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Paul Predki

Research Profile

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Protein Array Analysis

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TOP 3
Lihao Meng; Dawn Mattoon; Paul Predki
Small molecule protein interaction profiling with functional protein microarrays.
Xiquan Liang; Jarkko Huuskonen; Mahbod Hajivandi; Raul Manzanedo; Paul Predki; Joseph R Amshey; Marshall pope
Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell lines.
Xiquan Liang; Geir Fonnum; Mahbod Hajivandi; Torkel Stene; Nini H Kjus; Erlend Ragnhildstveit; Joseph W Amshey; Paul Predki; Marshall pope
Quantitative comparison of IMAC and TiO2 surfaces used in the study of regulated, dynamic protein phosphorylation.

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All Publications

2009: Lihao Meng; Dawn Mattoon; Paul Predki
Small molecule protein interaction profiling with functional protein microarrays.
Methods in molecular biology (Clifton, N.J.) 2009;572():177-88.
2009: Xiquan Liang; Jarkko Huuskonen; Mahbod Hajivandi; Raul Manzanedo; Paul Predki; Joseph R Amshey; Marshall pope
Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell lines.
Proteomics 2009;9(1):182-93.
2007: Xiquan Liang; Geir Fonnum; Mahbod Hajivandi; Torkel Stene; Nini H Kjus; Erlend Ragnhildstveit; Joseph W Amshey; Paul Predki; Marshall pope
Quantitative comparison of IMAC and TiO2 surfaces used in the study of regulated, dynamic protein phosphorylation.
Journal of the American Society for Mass Spectrometry 2007;18(11):1932-44.
2007: Scott N Boyle; Gregory A Michaud; Barry Schweitzer; Paul Predki; Anthony J Koleske
A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsal-wave formation.
Current biology : CB 2007;17(5):445-51.
2007: Michael Salcius; Gregory A Michaud; Barry Schweitzer; Paul Predki
Identification of small molecule targets on functional protein microarrays.
Methods in molecular biology (Clifton, N.J.) 2007;382():239-48.
2006: Fulai Jin; Tony R Hazbun; Gregory A Michaud; Michael Salcius; Paul Predki; Stanley Fields; Jing Huang
A pooling-deconvolution strategy for biological network elucidation.
Nature methods 2006;3(3):183-9.
2006: Gregory A Michaud; Michael Salcius; Fang Zhou; Vladimir V Papov; Janie Merkel; Michael Murtha; Paul Predki; Barry Schweitzer
Applications of protein arrays for small molecule drug discovery and characterization.
Biotechnology & genetic engineering reviews 2006;22():197-211.
2005: Jason Ptacek; Geeta Devgan; Gregory A Michaud; Heng Zhu; Xiaowei Zhu; Joseph Fasolo; Hong Guo; Ghil Jona; Ashton Breitkreutz; Richelle Sopko; Rhonda R McCartney; Martin C Schmidt; Najma Rachidi; Soo-Jung Lee; Angie S Mah; Lihao Meng; Michael J R Stark; David F Stern; Claudio de Virgilio; Mike Tyers; Brenda Andrews; Mark Gerstein; Barry Schweitzer; Paul Predki; Michael Snyder
Global analysis of protein phosphorylation in yeast.
Nature 2005;438(7068):679-84.
2005: Janie S Merkel; Gregory A Michaud; Michael Salcius; Barry Schweitzer; Paul Predki
Functional protein microarrays: just how functional are they?
Current opinion in biotechnology 2005;16(4):447-52.
2005: Z Lu; Eric Altermann; Frederick Breidt; Paul Predki; Henry P Fleming; Todd R Klaenhammer
Sequence analysis of the Lactobacillus plantarum bacteriophage PhiJL-1.
Gene 2005;348():45-54.
2005: Paul Predki; Dawn Mattoon; Rhonda Bangham; Barry Schweitzer; Gregory A Michaud
Protein microarrays: a new tool for profiling antibody cross-reactivity.
