Literature DB >> 21148691

mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.

L Safak Yilmaz1, Shreyas Parnerkar, Daniel R Noguera.   

Abstract

Mathematical models of RNA-targeted fluorescence in situ hybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.

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Year:  2010        PMID： 21148691      PMCID： PMC3028703          DOI： 10.1128/AEM.01733-10

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  24 in total

1.  probeBase: an online resource for rRNA-targeted oligonucleotide probes.

Authors:  Alexander Loy; Matthias Horn; Michael Wagner
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 2.  Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes.

Authors:  Michael Wagner; Matthias Horn; Holger Daims
Journal:  Curr Opin Microbiol       Date:  2003-06       Impact factor: 7.934

3.  Detection and differentiation of chlamydiae by fluorescence in situ hybridization.

Authors:  Sven Poppert; Andreas Essig; Reinhard Marre; Michael Wagner; Matthias Horn
Journal:  Appl Environ Microbiol       Date:  2002-08       Impact factor: 4.792

4.  ARB: a software environment for sequence data.

Authors:  Wolfgang Ludwig; Oliver Strunk; Ralf Westram; Lothar Richter; Harald Meier; Arno Buchner; Tina Lai; Susanne Steppi; Gangolf Jobb; Wolfram Förster; Igor Brettske; Stefan Gerber; Anton W Ginhart; Oliver Gross; Silke Grumann; Stefan Hermann; Ralf Jost; Andreas König; Thomas Liss; Ralph Lüssmann; Michael May; Björn Nonhoff; Boris Reichel; Robert Strehlow; Alexandros Stamatakis; Norbert Stuckmann; Alexander Vilbig; Michael Lenke; Thomas Ludwig; Arndt Bode; Karl-Heinz Schleifer
Journal:  Nucleic Acids Res       Date:  2004-02-25       Impact factor: 16.971

5.  Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes.

Authors:  N Sugimoto; S Nakano; M Katoh; A Matsumura; H Nakamuta; T Ohmichi; M Yoneyama; M Sasaki
Journal:  Biochemistry       Date:  1995-09-05       Impact factor: 3.162

6.  In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.

Authors:  Sebastian Behrens; Caroline Rühland; João Inácio; Harald Huber; A Fonseca; I Spencer-Martins; Bernhard M Fuchs; Rudolf Amann
Journal:  Appl Environ Microbiol       Date:  2003-03       Impact factor: 4.792

7.  Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells.

Authors:  E F DeLong; G S Wickham; N R Pace
Journal:  Science       Date:  1989-03-10       Impact factor: 47.728

8.  Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria.

Authors:  Annelie Pernthaler; Jakob Pernthaler; Rudolf Amann
Journal:  Appl Environ Microbiol       Date:  2002-06       Impact factor: 4.792

9.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors:  J D Thompson; D G Higgins; T J Gibson
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971

10.  The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function.

Authors:  Justyna Adamczyk; Martin Hesselsoe; Niels Iversen; Matthias Horn; Angelika Lehner; Per Halkjaer Nielsen; Michael Schloter; Peter Roslev; Michael Wagner
Journal:  Appl Environ Microbiol       Date:  2003-11       Impact factor: 4.792
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  61 in total

1.  Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes.

Authors:  Karel Šimek; Vesna Grujčić; Indranil Mukherjee; Vojtěch Kasalický; Jiří Nedoma; Thomas Posch; Maliheh Mehrshad; Michaela M Salcher
Journal:  FEMS Microbiol Ecol       Date:  2020-10-06       Impact factor: 4.194

2.  A straightforward DOPE (double labeling of oligonucleotide probes)-FISH (fluorescence in situ hybridization) method for simultaneous multicolor detection of six microbial populations.

Authors:  Faris Behnam; Andreas Vilcinskas; Michael Wagner; Kilian Stoecker
Journal:  Appl Environ Microbiol       Date:  2012-05-11       Impact factor: 4.792

3.  Simultaneous specific in planta visualization of root-colonizing fungi using fluorescence in situ hybridization (FISH).

Authors:  Pál Vági; Dániel G Knapp; Annamária Kósa; Diána Seress; Áron N Horváth; Gábor M Kovács
Journal:  Mycorrhiza       Date:  2013-11-13       Impact factor: 3.387

4.  Optimization of a two-step permeabilization fluorescence in situ hybridization (FISH) assay for the detection of Staphylococcus aureus.

Authors:  Thomas S Lawson; Russell E Connally; Subramanyam Vemulpad; James A Piper
Journal:  J Clin Lab Anal       Date:  2011       Impact factor: 2.352

5.  Community shift from phototrophic to chemotrophic sulfide oxidation following anoxic holomixis in a stratified seawater lake.

Authors:  Petra Pjevac; Marino Korlević; Jasmine S Berg; Elvira Bura-Nakić; Irena Ciglenečki; Rudolf Amann; Sandi Orlić
Journal:  Appl Environ Microbiol       Date:  2014-10-24       Impact factor: 4.792

6.  Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.

Authors:  Roberta M O'Connor; Jennifer M Fung; Koty H Sharp; Jack S Benner; Colleen McClung; Shelley Cushing; Elizabeth R Lamkin; Alexey I Fomenkov; Bernard Henrissat; Yuri Y Londer; Matthew B Scholz; Janos Posfai; Stephanie Malfatti; Susannah G Tringe; Tanja Woyke; Rex R Malmstrom; Devin Coleman-Derr; Marvin A Altamia; Sandra Dedrick; Stefan T Kaluziak; Margo G Haygood; Daniel L Distel
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-10       Impact factor: 11.205

7.  Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.

Authors:  Erik S Wright; L Safak Yilmaz; Andrew M Corcoran; Hatice E Ökten; Daniel R Noguera
Journal:  Appl Environ Microbiol       Date:  2014-06-13       Impact factor: 4.792

8.  Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms.

Authors:  Reiko Ueoka; Agustinus R Uria; Silke Reiter; Tetsushi Mori; Petra Karbaum; Eike E Peters; Eric J N Helfrich; Brandon I Morinaka; Muriel Gugger; Haruko Takeyama; Shigeki Matsunaga; Jörn Piel
Journal:  Nat Chem Biol       Date:  2015-08-03       Impact factor: 15.040

9.  "Candidatus Finniella" (Rickettsiales, Alphaproteobacteria), Novel Endosymbionts of Viridiraptorid Amoeboflagellates (Cercozoa, Rhizaria).

Authors:  Sebastian Hess; Andreas Suthaus; Michael Melkonian
Journal:  Appl Environ Microbiol       Date:  2015-11-13       Impact factor: 4.792

10.  Mixed group of Rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness.

Authors:  Shyh-Ching Lo; Guo-Chiuan Hung; Bingjie Li; Haiyan Lei; Tianwei Li; Kenjiro Nagamine; Shien Tsai; Mark J Zucker; Ludmilla Olesnicky
Journal:  Int J Clin Exp Pathol       Date:  2015-11-01
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