Publications

TBD

Gan, HM, Dailey, L*, Wenger, P*, Halliday, M, Williams, P, Hudson, AO, Savka, MA (2024). Quorum sensing signals of grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: Use of inducible expression and polymeric resin to sequester acyl-homoserine lactones. PeerJ 12:e18657. https://doi.org/10.7717/peerj.18657.

Cavanaugh, N, Kumar, G, Frignani, MC, Thewedros, N, Twashirwa, M, Riquelme, C, Hudson, AO, Chai, Y, Codoy-Carter, V. (2024). Whole-genome sequencing of three extremophile Bacillus sp. Strains isolated from the Atacama desert. Microbiol Resour Announc. doi: 10.1128/mra.00679-24.

Cavanaugh, N, Kumar, G, Reverdy-Pearson, A, Colbert, J, Riquelme, C, Hudson, AO, Chai, Y, Codoy-Carter. (2024). Whole-Genome Sequencing of a Janthinobacterium sp. Isolated from the Patagonian Desert. Microbiol Resour Announc. doi: 10.1128/mra.00600-24.

Bedore, TJ*, Kumar, G, McIntyre, C***, Alvarez, A***, Leslie, A***, Snead, A***, Hudson, AO.(2024). Genomic Analysis of five antibiotic-resistant bacteria isolated from the environment. Microbiol Resour Announc. 0:e00751-24. https://doi.org/10.1128/mra.00751-24.

Parthasarathy, A**, Miranda, RR**, Bedore, TJ*, Watts L*, Mantravadi, P, Wong, N, Chu, J*, Adjei J*, Rana, A, Savka, MA, Bulman, Z, Borrego, EJ, Hudson, AO. (2024). Interaction of Acinetobacter sp. RIT 592 induces the production of broad-spectrum antibiotics in Exiguobacterium sp. RIT 594. Front. Pharmacol. 15. doi: 10.3389/fphar.2024.1456027.

Olatunji, I*, Bardaji, DKR**, Miranda, RR, Savka, MA, Hudson, AO (2024). Artificial intelligence tools for the identification of antibiotic resistance genes. Front. Microbiol. 15:1437602. doi: 10.3389/fmicb.2024.1437602.

Gilkes, JM, Frampton, RA, Board, AJ, Hudson, AO, Price, Morris, VK, TG, Crittenden, DL, Muscroft-Taylor ,AC,  Sheen, CR, Smith, GR, Dobson, RCJ. (2024). A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction. Protein Science: 33:e5083. https://doi.org/10.1002/pro.5083.

Chomiak, K*, Owens, WA*, Bangkong, CM*, Day, S, Eddingsaas, NC, Hoffman, MJ, Hudson, AO, Tyler, AC (2024). Impact of microplastic on freshwater sediment biogeochemistry and microbial communities is polymer specific. Water: 6 (2): 348.

Mak, DA, Dunn, S, Coombes, D, Carere, C, Allison, J, Nock, V, Hudson, AO, Dobson, RCJ. (2024). Enzyme Kinetics Analysis (EKA): an online tool for analysing enzyme initial rate data and teaching enzyme kinetics. BMC. Bioinformatics. Biochem Mol Biol Educ: 1–11. https://doi.org/10.1002/bmb.21823.(Co-corresponding author).

Tuytschaevers, S*, Aden***, L, Greene, Z***, Nixon, C***, Shaw, W***, Kumar, G, Miranda, RR, Hudson, AO (2024). Isolation, whole-genome sequencing, annotation of two antibiotic-producing and antibiotic-resistant bacteria Pantoea rodasii RIT 836, and Pseudomonas soli RIT 838 collected from the environment. PLoS ONE: 19(2): e0293943. https://doi.org/10.1371/journal.pone.0293943.

Kumar, G, Gan, HM, Wengert, P*, Penix, T*, Parthasarathy, A**, Hudson, AO, Savka, MA (2024). Whole-genome sequencing of four culurable endophytic bacteria from German hard neck garlic cloves (Allium sativum L.). Microbiol Resour Announc. 2024 Mar 12:e0122523. doi: 10.1128/mra.01225-23.

