Patents

Promoters from corynebacterium glutamicum and uses thereof in regulating ancillary gene expression. Native promoters and promoter ladders from Corynebacterium glutamicum which may be used to regulate on- and off-pathway gene expression. Zach Serber, Katherine G Gora, Shawn Manchester, Peter Enyeart, Alexander Shearer.

Prioritization of genetic modifications to increase throughput of phenotypic optimization. Systems and methods for determining modifications to apply to genres within at least one microbial strain to improve phenotypic performance (based on a first round of modifications). Anupam Chowdhury, Peter Enyeart, Michael Flashman, Alexander Shearer, Kurt Thorn.

Bioreachable prediction tool. Systems and methods for predicting the viability of producing target molecules in a host organism. Alexander G Shearer and Michelle L Wynn.

Engineered biosynthetic pathways for production of tyramine by fermentation. Engineering of microbial cells for fermentative production of tyramine. Michael S Siddiqui, Stefan De Kok, Alexander Shearer, Franklin Lu, Cara Tracewell, Steven Edgar.

Publications

Shearer AG, Altman T, Rhee CD. “Finding sequences for over 270
orphan enzymes.” PLoS ONE 9(5):e97250. 2014. Click here to read the article

Ramkissoon KR, Miller JK, Ojha S, Watson DS, Bomar MG, Galande AK, Shearer AG. “Rapid identification of sequences for orphan enzymes to power accurate protein annotation.” PLoS ONE 8(12): e84508. 2013. Click here to read the article

Mackie A, Paley S, Keseler IM, Shearer A, Paulsen IT, Karp PD. “Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database.” J Bacteriol. 196(5):982-8. 2014. PubMed

Eker S, Krummenacker M, Shearer AG, Tiwari A, Keseler IM, Talcott, C, Karp PD. “Computing minimal nutrient sets from metabolic networks via linear constraint solving.” BMC Bioinformatics. 14:114. 2013. Pubmed

Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martinez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD. “EcoCyc: fusing model organism databases with systems biology.” Nucleic Acids Research. 41(D1):D605-12. 2013. Pubmed

Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD. “The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.” Nucleic Acids Research. 40:D742-53. 2012. PubMed

Ferrer L, Shearer AG, Karp PD. “Discovering novel subsystems using comparative genomics.” Bioinformatics. 27(18):2478-85. 2011. PubMed

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD. “EcoCyc: a comprehensive database of Escherichia coli biology.” Nucleic Acids Research. 39:D583-90. 2011. PubMed

Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD. “The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.” Nucleic Acids Research. 38:D473-9. 2010. PubMed

Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. “EcoCyc: a comprehensive view of Escherichia coli biology.” Nucleic Acids Research. 37:D464-70. 2009. PubMed

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD. “The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.” Nucleic Acids Research. 36:D623-31. 2008. PubMed

Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides K, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Bonavides-Martinez C, Ingraham J. “Multidimensional annotation of the Escherichia coli K-12 genome.” Nucleic Acids Research. 35(22):7577-90. 2007. PubMed

Flury I, Garza R, Shearer A, Rosen J, Cronin S, Hampton RY. “INSIG: a broadly conserved transmembrane chaperone for sterol-sensing domain proteins.” EMBO Journal. 24(22):3917-26. 2005. PubMed

Shearer AG, Hampton RY. “Lipid-mediated reversible misfolding of a sterol-sensing domain (SSD) protein.”  EMBO Journal. 24(1):149-59. 2005. PubMed

Shearer AG, Hampton RY. “Structural control of endoplasmic reticulum-associated degradation: effect of chemical chaperones on 3-hydroxy-3-methylglutaryl-CoA reductase.” The Journal of Biological Chemistry. 279(1):188-96. 2004. PubMed

Gardner RG, Shearer AG, Hampton RY. “In vivo action of the HRD ubiquitin ligase complex: mechanisms of endoplasmic reticulum quality control and sterol regulation.” Molecular and Cellular Biology. 21(13):4276-91. 2001. PubMed