Dr. Frederick Russell Blattner (born 1940)

B.Sc. (Physics), Oberlin College, 1962
Ph.D. (Biophysics), The Johns Hopkins University, 1968
Postdoctoral Research: Harvard Medical School
Postdoctoral Research: McArdle Laboratory for Cancer Research, University of Wisconsin

Scarab Genomics, LLC

1202 Ann Street

Madison, WI 53713

Email: fred@genome.wisc.edu

Research Description

Genomics, gene regulation, bacteria, bioinformatics, DNA chips, genome engineering

One of the early leaders of the genomics revolution, Fred Blattner was the first to propose sequencing the entire genome of an organism. After accomplishing that, sequencing the genome of Escherichia coli K-12, his lab turned to large scale functional genomics of E. coli through DNA chip analysis of global gene expression, and by phenotypic analysis of conditional knock-out mutations.

Interested in hypothesis-driven comparative and evolutionary genomics, the lab sequenced the genomes of several pathogens related to E. coli K-12. The first strain selected for comparison was the infamous O157:H7 “hamburger strain” of E. coli, followed by a uropathogenic strain of E. coli and a strain causing neonatal sepsis and meningitis. They also sequenced Yersinia pestis (plague), Shigella flexneri (dysentary), and Salmonella Typhi (typhoid fever). It turns out that many virulence determinants of the different pathogens are similar, allowing identification of a “pathosphere” of virulence genes that make up the pathogenic potential of these bacteria.

Other interests include bioinformatics, technology development, and genetic engineering/re-engineering of bacterial genomes. Dr. Blattner retired from the university in July, 2011, but remains active at the helm of two companies he founded. DNASTAR, Inc., established in 1984, develops bioinformatics software for scientists to analyze DNA sequences, gene expression, protein structure, and more. Scarab Genomics, LLC was established in 2002 to commercialize the reduced genome technology arising from research in his campus lab. A third company, NimbleGen Systems, was created in 1999 based on the work of Blattner, UW scientists Franco Cerrina and Michael Sussman, and then-graduate student Roland Green. The company developed a faster, less-expensive way to make gene chips and was sold to Swiss pharmaceutical giant Roche in 2007.