Human antibodies 2005;14(1-2):7-15.
2005: Rhonda Bangham; Gregory A Michaud; Barry Schweitzer; Paul Predki
Protein microarray-based screening of antibody specificity.
Methods in molecular medicine 2005;114():173-82.
2004: Joel Martin; Cliff Han; Laurie A Gordon; Astrid Terry; Shyam Prabhakar; Xinwei She; Gary Xie; Uffe Hellsten; Yee Man Chan; Michael Altherr; Olivier Couronne; Andrea Aerts; Eva Bajorek; Stacey Black; Heather Blumer; Elbert Branscomb; Nancy C Brown; William J Bruno; Judith M Buckingham; David F Callen; Connie S Campbell; Mary L Campbell; Evelyn W Campbell; Chenier Caoile; Jean F Challacombe; Leslie A Chasteen; Olga Chertkov; Han C Chi; Mari Christensen; Lynn M Clark; Judith D Cohn; Mirian Denys; John C Detter; Mark Dickson; Mira Dimitrijevic-Bussod; Julio Escobar; Joseph J Fawcett; Dave Flowers; Dea Fotopulos; Tijana Glavina; Maria Gomez; Eidelyn Gonzales; David Goodstein; Lynne A Goodwin; Deborah L Grady; Igor Grigoriev; Matthew Groza; Nancy Hammon; Trevor Hawkins; Lauren Haydu; Carl E Hildebrand; Wayne Huang; Sanjay Israni; Jamie Jett; Phillip B Jewett; Kristen Kadner; Heather Kimball; Arthur Kobayashi; Marie-Claude Krawczyk; Tina Leyba; Jonathan L Longmire; Frederick Lopez; Yunian Lou; Steve Lowry; Thom Ludeman; Chitra F Manohar; Graham A Mark; Kimberly L McMurray; Linda J Meincke; Jenna Morgan; Robert K Moyzis; Mark O Mundt; A Christine Munk; Richard D Nandkeshwar; Sam Pitluck; Martin Pollard; Paul Predki; Beverly Parson-Quintana; Lucia Ramirez; Sam Rash; James Retterer; Darryl O Ricke; Donna L Robinson; Alex Rodriguez; Asaf Salamov; Elizabeth H Saunders; Duncan Scott; Timothy Shough; Raymond L Stallings; Malinda Stalvey; Robert D Sutherland; Roxanne Tapia; Judith G Tesmer; Nina Thayer; Linda S Thompson; Hope Tice; David C Torney; Mary Tran-Gyamfi; Ming Tsai; Levy E Ulanovsky; Anna Ustaszewska; Nu Vo; P Scott White; Albert L Williams; Patricia L Wills; Jung-Rung Wu; Kevin Wu; Joan Yang; Pieter Dejong; David Bruce; Norman A Doggett; Larry Deaven; Jeremy Schmutz; Jane Grimwood; Paul Richardson; Daniel S Rokhsar; Evan E Eichler; Paul Gilna; Susan M Lucas; Richard Myers; Edward M Rubin; Len A Pennacchio
The sequence and analysis of duplication-rich human chromosome 16.
Nature 2004;432(7020):988-94.
