-77.
2004: Coralie Fouquet; Martine Antoine; Pascaline Tisserand; Reyna Favis; Marie Wislez; Frédéric Commo; Nathalie Rabbe; Marie-France Carette; Bernard Milleron; Francis Barany; Jacques Cadranel; Gérard Zalcman; thierry soussi
Rapid and sensitive p53 alteration analysis in biopsies from lung cancer patients using a functional assay and a universal oligonucleotide array: a prospective study.
Clinical cancer research : an official journal of the American Association for Cancer Research 2004;10(10):3479-89.
2004: Hanna Pincas; Maneesh R Pingle; Jianmin Huang; kaiqin lao; Philip B Paty; Alan Friedman; Francis Barany
High sensitivity EndoV mutation scanning through real-time ligase proofreading.
Nucleic acids research 2004;32(19):e148.
2003: Michael Overholtzer; Pulivarthi H Rao; Reyna Favis; Xin-Yan Lu; Michael B Elowitz; Francis Barany; Marc Ladanyi; Richard Gorlick; Arnold J Levine
The presence of p53 mutations in human osteosarcomas correlates with high levels of genomic instability.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11547-52.
2003: Garrett M Nash; Mark I Gimbel; Jinru Shia; Alfred T Culliford; Daniel R Nathanson; M Ndubuisi; Y Yamaguchi; Zhaoshi Zeng; Francis Barany; Philip B Paty
Automated, multiplex assay for high-frequency microsatellite instability in colorectal cancer.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2003;21(16):3105-12.
2003: Daniel R Nathanson; Alfred T Culliford; Jinru Shia; Beiyun Chen; Matthew D'Alessio; Zhaoshi Zeng; Garrett M Nash; William Gerald; Francis Barany; Philip B Paty
HER 2/neu expression and gene amplification in colon cancer.
International journal of cancer. Journal international du cancer 2003;105(6):796-802.
2003: Musundi B Wabuyele; Hannah Farquar; Wieslaw Stryjewski; Robert P Hammer; Steven A Soper; Yu-Wei Cheng; Francis Barany
Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes.
Journal of the American Chemical Society 2003;125(23):6937-45.
2003: Yun Wang; Bikas Vaidya; Hannah Farquar; Wieslaw Stryjewski; Robert P Hammer; Robin L McCarley; Steven A Soper; Yu-Wei Cheng; Francis Barany
Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations.
Analytical chemistry 2003;75(5):1130-40.
2002: Brian W Kirk; Matthew Feinsod; Reyna Favis; Richard M Kliman; Francis Barany
Single nucleotide polymorphism seeking long term association with complex disease.
Nucleic acids research 2002;30(15):3295-311.
2002: Jianmin Huang; Brian Kirk; Reyna Favis; thierry soussi; Philip B Paty; Weiguo Cao; Francis Barany
An endonuclease/ligase based mutation scanning method especially suited for analysis of neoplastic tissue.
Oncogene 2002;21(12):1909-21.
2001: Seung Myung Dong; Giovanni Traverso; C Johnson; L Geng; Reyna Favis; Kevin Boynton; K Hibi; Steven Goodman; M D'Allessio; Philip B Paty; Stanley R Hamilton; David Sidransky; Francis Barany; B Levin; Anthony P Shuber; Kenneth W Kinzler; Bert Vogelstein; Jin Jen
Detecting colorectal cancer in stool with the use of multiple genetic targets.
Journal of the National Cancer Institute 2001;93(11):858-65.
2000: Reyna Favis; JP Day; Norman P Gerry; Catherine M Phelan; Steven A Narod; Francis Barany
Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2.
Nature biotechnology 2000;18(5):561-4.
2000: Reyna Favis; Francis Barany
Mutation detection in K-ras, BRCA1, BRCA2, and p53 using PCR/LDR and a universal DNA microarray.
Annals of the New York Academy of Sciences 2000;906():39-43.
1999: Monib A Zirvi; DE Bergstrom; A S Saurage; Robert P Hammer; Francis Barany
Improved fidelity of thermostable ligases for detection of microsatellite repeat sequences using nucleoside analogs.
Nucleic acids research 1999;27(24):e41.
1999: Monib A Zirvi; T Nakayama; G Newman; TA McCaffrey; Philip B Paty; Francis Barany
Ligase-based detection of mononucleotide repeat sequences.
Nucleic acids research 1999;27(24):e40.
1999: Norman P Gerry; N E Witowski; J Day; Robert P Hammer; George Barany; Francis Barany
Universal DNA microarray method for multiplex detection of low abundance point mutations.
Journal of molecular biology 1999;292(2):251-62.
1999: M Khanna; Weiguo Cao; Monib A Zirvi; Philip B Paty; Francis Barany
Ligase detection reaction for identification of low abundance mutations.
Clinical biochemistry 1999;32(4):287-90.
1999: JP Day; Robert P Hammer; DE Bergstrom; Francis Barany
Nucleotide analogs and new buffers improve a generalized method to enrich for low abundance mutations.
Nucleic acids research 1999;27(8):1819-27.
1999: JP Day; DE Bergstrom; Robert P Hammer; Francis Barany
Nucleotide analogs facilitate base conversion with 3' mismatch primers.
Nucleic acids research 1999;27(8):1810-8.
1999: J Tong; Weiguo Cao; Francis Barany
Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D.