Representative Publications

Search PubMed for more publications by Frederick Blattner

Z. Lipinszki, V. Vernyik, N. Farago, T. Sari, L. G. Puskas, F. R. Blattner, G. Pósfai, & Z. Györfy (2018) Enhancing the translational capacity of E. coli by resolving the codon bias. ACS Synth Biol 7(11):2656-2664. Epub 2018 Nov 2. [PubMed]
I. Karcagi, G. Draskovits, K. Umenhoffer, G. Fekete, K. Kovács, O. Méhi, G. Balikó, B. Szappanos, Z. Györfy, T. Fehér, B. Bogos, F. R. Blattner, C. Pál, G. Pósfai, & B. Papp (2016) Indispensability of horizontally transferred genes and its impact on bacterial genome streamlining. Mol Biol Evol 33(5):1257-1269. Epub 2016 Jan 14. [PubMed]
Z. Györfy, G. Draskovits, V. Vernyik, F. R. Blattner, T. Gaal, & G. Pósfai (2015) Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number. Nucleic Acids Res 43(3):1783-1794. Epub 2015 Jan 23. [PubMed]
T. Fehér, I. Karcagi, F. R. Blattner, & G. Pósfai (2012) Bacteriophage recombineering in the lytic state using the lambda red recombinases. Microb Biotechnol 5(4):466-476. Epub 2011 Sep 13. [PubMed]
S. Förster, M. Brandt, D. S. Mottok, A. Zschüttig, K. Zimmermann, F. R. Blattner, F. Gunzer, & C. Pöhlmann (2013) Secretory expression of biologically active human Herpes virus interleukin-10 analogues in Escherichia coli via a modified Sec-dependent transporter construct. BMC Biotechnol 13, article number 82. [PubMed].
Csörgo, T. Fehér, E. Tímár, F. R. Blattner, & G. Pósfai (2012) Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs. Microb Cell Fact 11, article number 11. [PubMed]
C. Pöhlmann, M. Brandt, D. S. Mottok, A. Zschüttig, J. W. Campbell, F. R. Blattner, D. Frisch, & F. Gunzer (2012) Periplasmic delivery of biologically active human interleukin-10 in Escherichia coli via a sec-dependent signal peptide. J Mol Microbiol Biotechnol 22(1):1-9. Epub Feb 21. [PubMed]
K. Umenhoffer, T. Fehér, G. Balikó, F. Ayaydin, J. Pósfai, F. R. Blattner, & G. Pósfai (2010) Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications. Microb Cell Fact 9, article number 38. [PubMed]
J. H. Lee, B. H. Sung, M. S. Kim, F. R. Blattner, B. H. Yoon, J. H. Kim, & S. C. Kim (2009) Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production. Microb Cell Fact 8, article number 2. [PubMed]
T. Durfee, A. M. Hansen, H. Zhi, F. R. Blattner, & D. J. Jin (2008) Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 190(3):1084-1096. Epub 2007 Nov 26. [PubMed]
T. Durfee, R. Nelson, S. Baldwin, G. Plunkett III, V. Burland, B. Mau, J. F. Petrosino, X. Qin, D. M. Muzny, M. Ayele, R. A. Gibbs, B. Csörgo, G. Pósfai, G. M. Weinstock, & F. R. Blattner (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol 190(7):2597-2606. Epub 2008 Feb 1. [PubMed]
J. D. Glasner, G. Plunkett III, B. D. Anderson, D. J. Baumler, B. S. Biehl, V. Burland, E. L. Cabot, A. E. Darling, B. Mau, E. C. Neeno-Eckwall, D. Pot, Y. Qiu, A. I. Rissman, S. Worzella, S. Zaremba, J. Fedorko, T. Hampton, P. Liss, M. Rusch, M. Shaker, L. Shaull, P. Shetty, S. Thotakura, J. Whitmore, F. R. Blattner, J. M. Greene, & N. T. Perna (2008) Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Res 36(Database issue):D519-523. Epub 2007 Nov 13. [PubMed]
J. M. Greene, G. Plunkett III, V. Burland, J. Glasner, E. Cabot, B. Anderson, E. Neeno-Eckwall, Y. Qiu, B. Mau, M. Rusch, P. Liss, T. Hampton, D. Pot, M. Shaker, L. Shaull, P. Shetty, C. Shi, J. Whitmore, M. Wong, S. Zaremba, F. R. Blattner, & N. T. Perna (2007) A new asset for pathogen informatics — the Enteropathogen Resource Integration Center (ERIC), an NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Disease. Adv Exp Med Biol 603:28-42. [PubMed]
M. R. King, R. P. Vimr, S. M. Steenbergen, L. Spanjaard, G. Plunkett III, F. R. Blattner, & E. R. Vimr (2007) Escherichia coli K1-specific bacteriophage CUS-3 distribution and function in phase-variable capsular polysialic acid O acetylation. J Bacteriol 189(17):6447-6456. Epub 2007 Jun 29. [PubMed]
S. S. Sharma, J. W. Campbell, D. Frisch, F. R. Blattner, & S. W. Harcum (2007) Expression of two recombinant chloramphenicol acetyltransferase variants in highly reduced genome Escherichia coli strains. Biotechnol Bioeng 98(5):1056-1070. [PubMed]
S. S. Sharma, F. R. Blattner, & S. W. Harcum (2007) Recombinant protein production in an Escherichia coli reduced genome strain. Metab Eng 9(2):133-141. Epub 2006 Oct 21. [PubMed]
Y. Xie, V. Kolisnychenko, M. Paul-Satyaseela, S. Elliott, G. Parthasarathy, Y. Yao, G. Plunkett 3rd, F. R. Blattner, & K. S. Kim (2006) Identification and characterization of Escherichia coli RS218-derived islands in the pathogenesis of E. coli meningitis. J Infect Dis 194(3):358-364. Epub 2006 Jun 30. [PubMed]
G. Posfai, G. Plunkett III, T. Feher, D. Frisch, G. M. Keil, K. Umenhoffer, V. Kolisnychenko, B. Stahl, S. S. Sharma, M. de Arruda, V. Burland, S. W. Harcum, & F. R. Blattner (2006) Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044-1046. Epub 2006 Apr 27. [PubMed]
M. Riley, T. Abe, M. B. Arnaud, M. K. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, H. Mori, N. T. Perna, G. Plunkett III, K. E. Rudd, M. H. Serres, G. H. Thomas, N. R. Thomson, D. Wishart, & B. L. Wanner (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 34(1):1-9. [PubMed]
C. D. Herring, A. Raghunathan, C. Honisch, T. Patel, M. K. Applebee, A. R. Joyce, T. J. Albert, F. R. Blattner, D. van den Boom, C. R. Cantor, & B. Ø. Palsson (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38(12):1406-1412. Epub 2006 Nov 5. [PubMed]
J. P. Novak, S. Y. Kim, J. Xu, O. Modlich, D. J. Volsky, D. Honys, J. L. Slonczewski, D. A. Bell, F. R. Blattner, E. Blumwald, M. Boerma, M. Cosio, Z. Gatalica, M. Hajduch, J. Hidalgo, R. R. McInnes, M. C. Miller III, M. Penkowa, M. S. Rolph, J. Sottosanto, R. St-Arnaud, M. J. Szego, D. Twell, & C. Wang (2006) Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution. Biol Direct 1, article number 27. [PubMed]
C. Brinkley, V. Burland, R. Keller, D. J. Rose, A. T. Boutin, S. A. Klink, F. R. Blattner, & J. B. Kaper (2006) Nucleotide sequence analysis of the enteropathogenic Escherichia coli adherence factor plasmid pMAR7. Infect Immun 74(9):5408-5413. [PubMed]
