Publications

Orcid

Esser SP, Rahlff J, Zhao W§, Predl M, Plewka J, Sures K, Wimmer F, Lee J, Adam PS, McGonigle J, Turzynski V, Banas I, Schwank K, Krupovic M, Bornemann TLV, Figueroa-Gonzalez PA, Jarett J, Rattei T, Amano Y, Blaby IK, Cheng J, Brazelton WJ, Beisel CL, Woyke T, Zhang Y, and Probst AJ. (2023) A predicted CRISPR-mediated symbiosis between uncultivated archaea. Nature Microbiology, Under Review.

* Vailionis J§, Zhao W§, Zhang K§, Rodionov D., Lipscomb GL, Tanwee TNN, O’Quinn HC, Kelly RM, Adams MWW, and Zhang Y. (2023). Optimizing strategies for bio-based ethanol production using genome-scale metabolic modeling of the hyperthermophilic archaeon, Pyrococcus furiosus. Applied and Environmental Microbiology, e00563-23. doi: 10.1128/aem.00563-23.

Lipscomb GL, Crowley AT, Nguyen DMN, Keller MW, Vailionis J§, Zhang K§, Zhang Y, Kelly RM, and Adams, MWW. (2023). Manipulating Fermentation Pathways in the Hyperthermophilic Archaeon Pyrococcus furious for Ethanol Production up to 95°C Driven by Carbon Monoxide Oxidation. Applied and Environmental Microbiology, e00012-23. doi: 10.1128/aem.00012-23.

* Cres CM§, Tritt A, Bouchard KE, Zhang Y. DL-TODA: A Deep Learning Tool for Omics Data Analysis. Biomolecules. 2023; 13(4):585. doi: 10.3390/biom13040585.

* Powers C§, Gomaa F, Billings EB§, Utter DR, Beaudoin DJ, Edgcomb VP, Hansel CM, Wankel SD, Filipsson HL, Zhang Y, Bernhard JM. (2022) Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms. Frontiers in Marine Science, doi: 10.3389/fmars.2022.1010319.

* Pimentel ZT§, Thibodeau PS, Song B, Zhang Y. (2022) A Mollicutes Metagenome-Assembled Genome from the Gut of the Pteropod Limacina rangii. Microbiology, doi: 10.1128/mra.00752-22.

Crosby JR, Laemthong T, Bing RG, Zhang K§, Tanwee TNN, Lipscomb GL, Rodionov DA, Zhang Y, Adams MWW, Kelly RM. (2022) Biochemical and Regulatory Analyses of Xylanolytic Regulons in Caldicellulosiruptor bescii Reveal Genus-Wide Features of Hemicellulose Utilization. Appl Environ Microbiol. 88(21):e0130222. doi: 10.1128/aem.01302-22.

Liu F, Meamardoost S, Gunawan R, Komiyama T, Mewes C, Zhang Y, Hwang E, Wang L. (2022) Deep learning for neural decoding in motor cortex. Journal of Neural Engineering. 19(5). doi: 10.1088/1741-2552/ac8fb5.

* Dufault-Thompson K§, Nie C, Jian H, Wang F, and Zhang Y. (2022) Reconstruction and analysis of thermodynamically constrained metabolic models reveal mechanisms of metabolic remodeling under temperature perturbations of a deep-sea bacterium. mSystems, DOI: https://doi.org/10.1128/msystems.00588-22.

Hwang Y, Schulze-Makuch D, Arens FL, Saenz JS, Adam PS, Sager C, Bornemann TLV, Zhao W§, Zhang Y, Airo A, Schloter M, Probst AJ. (2021) Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core. Microbiome 9, 234. https://doi.org/10.1186/s40168-021-01177-9

Meamardoost S, Bhattacharya M, Hwang EJ, Komiyama T, Mewes C, Wang L, Zhang Y, Gunawan R. (2021) FARCI: Fast and Robust Connectome Inference. Brain Sciences 11(12):1556. https://doi.org/10.3390/brainsci11121556

* Zhang K§, Zhao W§, Rodionov D, Rubinstein GM, Nguyen DN, Crosby J, Bing RG, Kelly RM, Adams MWW, Zhang Y. (2021) Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production. mSystems 6:e01351-20. doi: 10.1128/mSystems.01351-20.

Rodionov DA, Rodionova IA, Rodionov VA, Arzamasov AA, Zhang K§, Rubinstein GM, Tanwee TNN, Bing RG, Crosby J, Nookaew I, Basen M, Brown SD, Wilson CM, Klingeman DM, Poole FL, Zhang Y, Kelly RM, Adams M. (2021) Transcriptional regulation of plant biomass degradation and carbohydrate utilization genes in the extreme thermophile Caldicellulosiruptor bescii. mSystems 6:e01345-20. doi: 10.1128/mSystems.01345-20.