2004: Jeremy Schmutz; Joel Martin; Astrid Terry; Olivier Couronne; Jane Grimwood; Steve Lowry; Laurie A Gordon; Duncan Scott; Gary Xie; Wayne Huang; Uffe Hellsten; Mary Tran-Gyamfi; Xinwei She; Shyam Prabhakar; Andrea Aerts; Michael Altherr; Eva Bajorek; Stacey Black; Elbert Branscomb; Chenier Caoile; Jean F Challacombe; Yee Man Chan; Mirian Denys; John C Detter; Julio Escobar; Dave Flowers; Dea Fotopulos; Tijana Glavina; Maria Gomez; Eidelyn Gonzales; David Goodstein; Igor Grigoriev; Matthew Groza; Nancy Hammon; Trevor Hawkins; Lauren Haydu; Sanjay Israni; Jamie Jett; Kristen Kadner; Heather Kimball; Arthur Kobayashi; Frederick Lopez; Yunian Lou; Diego Martinez; Catherine Medina; Jenna Morgan; Richard Nandkeshwar; James P Noonan; Sam Pitluck; Martin Pollard; Paul Predki; James Priest; Lucia Ramirez; James Retterer; Alex Rodriguez; Stephanie Rogers; Asaf Salamov; Angelica Salazar; Nina Thayer; Hope Tice; Ming Tsai; Anna Ustaszewska; Nu Vo; Jeremy Wheeler; Kevin Wu; Joan Yang; Mark Dickson; Jan-Fang Cheng; Evan E Eichler; Anne Olsen; Len A Pennacchio; Daniel S Rokhsar; Paul Richardson; Susan M Lucas; Richard Myers; Edward M Rubin
The DNA sequence and comparative analysis of human chromosome 5.
Nature 2004;431(7006):268-74.
2004: Fang X Zhou; Jaclyn Bonin; Paul Predki
Development of functional protein microarrays for drug discovery: progress and challenges.
Combinatorial chemistry & high throughput screening 2004;7(6):539-46.
2004: Jane Grimwood; Laurie A Gordon; Anne Olsen; Astrid Terry; Jeremy Schmutz; Jane Lamerdin; Uffe Hellsten; David Goodstein; Olivier Couronne; Mary Tran-Gyamfi; Andrea Aerts; Michael Altherr; Linda Ashworth; Eva Bajorek; Stacey Black; Elbert Branscomb; Sean Caenepeel; Anthony Carrano; Chenier Caoile; Yee Man Chan; Mari Christensen; Catherine A Cleland; Alex Copeland; Eileen Dalin; Paramvir Dehal; Mirian Denys; John C Detter; Julio Escobar; Dave Flowers; Dea Fotopulos; Carmen Garcia; Anca M Georgescu; Tijana Glavina; Maria Gomez; Eidelyn Gonzales; Matthew Groza; Nancy Hammon; Trevor Hawkins; Lauren Haydu; Isaac Ho; Wayne Huang; Sanjay Israni; Jamie Jett; Kristen Kadner; Heather Kimball; Arthur Kobayashi; Vladimer Larionov; Sun-Hee Leem; Frederick Lopez; Yunian Lou; Steve Lowry; Stephanie Malfatti; Diego Martinez; Paula McCready; Catherine Medina; Jenna Morgan; Kathryn Nelson; Matt Nolan; Ivan Ovcharenko; Sam Pitluck; Martin Pollard; Anthony P Popkie; Paul Predki; Glenda Quan; Lucia Ramirez; Sam Rash; James Retterer; Alex Rodriguez; Stephanine Rogers; Asaf Salamov; Angelica Salazar; Xinwei She; Doug Smith; Tom Slezak; Victor Solovyev; Nina Thayer; Hope Tice; Ming Tsai; Anna Ustaszewska; Nu Vo; Mark Wagner; Jeremy Wheeler; Kevin Wu; Gary Xie; Joan Yang; Inna Dubchak; Terrence S Furey; Pieter DeJong; Mark Dickson; David Gordon; Evan E Eichler; Len A Pennacchio; Paul Richardson; Lisa Stubbs; Daniel S Rokhsar; Richard Myers; Edward M Rubin; Susan M Lucas
The DNA sequence and biology of human chromosome 19.
Nature 2004;428(6982):529-35.
2004: Paul Predki
Functional protein microarrays: ripe for discovery.
Current opinion in chemical biology 2004;8(1):8-13.
2004: Paul Predki; Christopher Elkin; Hitesh Kapur; Jamie Jett; Susan Lucas; Tijana Glavina; Trevor L Hawkins
Rolling circle amplification for sequencing templates.
Methods in molecular biology (Clifton, N.J.) 2004;255():189-96.