J. L. Giel, D. Rodionov, M. Liu, F. R. Blattner, & P. J. Kiley (2006) IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Mol Microbiol 60(4):1058-1075. [PubMed]
B. H. Sung, C. H. Lee, B. J. Yu, J. H. Lee, J. Y. Lee, M. S. Kim, F. R. Blattner, & S. C. Kim (2006) Development of a biofilm production-deficient Escherichia coli strain as a host for biotechnological applications. Appl Environ Microbiol 72(5):3336-3342. [PubMed]
S.S. Fong, A. P. Burgard, C. D. Herring, E. M. Knight, F. R. Blattner, C. D. Maranas, & B. Ø. Palsson (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91(5):643-648. [PubMed]
A. M. Hansen, Y. Qiu, N. Yeh, F. R. Blattner, T. Durfee, & D. J. Jin (2005) SspA is required for acid resistance in stationary phase by downregulation of H-NS in Escherichia coli. Mol Microbiol 56(3):719-734. [PubMed]
M. Liu, T. Durfee, J. E. Cabrera, K. Zhao, D. J. Jin, & F. R. Blattner (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280(16):15921-15927. Epub 2005 Feb 10. [PubMed]
Y. Kang, K. D. Weber, Y. Qiu, P. J. Kiley, & F. R. Blattner (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187(3):1135-1160. [PubMed]
S. Zhou, A. Kile, M. Bechner, M. Place, E. Kvikstad, W. Deng, J. Wei, J. Severin, R. Runnheim, C. Churas, D. Forrest, E. T. Dimalanta, C. Lamers, V. Burland, F. R. Blattner, & D. C. Schwartz (2004) Single-molecule approach to bacterial genomic comparisons via optical mapping. J Bacteriol 186(22):7773-7782. [PubMed]
C. D. Herring & F. R. Blattner (2004) Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR. J Bacteriol 186(20):6714-6720. [PubMed]
Y. Kang, T. Durfee, J. D. Glasner, Y. Qiu, D. Frisch, K. M. Winterberg, & F. R. Blattner (2004) Systematic mutagenesis of the Escherichia coli genome. J Bacteriol 186(15):4921-4930. Erratum in: J Bacteriol 186(24):8548. [PubMed]
A. C. Darling, B. Mau, F. R. Blattner, & N. T. Perna (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394-1403. [PubMed]
E. L. Buckles, F. K. Bahrani-Mougeot, A. Molina, C. V. Lockatell, D. E. Johnson, C. B. Drachenberg, V. Burland, F. R. Blattner, & M. S. Donnenberg (2004) Identification and characterization of a novel uropathogenic Escherichia coli-associated fimbrial gene cluster. Infect Immun 72(7):3890-3901. [PubMed]
C. D. Herring & F. R. Blattner (2004) Conditional lethal amber mutations in essential Escherichia coli genes. J Bacteriol 186(9):2673-2681. Erratum in: J Bacteriol 186(24):8547. [PubMed]
A. E. Darling, B. Mau, F. R. Blattner, & N. T. Perna (2004) GRIL: genome rearrangement and inversion locator. Bioinformatics 20(1):122-124. [PubMed]
M. B. Lobocka, D. J. Rose, G. Plunkett III, M. Rusin, A. Samojedny, H. Lehnherr, M. B. Yarmolinsky, & F. R. Blattner (2004) Genome of bacteriophage P1. J. Bacteriol 186(21):7032-7068. [PubMed]
R. M. Gutiérrez-Ríos, D. A. Rosenblueth, J. A. Loza, A. M. Huerta, J. D. Glasner, F. R. Blattner, & Collado-Vides J (2003) Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res 13(11):2435-2443. [PubMed]
T. E. Allen, M. J. Herrgård, M. Liu, Y. Qiu, J. D. Glasner, F. R. Blattner, & B. Ø. Palsson (2003) Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol 185(21):6392-6399. [PubMed]
J. Nishi, J. Sheikh, K. Mizuguchi, B. Luisi, V. Burland, A. Boutin, D. J. Rose, F. R. Blattner, & J. P. Nataro (2003) The export of coat protein from enteroaggregative Escherichia coli by a specific ATP-binding cassette transporter system. J Biol Chem 278(46):45680-45689. Epub 2003 Aug 21. [PubMed]
J. Bockhorst, Y. Qiu, J. Glasner, M. Liu, F. Blattner, & M. Craven (2003) Predicting bacterial transcription units using sequence and expression data. Bioinformatics 19 Suppl 1:i34-i43. [PubMed]
C. D. Herring, J. D. Glasner, & F. R. Blattner (2003) Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli. Gene 311:153-163. [PubMed]
P. L. Roesch, P. Redford, S. Batchelet, R. L. Moritz, S. Pellett, B. J. Haugen, F. R. Blattner, & R. A. Welch (2003) Uropathogenic Escherichia coli use D-serine deaminase to modulate infection of the murine urinary tract. Mol Microbiol 49(1):55-67. [PubMed]
J. Wei, M. B. Goldberg, V. Burland, M. M. Venkatesan, W. Deng, G. Fournier, G. F. Mayhew, G. Plunkett III, D. J. Rose, A. Darling, B. Mau, N. T. Perna, S. M. Payne, L. J. Runyen-Janecky, S. Zhou, D. C. Schwartz, & F. R. Blattner (2003) Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 71(5):2775-2786. [PubMed]
W. Deng, S.-R. Liou, G. Plunkett III, G. F. Mayhew, D. J. Rose, V. Burland, V. Kodoyianni, D. C. Schwartz, & F. R. Blattner (2003) Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol 185(7):2330-2337. [PubMed]
J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31(1):147-151. [PubMed]
R. A. Welch, V. Burland, G. Plunkett III , P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S.-R. Liou, A. Boutin, J. Hackett, D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T. Perna, H. L. T. Mobley, M. S. Donnenberg & F. R. Blattner (2002) Extensive mosiac structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99(26):17020-17024. [PubMed]
W. Deng, V. Burland, G. Plunkett III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plano, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner & R. D. Perry (2002) Genome sequence of Yersinia pestis KIM. J Bacteriol 184(16):4601-4611. [PubMed]
N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, J. Kim & F. R. Blattner (2002) Comparative Analyses of Enterobacterial Genomes. pp. 296-301 in: Biology of Plant-Microbe Interactions, Volume 3, S. A. Leong, C. Allen, & E. W. Triplett, eds. International Society for Molecular Plant-Microbe Interactions, St. Paul, Minnesota, U.S.A. (Proceedings of the 10th International Congress on Molecular Plant-Microbe Interactions, Madison, Wisconsin, U.S.A., July 10-14, 2001) [not indexed in PubMed]
V. Kolisnychenko, G. Plunkett III, C. D. Herring, T. Feher, J. Pósfai, F. R. Blattner & G. Pósfai (2002) Engineering a reduced Escherichia coli genome. Genome Res 12(4):640-647. [PubMed]
E. F. Nuwaysir, W. Huang, T. J. Albert, J. Singh, K. Nuwaysir, A. Pitas, T. Richmond, T. Gorski, J. P. Berg, J. Ballin, M. McCormick, J. Norton, T. Pollock, T. Sumwalt, L. Butcher, D. Porter, M. Molla, C. Hall, F. Blattner, M. R. Sussman, R. L. Wallace, F. Cerrina, & R. D. Green (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12(11):1749-1755. [PubMed]