Nucleic acids research 1999;27(3):788-94.
1999: M Khanna; P Park; Monib A Zirvi; Weiguo Cao; Antonio Picon; J Day; Philip B Paty; Francis Barany
Multiplex PCR/LDR for detection of K-ras mutations in primary colon tumors.
Oncogene 1999;18(1):27-38.
1998: Weiguo Cao; Francis Barany
Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage.
The Journal of biological chemistry 1998;273(49):33002-10.
1998: Weiguo Cao; J Lu; SG Welch; RA Williams; Francis Barany
Cloning and thermostability of TaqI endonuclease isoschizomers from Thermus species SM32 and Thermus filiformis Tok6A1.
The Biochemical journal 1998;333 ( Pt 2)():425-31.
1997: Weiguo Cao; J Lu; Francis Barany
Nucleotide sequences and gene organization of TaqI endonuclease isoschizomers from Thermus sp. SM32 and Thermus filiformis Tok6A1.
Gene 1997;197(1-2):205-14.
1996: D J Day; Phyllis W Speiser; E Schulze; M Bettendorf; J Fitness; Francis Barany; P C White
Identification of non-amplifying CYP21 genes when using PCR-based diagnosis of 21-hydroxylase deficiency in congenital adrenal hyperplasia (CAH) affected pedigrees.
Human molecular genetics 1996;5(12):2039-48.
1996: J Luo; Francis Barany
Identification of essential residues in Thermus thermophilus DNA ligase.
Nucleic acids research 1996;24(15):3079-85.
1996: J Luo; D E Bergstrom; Francis Barany
Improving the fidelity of Thermus thermophilus DNA ligase.
Nucleic acids research 1996;24(15):3071-8.
1995: D J Day; Phyllis W Speiser; P C White; Francis Barany
Detection of steroid 21-hydroxylase alleles using gene-specific PCR and a multiplexed ligation detection reaction.
Genomics 1995;29(1):152-62.
1995: Weiguo Cao; Alan N Mayer; Francis Barany
Stringent and relaxed specificities of TaqI endonuclease: interactions with metal cofactors and DNA sequences.
Biochemistry 1995;34(7):2276-83.
1995: Alan N Mayer; Francis Barany
Photoaffinity cross-linking of TaqI restriction endonuclease using an aryl azide linked to the phosphate backbone.
Gene 1995;153(1):1-8.
1994: Alan N Mayer; Francis Barany
Interaction of TaqI endonuclease with the phosphate backbone. Effects of stereospecific phosphate modification.
The Journal of biological chemistry 1994;269(46):29067-76.
1993: J A Zebala; Francis Barany
Implications for the ligase chain reaction in gastroenterology.
Journal of clinical gastroenterology 1993;17(2):171-5.
1992: J A Zebala; J Choi; G L Trainor; Francis Barany
DNA recognition of base analogue and chemically modified substrates by the TaqI restriction endonuclease.
The Journal of biological chemistry 1992;267(12):8106-16.
1992: J A Zebala; J Choi; Francis Barany
Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease.
The Journal of biological chemistry 1992;267(12):8097-105.
1992: Francis Barany; Barton Slatko; M Danzitz; David Cowburn; Schildkraut Ira; G G Wilson
The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap.
Gene 1992;112(1):91-5.
1992: Francis Barany; J Zebala
Correlation between insertion mutant activities and amino acid sequence identities of the TaqI and TthHB8 restriction endonucleases.
Gene 1992;112(1):13-20.
1992: Francis Barany; M Danzitz; J Zebala; Alan N Mayer
Cloning and sequencing of genes encoding the TthHB8I restriction and modification enzymes: comparison with the isoschizomeric TaqI enzymes.
Gene 1992;112(1):3-12.
1991: Francis Barany; D H Gelfand
Cloning, overexpression and nucleotide sequence of a thermostable DNA ligase-encoding gene.
Gene 1991;109(1):1-11.
1991: Francis Barany
The ligase chain reaction in a PCR world.
PCR methods and applications 1991;1(1):5-16.
1991: J Zebala; Francis Barany
Mapping catalytically important regions of an enzyme using two-codon insertion mutagenesis: a case study correlating beta-lactamase mutants with the three-dimensional structure.
Gene 1991;100():51-7.
1991: Francis Barany
Genetic disease detection and DNA amplification using cloned thermostable ligase.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(1):189-93.
1989: J Glushka; Francis Barany; David Cowburn
Observation of arginyl-deoxyoligonucleotide interactions in Taq I endonuclease by detection of specific 1H NMR signals from 140kD [N eta 1, N eta 2, 15N Arg]Taq I/oligomer complexes.
Biochemical and biophysical research communications 1989;164(1):88-93.
1988: Francis Barany
How TaqI endonuclease recognizes its cognate sequence.
Gene 1988;74(1):63-5.
1988: Francis Barany
Overproduction, purification and crystallization of TaqI restriction endonuclease.
Gene 1988;65(2):167-77.
1988: Francis Barany
The TaqI 'star' reaction: strand preferences reveal hydrogen-bond donor and acceptor sites in canonical sequence recognition.
Gene 1988;65(2):149-65.
1987: Francis Barany
A genetic system for isolation and characterization of TaqI restriction endonuclease mutants.
Gene 1987;56(1):13-27.