2003: Gregory A Michaud; Michael Salcius; Fang Zhou; Rhonda Bangham; Jaclyn Bonin; Hong Guo; Michael Snyder; Paul Predki; Barry Schweitzer
Analyzing antibody specificity with whole proteome microarrays.
Nature biotechnology 2003;21(12):1509-12.
2003: Barry Schweitzer; Paul Predki; Michael Snyder
Microarrays to characterize protein interactions on a whole-proteome scale.
Proteomics 2003;3(11):2190-9.
2003: Paul M Richardson; Chris Detter; Barry Schweitzer; Paul Predki
Practical applications of rolling circle amplification of DNA templates.
Genetic engineering 2003;25():51-63.
2002: Elbert Branscomb; Paul Predki
On the high value of low standards.
Journal of bacteriology 2002;184(23):6406-9; discussion 6409.
2002: Amber Vanden Wymelenberg; Stuart Denman; Diane Dietrich; Jennifer Bassett; Xiaochun Yu; Rajai Atalla; Paul Predki; Ulla Rudsander; Tuula T Teeri; Dan Cullen
Transcript analysis of genes encoding a family 61 endoglucanase and a putative membrane-anchored family 9 glycosyl hydrolase from Phanerochaete chrysosporium.
Applied and environmental microbiology 2002;68(11):5765-8.
2002: Anamitra Bhattacharyya; Stephanie Stilwagen; Gary Reznik; Helene Feil; William S Feil; Iain Anderson; Axel Bernal; Mark D'Souza; Natalia Ivanova; Vinayak Kapatral; Niels Larsen; Tamara Los; Athanasios Lykidis; Eugene Selkov; Theresa Walunas; Alexander H Purcell; Robert A Edwards; Trevor L Hawkins; Robert Haselkorn; Ross Overbeek; Nikos Kyrpides; Paul Predki
Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights.
Genome research 2002;12(10):1556-63.
2002: Anamitra Bhattacharyya; Stephanie Stilwagen; Natalia Ivanova; Mark D'Souza; Axel Bernal; Athanasios Lykidis; Vinayak Kapatral; Iain Anderson; Niels Larsen; Tamara Los; Gary Reznik; Eugene Selkov; Theresa Walunas; Helene Feil; William S Feil; Alexander H Purcell; Jean-Louis Lassez; Trevor L Hawkins; Robert Haselkorn; Ross Overbeek; Paul Predki; Nikos Kyrpides
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(19):12403-8.
2002: Samuel Aparicio; Jarrod Chapman; Elia Stupka; Nicholas Putnam; Jer-Ming Chia; Paramvir Dehal; Alan Christoffels; Sam Rash; Shawn Hoon; Arian Smit; Maarten D Sollewijn Gelpke; Jared Roach; Tania Oh; Isaac Y Ho; Marie Wong; Chris Detter; Frans Verhoef; Paul Predki; Alice Tay; Susan Lucas; Paul Richardson; Sarah F Smith; Melody S Clark; Yvonne Jemimah Edwards; Norman Doggett; Andrey Zharkikh; Sean V Tavtigian; Dmitry Pruss; Mary Barnstead; Cheryl Evans; Holly Baden; Justin Powell; Gustavo Glusman; Lee Rowen; Leroy Hood; Y H Tan; greg elgar; Trevor Hawkins; Byrappa Venkatesh; Daniel Rokhsar; Sydney Brenner
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.
Science (New York, N.Y.) 2002;297(5585):1301-10.
2001: Paramvir Dehal; Paul Predki; Anne S Olsen; A Kobayashi; P Folta; Susan Lucas; Miriam Land; A Terry; C L Ecale Zhou; S Rash; Q Zhang; Laurie Gordon; Joomyeong Kim; Christopher Elkin; M J Pollard; Paul Richardson; Dan S Rokhsar; Edward C Uberbacher; Trevor L Hawkins; Elbert Branscomb; Lisa Stubbs
Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution.
Science (New York, N.Y.) 2001;293(5527):104-11.