A. G. Torres, J. A. Giron, N. T. Perna, V. Burland, F. R. Blattner, F. Avelino-Flores, & J. B. Kaper (2002) Identification and characterization of lpfABCC'DE, a fimbrial operon of enterohemorrhagic Escherichia coli O157:H7. Infect Immun 70(10):5416-5427. [PubMed]
A. G. Torres, N. T. Perna, V. Burland, A. Ruknudin, F. R. Blattner, & J. B. Kaper (2002) Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli. Mol Microbiol 45(4):951-966. [PubMed]
Z. Cheng, F. Dong, T. Langdon, S. Ouyang, C. R. Buell, M. Gu, F. R. Blattner, & J. Jiang (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14(8):1691-1704. [PubMed]
D. E. Taylor, M. Rooker, M. Keelan, L. K. Ng, I. Martin, N. T. Perna, V. Burland, & F. R. Blattner (2002) Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates. J Bacteriol 184(17):4690-4698. [PubMed]
I. T. Kudva, P. S. Evans, N. T. Perna, T. J. Barrett, G. J. DeCastro, F. M. Ausubel, F. R. Blattner, & S. B. Calderwood (2002) Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing. J Clin Microbiol 40(4):1152-1159. [PubMed]
I. T. Kudva, P. S. Evans, N. T. Perna, T. J. Barrett, F. M. Ausubel, F. R. Blattner, & S. B. Calderwood (2002) Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol 184(7):1873-1879. [PubMed]
S. R. Heimer, R. A. Welch, N. T. Perna, G. Posfai, P. S. Evans, J. B. Kaper, F. R. Blattner, & H. L. Mobley (2002) Urease of enterohemorrhagic Escherichia coli: evidence for regulation by Fur and a trans-acting factor. Infect Immun 70(2):1027-1031. [PubMed]
M. A. Newton, C. M. Kendziorski, C. S. Richmond, F. R. Blattner, & K. W. Tsui (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comput Biol 8(1):37-52. [PubMed]
M. M. Venkatesan, M. B. Goldberg, D. J. Rose, E. J. Grotbeck, V. Burland, & F. R. Blattner (2001) Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun 69(5):3271-3285. [PubMed]
Y. Dong, J. D. Glasner, F. R. Blattner, & E. W. Triplett (2001) Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames. Appl Environ Microbiol 67(4):1911-1921. [PubMed]
Y. Wei, J. M. Lee, C. Richmond, F. R. Blattner, J. A. Rafalski, & R. A. LaRossa (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 183(2):545-556. [PubMed]
N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Pósfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, & F. R. Blattner (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409(6819):529-533. Erratum in: Nature 410(6825):240. [PubMed]
A. Lim, E. T. Dimalanta, K. D. Potamousis, G. Yen, J. Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. Hackett, F. R. Blattner, T. S. Anantharaman, B. Mishra & D. C. Schwartz (2001) Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome Res 11(9):1584-1593. [PubMed]
D. W. Selinger, K. J. Cheung, R. Mei, E. M. Johansson, C. S. Richmond, F. R. Blattner, D. J. Lockhart, & G. M. Church (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18(12):1262-1268. [PubMed]
R. H. Ffrench-Constant, N. Waterfield, V. Burland, N. T. Perna, P. J. Daborn, D. Bowen, & F. R. Blattner (2000) A genomic sample sequence of the entomopathogenic bacterium Photorhabdus luminescens W14: potential implications for virulence. Appl Environ Microbiol 66(8):3310-3329. [PubMed]
C. K. Sherburne, T. D. Lawley, M. W. Gilmour, F. R. Blattner, V. Burland, E. Grotbeck, D. J. Rose, & D. E. Taylor (2000) The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer. Nucleic Acids Res 28(10):2177-2186. [PubMed]
G. Plunkett III, D. J. Rose, T. J. Durfee, & F. R. Blattner (1999) Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J Bacteriol 181(6):1767-1778. [PubMed]
J. Mahillon, H. A. Kirkpatick, H. L. Kijenski, C. A. Bloch, C. K. Rode, G. F. Mayhew, D. J. Rose, G. Plunkett III, V. Burland, & F. R. Blattner (1998) Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites. Gene 223(1-2):47-54. [PubMed]
V. Burland, Y. Shao, N. T. Perna, G. Plunkett III, H. J. Sofia, & F. R. Blattner (1998) The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res 26(18):4196-4204. [PubMed]
F. R. Blattner, G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, & Y. Shao (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453-1462. [PubMed]
F. R. Blattner, G. Plunkett III, G. F. Mayhew, J. Gregor, W. Davis, M. Goeden, N. Perna, D. Rose, Y. Shao, H. Kirkpatrick, C. Bloch, G. Pósfai, & C. Rode (1996) E. coli Genome Project. Microb Comp Genomics 1(4):357. [not indexed in PubMed]
V. Burland, G. Plunkett III, H. J. Sofia, D. L. Daniels, & F. R. Blattner (1995) Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res 23(12):2105-2119. [PubMed]
H. J. Sofia, V. Burland, D. L. Daniels, G. Plunkett III, & F. R. Blattner (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res 22(13):2576-2586. [PubMed]
F. R. Blattner, V. Burland, G. Plunkett III, H. J. Sofia, & D. L. Daniels (1993) Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res 21(23):5408-5417. [PubMed]
S.-E. Chuang, V. Burland, G. Plunkett III, D. L. Daniels, & F. R. Blattner (1993) Sequence analysis of four new heat-shock genes constituting the hslTS/ibpAB and hslVU operons in Escherichia coli. Gene 134(1):1-6. [PubMed]
G. Plunkett III, V. Burland, D. L. Daniels, & F. R. Blattner (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21(15):3391-3398. [PubMed]
V. Burland, D. L. Daniels, G. Plunkett III, & F. R. Blattner (1993) Genome sequencing on both strands: the Janus strategy. Nucleic Acids Res 21(15):3385-3390. [PubMed]
V. Burland, G. Plunkett III, D. L. Daniels, & F. R. Blattner (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16(3):551-561. [PubMed]
F. R. Blattner, D. L. Daniels, V. D. Burland, G. Plunkett III, & S.-E. Chuang (1992) The E. coli genome project: towards the first megabase. pp. 43-59, in: The Chromosome (John Innes Symposium, Norwich, England), J.S. Heslop-Harrison & R.B. Flavell, eds. Bios Scientific Publishers, Oxford, UK. [not indexed in PubMed]
D. L. Daniels, G. Plunkett III, V. Burland, & F. R. Blattner (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257(5071):771-778. [PubMed]