Gomaa F, Utter DR, Powers C§, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. (2021) Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. Science Advances 7(22):eabf1586. doi: 10.1126/sciadv.abf1586.

* Pimentel ZT§, Dufault-Thompson K§, Russo KT§, Scro AK, Smolowitz RM, Gomez-Chiarri M, Zhang Y. (2021) Microbiome analysis reveals diversity and function of Mollicutes associated with the eastern oyster, Crassostrea virginica. mSphere 6:e00227-21. doi:10.1128/mSphere.00227-21.

Bhuta R, DeNardo B, Wang J§, Atoyan J, Zhang Y, Nelson D, Shapiro J. (2021) Durable changes in the gut microbiome in survivors of childhood acute lymphoblastic leukemia. Pediatric Blood & Cancer Aug 31:e29308. doi: 10.1002/pbc.29308.

Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K§, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao Y, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Goff G, Trionnaire G, Librado P, Liu S, Lombaert E, Lu H, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre R-F, Tang M, Tian W, Umina PA, Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, and Tagu D. (2020) The Genome Sequence of the Grape Phylloxera Provides Insights into the Evolution, Adaptation, and Invasion Routes of an Iconic Pest. BMC Biology 18, 90. doi:10.1186/s12915-020-00820-5.

Williams LE, Cullen N, DeGiorgis JA, Martinez KJ, Mellone J, Oser M, Wang J§, Zhang Y. (2019) Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100. Microbiology. doi: 10.1099/mic.0.000861.

Fernández Robledo JA, Yadavalli R, Allam B, Pales Espinosa E, Gerdol M, Greco S, Gomez-Chiarri M, Stevick RJ, Zhang Y, Heil C, Bishop-Bailey D, Metzger MJ. (2019) From the raw bar to the bench: Bivalves as models for human health. Developmental and Comparative Immunology 92, 260–282. doi:10.1016/j.dci.2018.11.020.

* Pimentel ZT§ and Zhang Y. (2018) Evolution of the natural transformation protein, ComEC, in Bacteria. Frontiers in Microbiology 9:2980. doi:10.3389/fmicb.2018.02980.

Mokszycki ME, Leatham-Jensen M, Steffensen JL, Zhang Y, Krogfelt KA, Caldwell ME, Conway T, and Cohen PS. (2018) A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus. Applied and Environmental Microbiology. doi:10.1128/AEM.02166-18.

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG and Hugenholtz P. (2018) Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology 9:772. doi: 10.3389/fmicb.2018.00772

* Steffensen JL§, Dufault-Thompson K§, Zhang Y. (2018) FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks. PLoS ONE 13(2): e0192891.

* Dufault-Thompson K§, Steffensen JL§, Zhang Y (2018) Using PSAMM for the curation and analysis of genome-scale metabolic models. In: Fondi M, editor. Metabolic Network Reconstruction and Modeling: Methods and Protocols. New York, NY: Springer New York. pp. 131–150. doi:10.1007/978-1-4939-7528-0_6. (Invited book chapter)

* Dufault-Thompson K§, Jian H, Cheng R, Li J, Wang F, and Zhang Y. (2017) A genome-scale model of Shewanella piezotolerans simulates mechanisms of metabolic diversity and energy conservation. mSystems (ASM), 2, e00165-16.

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P. (2017) Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology. 8:682.

* Steffensen JL§, Dufault-Thompson K§, and Zhang Y. (2016). PSAMM: a portable system for the analysis of metabolic models. PLoS Computational Biology 12(2): e1004732. doi:10.1371/journal.pcbi.1004732.

* Zhang Y and Sievert SM. (2014) Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. Frontiers in Microbiology 5:110. doi: 10.3389/fmicb.2014.00110.

Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. (2011) The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Computational Biology 7(12): e1002318.

Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. (2011) Structural determinants of limited proteolysis. Journal of Proteome Research 10(8): 3642-51.

Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 325, 1544-1549.

Burra PV, Zhang Y, Godzik A, Stec B. (2009) Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc. Natl. Acad. Sci. U. S. A. 106, 10505-10.

Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. (2009). PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Research 37, D611-8.

Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, and Godzik A. (2007) CutDB: a proteolytic event database. Nucleic Acids Research 35, D546-549.

Zhang Y, Stec B, and Godzik A. (2007) Between order and disorder in protein structures: analysis of “dual personality” fragments in proteins. Structure 15, 1141-1147.