2001: Christopher Elkin; Paul M Richardson; H M Fourcade; N M Hammon; M J Pollard; Paul Predki; Tijana Glavina; Trevor L Hawkins
High-throughput plasmid purification for capillary sequencing.
Genome research 2001;11(7):1269-74.
2001: Colin Collins; Stanislav Volik; David Kowbel; David Ginzinger; Bauke Ylstra; T Cloutier; Trevor L Hawkins; Paul Predki; C Martin; M Wernick; Wen-Lin Kuo; ARTHUR S ALBERTS; Joe Gray
Comprehensive genome sequence analysis of a breast cancer amplicon.
Genome research 2001;11(6):1034-42.
2001: Latif Shooshtari Nasrin; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; N Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; John E Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; Andrew Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; Michael Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; Paul Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; John Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; Susan Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; Anna Pia Abola; M J Proctor; Richard Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; Roger A Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; Evan E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; Henning Hermjakob; K Hokamp; W Jang; L Steven Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W James Kent; P Kitts; E V Koonin; Ian F Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; John V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; Elia Stupka; J Szustakowski; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Initial sequencing and analysis of the human genome.
Nature 2001;409(6822):860-921.
1999: Richard A Shimkets; DG Lowe; J T Tai; PD Sehl; H Jin; R Yang; Paul Predki; B E Rothberg; M T Murtha; M E Roth; SG Shenoy; A Windemuth; JW Simpson; Jan Fredrik Simons; M P Daley; S A Gold; McKenna Michael; Kenneth J Hillan; G T Went; Jonathan M Rothberg
Gene expression analysis by transcript profiling coupled to a gene database query.
Nature biotechnology 1999;17(8):798-803.
1996: Paul Predki; V Agrawal; Axel T Brünger; Lynne Regan
Amino-acid substitutions in a surface turn modulate protein stability.
Nature structural biology 1996;3(1):54-8.
1995: Paul Predki; Lynne Regan
Redesigning the topology of a four-helix-bundle protein: monomeric Rop.
Biochemistry 1995;34(31):9834-9.
1995: Paul Predki; Bibudhendra Sarkar
Cooperative interaction of oestrogen receptor 'zinc finger' domain polypeptides on DNA binding.
The Biochemical journal 1995;305 ( Pt 3)():805-10.
1995: Paul Predki; L M Nayak; M B Gottlieb; Lynne Regan
Dissecting RNA-protein interactions: RNA-RNA recognition by Rop.
Cell 1995;80(1):41-50.
1994: Paul Predki; Bibudhendra Sarkar
Metal replacement in "zinc finger" and its effect on DNA binding.
Environmental health perspectives 1994;102 Suppl 3():195-8.
1994: Mary Munson; Paul Predki; Lynne Regan
ColE1-compatible vectors for high-level expression of cloned DNAs from the T7 promoter.
Gene 1994;144(1):59-62.
1994: Paul Predki; D Zamble; Bibudhendra Sarkar; Vincent Giguère
Ordered binding of retinoic acid and retinoid-X receptors to asymmetric response elements involves determinants adjacent to the DNA-binding domain.
Molecular endocrinology (Baltimore, Md.) 1994;8(1):31-9.
1992: Paul Predki; C Harford; P Brar; Bibudhendra Sarkar
Further characterization of the N-terminal copper(II)- and nickel(II)-binding motif of proteins. Studies of metal binding to chicken serum albumin and the native sequence peptide.
The Biochemical journal 1992;287 ( Pt 1)():211-5.
1992: Paul Predki; Bibudhendra Sarkar
Effect of replacement of "zinc finger" zinc on estrogen receptor DNA interactions.
The Journal of biological chemistry 1992;267(9):5842-6.
1992: Paul Predki; Dennis M Whitfield; Bibudhendra Sarkar
Characterization and cellular distribution of acidic peptide and oligosaccharide metal-binding compounds from kidneys.
The Biochemical journal 1992;281 ( Pt 3)():835-41.