Patents

US 8,367,380 Compositions and methods for amino acid biosynthesis
US 8,178,339 Reduced genome E. coli
US 8,119,365 Insertion sequence-free bacteria
US 8,043,842 Bacteria with reduced genome
US 8,039,243 Insertion sequence-free bacteria
US 8,030,477 Methods for the synthesis of arrays of DNA probes
US 7,989,181 Methods and compositions for producing recombinant proteins using a gene for TRNA
US 7,935,505 Plasmid DNA preparations and methods for producing same
US 7,303,906 Competent bacteria
US 6,989,265 Bacteria with reduced genome
US 6,855,814 Sequences of E. coli O157
US 6,706,522 Plasmid DNA from Yersinia pestis
US 6,649,402 Microfabricated microbial growth assay method and apparatus
US 6,375,903 Method and apparatus for synthesis of arrays of DNA probes
US 6,365,723 Sequences of E. coli O157
US 6,223,128 DNA sequence assembly system
US 5,851,492 Microtiter plate sealing system
US 5,525,515 Process of handling liquids in an automated liquid handling apparatus
US 5,334,353 Micropipette device
US 5,227,288 DNA sequencing vector with reversible insert
US 4,771,384 System and method for fragmentation mapping

EVIDENCE TIMELINE

july 10 1971 - interesting wedding

https://www.newspapers.com/image/398283169/?terms=%22Frederick%20Blattner%22&match=1

update - Andria as of 2011 .. https://isthmus.com/news/news/everyday-scientists/

1976 (June 26)

https://www.newspapers.com/image/521365804/?terms=%22Frederick%20Blattner%22&match=1

1976-06-26-the-capital-times-madison-wisconsin-pg-17-clip-genetics.jpg

1977 (Jan 12)

https://www.newspapers.com/image/626742811/?terms=%22Frederick%20Blattner%22&match=1

1977-01-12-the-miami-herald-pg-19a-clip-gene-transplants.jpg

1977 (March 14)

https://www.newspapers.com/image/251101875/?terms=%22Frederick%20Blattner%22&match=1

