Jessica Schneider

Project

Development of novel bioinformatics tools for functional annotation and metabolic reconstruction of biotechnologically important yeasts.

Info

Area: polyomics
Project Start: 1.04.2009
Supervisor(s): Dr. Alexander Goesmann, Prof. Dr. Alfred Pühler, apl. Prof. Dr. Andreas Tauch
University: Bielefeld

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Alumna

Dr. Jessica Schneider was a fellow of the CLIB-Graduate Cluster from April 2009 until October 2012, when she successfully defended her thesis.

Project overview

Next-generation sequencing facilitates to sequence the genomes of industrially important yeast species. In this project, a bioinformatics pipeline including RAPYD and CARMEN was developed covering regional and functional annotation, metabolic pathway reconstruction, and comparative genomics. A RAPYD demo project was set up including the draft genome sequence of Wickerhamomyces anomalus. This non-conventional wine yeast exhibits antimicrobial activities and flavoring features.

Development of novel bioinformatics tools for functional annotation and metabolic reconstruction of biotechno-logically important yeasts.

Jessica’s website at the CeBiTec.

Publications

Schneider J, Andrea H, Blom J, Jaenicke S, Rückert C, Schorsch C, Szczepanowski R, Farwick M, Goesmann A, Pühler A, Schaffer S, Tauch A, Köhler T, Brinkrolf K (2012) Draft Genome Sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Eukaryotic Cell 11(12): 1582 - 1583.

Brinkrolf K, Schneider J, Knecht M, Rückert C, Tauch A (2012) Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear Fluid from a Child with Otitis Media. Journal of bacteriology 194(21): 5968 - 5969.

Schneider J, Rupp O, Trost E, Jaenicke S, Passoth V, Goesmann A, Tauch A, Brinkrolf K (2012) Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Research 12(3): 382 - 386.

Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A (2012) Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC genomics 13: 141.

Becker J, Hackel M, Jakobi T, Rupp O, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, Noll T, Pühler A, Tauch A, Brinkrolf K (2011) Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology 156(3): 227 - 235.

Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehöver P, Burkovski A, Soares SC, Almeida SS, Dorella FA, Miyoshi A, Azevedo V, Schneider MP, Silva A, Santos CS, Santos LS, Sabbadini P, Dias AA, Hirata RJ, Mattos-Guaraldi AL, Tauch A (2011) Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. BMC Genomics 12:383.

Brune I, Götker S, Schneider J, Rodionov DA, Tauch A (2011) Negative transcriptional control of biotin metabolism genes by the TetR-type regulator BioQ in biotin-auxotrophic Corynebacterium glutamicum ATCC 13032. Journal of Biotechnology.

Kueberl A, Schneider J, Thallinger GG, Anderl I, Wibberg D, Hajek T, Jaenicke S, Brinkrolf K, Goesmann A, Szczepanowski R, Pühler A, Schwab H, Glieder A, Pichler H (2011) High-quality genome sequence of Pichia pastoris CBS7435. Journal of Biotechnology 154(4): 312 - 320.

Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A (2011) RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology 155(1): 118 - 126.

Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Alves Dorella F, Souza Rocha F, de Castro Soares S, D’Afonseca V, Miyoshi A, Ruiz J, Silva A, Azevedo V, Burkovski A, Guiso N, Join-Lambert OF, Kayal S, Tauch A (2010) The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics 11:728.

Schneider J, Vorhölter F-J, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A (2010) CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. Genetics and Molecular Research 9(3): 1660 - 1672.

Trost E, Götker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehoever P, Arnold W, Bekel T, Blom J, Gartemann K-H, Linke B, Goesmann A, Pühler A, Shukla SK, Tauch A (2010) Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC Genomics 11(91).

Neuweger H, Persicke M, Albaum S, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A (2009) Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology 3:82.

Goesmann A, Schneider J, Trost E, Tauch A (2009) Entschlüsselung mikrobieller Genomsequenzen im Schnellverfahren. BIOspektrum 15(3): 279 - 281.

Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehöver P, Gartemann K-H, Arnold W, Blom J, Brinkrolf K, Brune I, Goetker S, Weisshaar B, Goesmann A, Droege M, Pühler A (2008) Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology 136(1-2): 22 - 30.

Document


Jessica’s project poster
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