1977-03-14-stevens-point-daily-journal-wisconsin-pg-3-clip-dna

1977 (April 20)

https://www.newspapers.com/image/85927277/?terms=%22Frederick%20Blattner%22&match=1

1977-04-20-the-la-crosse-tribune-wisconsin-pg-13-clip-germs.jpg

1978 (Dec 30) - cloned gene

https://www.newspapers.com/image/273262086/?terms=%22Frederick%20Blattner%22&match=1

1980 (Dec 30)

https://www.newspapers.com/image/405795251

https://www.newspapers.com/image/405795293/?terms=%22Frederick%20Blattner%22&match=1

1985

https://www.newspapers.com/image/401909314/?terms=%22Frederick%20Blattner%22&match=1

1989 (January 17)

https://www.newspapers.com/image/520019734/?terms=%22Frederick%20Blattner%22&match=1

1989-01-17-the-capital-times-madison-wisconsin-pg-23-clip-genetics

https://www.newspapers.com/image/520019736

1989-01-17-the-capital-times-madison-wisconsin-pg-24-clip-genetics

1995 (April 25) - NYTimes : "Bacterium's Full Gene Makeup Is Decoded"

1995-05-25-nytimes-bacterium-s-full-gene-makeup-is-decoded.pdf

https://www.nytimes.com/1995/05/26/us/bacterium-s-full-gene-makeup-is-decoded.html?searchResultPosition=8

By Nicholas Wade

May 26, 1995

For the first time, the entire DNA sequence of a free-living organism has been deciphered, displaying a full set of the genes needed for life, two scientists announced here on Wednesday night.

The sequence is a chain of 1,830,121 DNA bases, the chemical units of the genetic code, which constitute the entire genetic data base of the bacterium known as Hemophilus influenzae.

The result, announced at a meeting of the American Society for Microbiology, is a personal triumph for [Dr. John Craig Venter (born 1946)], the scientist who led the sequencing work.

Dr. Venter left the National Institutes of Health after disagreement about the best technical methods to be used in its Human Genome Project, and with private money has now won the race to sequence the first free-living organism. He first applied for Government funds to sequence the Hemophilus bacterium, but he said he was turned down on the ground that his approach would not work.

"This is really an incredible moment in history," Dr. Frederick R. Blattner of the University of Wisconsin said in an interview. "It demonstrates the ability to take the whole sequence of an organism and work down from that to its genes, which is what geneticists have been dreaming of for a long time."

Dr. Blattner heads the National Institutes of Health project, now almost half completed, to sequence the DNA of another bacterium, Escherichia coli.

[Dr. Francis Sellers Collins (born 1950)], director of the Center for Human Genome Research at the institutes, called Dr. Venter's sequencing of the bacterium "a significant milestone."

The importance of the Hemophilus sequence, in Dr. Blattner's view, is that in obtaining a full catalogue of an organism's genes, "the whole paradigm of genetics is reversed." Until now geneticists have discovered genes by seeing what function is impaired when a mutation, or change of bases, is made in a bacterium's DNA. With the full catalogue of genes in hand, they can start with a gene and search for its function.

Full genome sequences will also open the door to medical applications, like pinpointing a bacterium's virulent genes by comparing its harmless and disease-causing forms.

William A. Haseltine, chairman and chief executive officer of Human Genome Sciences, the company that has commercial rights to Dr. Venter's work, said that now that the surface proteins of Hemophilus can be inferred from the genes in the DNA sequence, it should be possible to design vaccines against them. Hemophilus influenzae, despite its name, usually causes an ear infection, not flu.

The task of sequencing Hemophilus was suggested by Dr. Hamilton O. Smith of Johns Hopkins University Medical School, who won a Nobel Prize for discovering special enzymes it possessed. Dr. Smith proposed a strategy for sequencing the bacterium and prepared a library of clones, or chopped up and amplified pieces of DNA, which he gave to Dr. Venter's laboratory, the Institute for Genomic Research in Gaithersburg, Md.

Although many viruses have been sequenced, their gene sets, or genomes, are quite small, since they replicate themselves by usurping the machinery of living cells and lack the genes for independent existence. Smallpox virus, for instance, has a genome of only 186,000 DNA bases. The Hemophilus genome sequenced by Dr. Smith and Dr. Venter is nearly 10 times as large. They have submitted articles about their work to the journal Science.

Dr. Venter said the sequencing took him just under a year. Genomes this big are usually tackled by first making a "map" of known chemical signposts along the DNA chain, and then sequencing between the signposts. He said his progress was so rapid because he had skipped the time-consuming mapping stage and relied on software programs he had developed to fit together the numerous pieces of the enormous jigsaw puzzle he had created.

With the full DNA sequence in hand, Dr. Venter has started to analyze it, although "it will take all of us months, if not years, to truly understand it," he said.

The Hemophilus genome seems to contain 1,749 genes. By comparing the sequence of these genes with those of known function from other organisms, Dr. Venter has predicted the biological role of most of them. They fall into 14 major categories that must include "all the enzymes necessary for life," Dr. Venter noted. Many of these genes are clustered into logical groups, corresponding to the series of enzymes needed at each step of a biochemical pathway.

Another feature of interest to microbiologists is the presence of a latent phage, a virus that infects bacteria, whose DNA sequence is nestled inside that of Hemophilus. The bacterium also has six identical sets, spread around its chromosome, of the genes that specify ribosomes, part of the cell's protein-making machinery, Dr. Venter said.

Dr. Venter's achievement threatens to make him part of the scientific establishment with which he has long been at odds because of his liking for short-cut approaches to genome sequencing that other experts say are unlikely to work.

In the case of Hemophilus, Dr. Venter said he applied for money to the National Center for Human Genome Research, a part of the National Institutes of Health. At the same time he started work on the project with other money he had available. When he had completed 90 percent of the sequence, he received a letter saying his application had been turned down, since the committee of experts that reviewed it felt he would be unable to close the remaining gaps between his assemblies of shorter sequences.

This well-known problem in sequencing arises because there are usually a few genes that produce proteins that are toxic to the cells in which they are growing, causing the puzzle to have missing pieces. But Dr. Venter sidestepped this problem with a second set of clones that did not produce proteins.

Dr. Robert L. Strausberg, an official who oversees the committee that recommended against Dr. Venter's application, confirmed that it was turned down because of concerns like that of gap closure. But he denied that the committee had made an error of judgment.

As if to prove that the Hemophilus sequence was no fluke, Dr. Venter at the end of his lecture produced another rabbit from his hat, the sequence of a second free-living organism. It was the 580,067 base pairs of Mycoplasma genitalium, which has one of the smallest genomes of any known bacterium. The Mycoplasma sequencing was completed in three months by a team under Dr. Claire Fraser, a member of his institute and also his wife. Dr. Venter said he chose the tiny Mycoplasma organism because it would help determine the minimum set of genes necessary for life.

Dr. Venter said he had money from the Department of Energy to sequence several other microbes and expected to finish a third organism, Methanococcus jannaschii, by the end of the year. The strange microbe, which lives in almost boiling water, is a member of an ancient family of bacteria known as Archaea. The Archaea genome, when compared with those of other bacteria as they become available, may help point toward the characteristics of the organisms that lived at the root of the tree of life.

1995 (July 18)

https://www.newspapers.com/image/167314207/?terms=%22Frederick%20Blattner%22&match=1

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1997 (Feb 24) - Letters to Dr. Joshua Lederberg

1997-02-24-profiles-nlm-nih-gov-letter-from-lederberg-to-frederick-blattner-download-page.pdf

1997-02-24-profiles-nlm-nih-gov-letter-from-lederberg-to-frederick-blattner.pdf

1997-02-24-profiles-nlm-nih-gov-letter-from-lederberg-to-frederick-blattner-img-1.jpg

https://profiles.nlm.nih.gov/spotlight/bb/catalog/nlm:nlmuid-101584906X12714-doc

Title: Letter from Joshua Lederberg to Frederick R. Blattner
Creator: Lederberg, Joshua
Recipient: Blattner, Frederick R.
Date: 24 February 1997
Location: Box: 40. Folder: 48
Legacy ID : BBBCBJ / NLM ID : 101584906X12714
Profiles Collection : The Joshua Lederberg Papers
Shareable Link : https://profiles.nlm.nih.gov/101584906X12714

1997 (April 10) - Wisconsin State Journal : "Science a difficult, high-stakes venture"

Full Page 1A : [HN01P8][GDrive] / Clip above : [HN01P9][GDrive]

Full Page 3A : [HN01PB][GDrive] / Clip above : [HN01PC][GDrive]

1997 (Sep 05)

https://www.newspapers.com/image/139139087/?terms=%22Frederick%20Blattner%22&match=1

2001 (Jan 25) - NYTimes : "Decoding of Genome Could Help to Fight E. Coli Infections"

https://www.nytimes.com/2001/01/25/us/decoding-of-genome-could-help-to-fight-e-coli-infections.html?searchResultPosition=7

2001-01-25-nytimes-decoding-of-genome-could-help-to-fight-e-coli-infections.pdf

By Kenneth Chang

Jan. 25, 2001

Scientists have decoded the genome of a deadly strain of E. coli bacteria, and they say the work could aid in the development of diagnostic tests and treatments.

Writing in today's issue of the journal Nature, researchers from the University of Wisconsin and other institutes report that the bacterium, a strain known as O157:H7, is much more complex than its benign relatives. Its DNA, with more than 5,400 genes, is one-quarter longer and contains blueprints for a host of biological machinery to wreak havoc within people's intestines, the researchers said.

''That was one of the big surprises of this comparison,'' said Dr. Nicole T. Perna, a professor of animal health and biomedical sciences at Wisconsin and the lead author of the paper.

Harmless versions of E. coli live in the intestines of people and other mammals, but some E. coli can cause severe health problems. First identified in 1982, O157:H7 is now a common cause of food poisoning, inflicting diarrhea on 73,000 people in the United States each year. Of those, about 2,000 are hospitalized with more serious symptoms like bloody diarrhea and kidney trouble, and about 60 die. Children and the elderly are the most vulnerable.

When researchers started the project, they expected the DNA of O157:H7 to resemble that of a harmless strain they had decoded in 1997, with a few additional genes to manufacture the toxins.

The two strains share more than 4,000 genes, or what Dr. Frederick R. Blattner, the director of the Genome Center of Wisconsin, calls a common ''backbone.'' But Dr. Blattner, who led the research, said, ''then you've got these wild things just stuck in there.''

Interspersed along the O157:H7's backbone are 177 new chunks of DNA containing 1,387 genes, the researchers reported. The harmless strain also contains about 500 genes not found in O157:H7.

The immense differences between the genetic makeup of the two types indicate that E. coli swap DNA much more readily than other bacteria, the researchers said. Some of the DNA, including the genes that produce the toxins, appears to have been implanted by viruses.

2001 (Jan 30) - NYTimes : "The Week in Science: Rats and Reindeer"

https://www.nytimes.com/2001/01/30/science/the-week-in-science-rats-and-reindeer.html?searchResultPosition=1

2001-01-30-nytimes-the-week-in-science-rats-and-reindeer.pdf

By Nicholas Wade

Jan. 30, 2001

Rats and reindeer were the stars of this week's scientific news.

Biologists at MIT have gained the most curious and intimate insight into a rat's mind: they have eavesdropped on its dreams .

When rats are trained to run mazes, their initial memories are laid down in cells in an organ of the brain called the hippocampus. By sticking very fine recording needles into the hippocampal cells, biologists can even tell where in the maze the rat is at any given moment.

In an extension of this experiment, some MIT rats were trained to run a maze in the usual way but the biologists continued to record from the hippocampal cells while the rats were asleep.

When the rats entered the phase of sleep during which dreams occur, at least in people, the hippocampal cells started firing, presumably activated by a rat dream. And the researchers could tell, as before, exactly where in the maze the dreaming rat imagined it was.

The research seems to corroborate the long-standing idea that the function of dreams is to let the brain consolidate memories laid down the previous day.

What's the difference between a reindeer and a caribou ? Far too little, it seems, at least in the view of Alaskan reindeer herders. Both ungulates belong to the same species, Rangifer tarandus, but the reindeer have been domesticated for 7,000 years. They have acquired a small behavioral difference that makes them easier to herd - they tend to move in circles instead of straight lines. And domestication has left them with less endurance than their wild cousins.

These arcane attributes would matter less if it were not for the unexpected resurgence of Alaska's caribou herd, which now numbers 400,000 animals. The caribou have spread into areas where the free ranging reindeer herds are kept, and nothing can stop the reindeer from following their cousins' annual migration to their calving grounds.

Six of the 7 reindeer herds in Alaska have been lost this way. The only way of separating the reindeer from the caribou is to chase them in a helicopter - the reindeer lag behind because of their lesser endurance. But to little avail - they just get caught up in another caribou herd.

Two important genomes were sequenced this week. One was the genome of rice, an immensely important food crop . Rice, the second plant to be sequenced, has 430 million units of DNA in its genome and is only the second plant genome to be sequenced. It will probably take several years for biologists to figure out where all the genes are located and what they do. But having the genome in hand provides an excellent foundation for improving the rice plant and adapting it to special conditions.

The other genome belongs to the pathogenic variety of Escherichia coli, known as E. coli O157:H7 . E. coli itself is a harmless inhabitant of the human gut but its evil twin is responsible for food poisoning that affects 73,000 people a year, sends 2,000 to hospital and kills about 60. The pathogenic variety has now been sequenced by Fred Blattner of the University of Wisconsin, whose team also sequenced E. coli. E. coli O157:H7 turns out to have 25% more DNA than the ordinary bacterium and 1,387 extra genes, which are presumably the cause of its pathogenicity.

Australian scientists announced that they had managed to soup up the mouse pox virus so that it killed even mice that were vaccinated against the ordinary virus . They said it would be serious if anyone were to try the same thing the same with smallpox, the equivalent virus in humans, and therefore that the Biological Weapons Convention should be strengthened. The mousepox virus was enhanced by addition of the mouse gene that makes interleukin-4, one of the signals that primes the immune system for action. It seems that by forcing cells to make extra amounts of the interleukin, the genetically engineered virus deranged the mouse's immune system and so was able to kill the animals.

Talking of ominous news, there were more bad tidings from the global climate front . Samples of coral from Papua-New Guinea suggests that the cycle of warm and cold water in the Pacific, known as El Nino and La Nina, has been more intense this century than at any time in the last 130,000 years. The intense phase started well before the peak of industrial waste gases thought to be triggering the current phase of global warming, so presumably has a separate cause. But the warming could make worse the tendency of the El Nino cycle to cause disruptive weather.

2006 (May 02) - removing DNA may make ecoli safe, help vaccines

https://www.newspapers.com/image/518805295/?terms=%22Frederick%20Blattner%22&match=1

2006-05-02-the-times-tribune-scranton-pennsylvania-pg-c6

2006-05-02-the-times-tribune-scranton-pennsylvania-pg-c6-clip-ecoli.jpg

https://profiles.nlm.nih.gov/spotlight/bb/catalog?utf8=%E2%9C%93&exhibit_id=bb&search_field=all_fields&q=blattner

march 5 2000

https://www.newspapers.com/image/397136036/?terms=%22Frederick%20Blattner%22&match=1

August 19 1999 - Lederberg, Blattner - Giants at UW

https://www.newspapers.com/image/402026623/?terms=%22Frederick%20Blattner%22&match=1

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