Kumar, G, Gan, HM, Popielarz*, H, Steele, J*, Parthasarathy, A**, Hudson, AO, Savka, MA. (2023). Endophytic bacteria associated with wild-type banana seed (Musa balbisiana): Whole genome sequencing. Microbiol Resour Announc: e0065023. doi: 10.1128/MRA.00650-23

Freezman*, I, Parthasarathy**, A, Miranda, RR**, Watts, LM*, Hudson AO. (2023). Chromatographic isolation of potentially novel antibiotic compounds produced by Yimella sp. RIT 621. BMC Res Notes 16, 114 (2023). https://doi.org/10.1186/s13104-023-06393-0.

Gan, HM, Penix, T*, Wengert, P*, Wong,N, Hudson, AO,  Kumar, G,  Savka MA (2022). Whole Genome Sequence of Endophytic Bacteria Associated with Poison Ivy Vine (Toxicodendron radicans). Microbiol Resour Announc. 15: e0123222.doi: 10.1128/mra.01232-22.

Kesel, E*, Hudson, AO, Osier, MV (2022). Whole-genome sequence, assembly and annotation of an invasive plant, Amur Lonicera maackii (honeysuckle). Plants, 11(23), 3253; https://doi.org/10.3390/plants11233253.  (Co-corresponding author)

Mozrall, AR***, Miranda, RR**, Kumar, G, Wadsworth, CB, Hudson, AO. (2022). Isolation, whole-genome sequencing and annotation of two antibiotic producing and resistant bacteria, Enterobacter roggenkampii sp RIT 834 and Acinetobacter pittii sp RIT 835 from disposable masks collected from the environment. Microbiol Resour Announc. 12:e0075722. doi: 10.1128/mra.00757-22.

Reilly, E*, Alfaro, J*, Borzelleri, A*, Branco, E, Conklin*, D, Held, E*, Kulee, F*, Kuzman, A*, Langdon, N*, Lasko, A*, Neri, S*, Nichols, H*, Olawuyi, T*, Park, E*, Rugullies, K*, Wilkie, C*, Krebs, L*, Carter, D, Hudson, AO, Wadsworth. (2022). Draft genome sequences of three antibiotic-producing soil bacteria with growth inhibiting effects against commensal Neisseria. Microbiol Resour Announc. 12:e0062722. doi: 10.1128/mra.00627-22.

Parthasarathy, A.** Miranda, R.R**, Eddingsaas, N.C.; Chu, J*. Freezman, I.M*, Tyler, A.C, Hudson, A.O. Polystyrene Degradation by Exiguobacterium sp. RIT 594: Preliminary Evidence for a Pathway Containing an Atypical Oxygenase. Microorganisms 2022, 10, 1619. https://doi.org/10.3390/microorganisms10081619.

Miranda, RR**, Parthasarathy, A**, Hudson AO (2022). Exploration of chemical biology approaches to facilitate the discovery and development of novel antibiotics.Front.Trop. Dis. doi: 10.3389/fitd.2022.845469.

Raisman, JC*, Fiore, MA*, Tomin, L*, Adjei, JKO*, Aswad, V*, Chu, J*, Domondon, CH*, Donahue, BA*, Masciotti, CA*, McGrath, CG*, Melita, J*, Podbielski, PA*, Schreiner, MR*, Trumpore, LJ*, Wenger, PC*, Wrightstone, EA*, Hudson, AO, Wadsworth, CB. (2022). Evolutionary paths to macrolide resistance in a Neisseria commensal coverage on ribosomal gene through short sequence duplications. PLoS One. 17(1):e0262370. doi: 10.1371/journal.pone.0262370.

Schroeter, MN*, Gazali, SJ*, Parthasarathy, A**, Wadsworth, CB, Miranda, RR**, Hudson, AO. (2021). Isolation, whole-genome sequencing and annotation of three unclassified antibiotic-producting bacteria, Enterobacter sp. RIT 637, Pseudomonas sp. RIT 778 and Deinococcus sp. RIT 780. Microbiol Resour Announc. 10(48):e00863-21. doi: 10.1128/MRA.00863-21.

Rynkiewicz, P*, Babbitt, GA, Cui, F, Hudson, AO, Lynch, ML. (2021). A comparative survey of survey of betacoronaviruses strain molecular dynamics identifies key ACE2 binding sites. J Biomol Strcut Dyn. doi: 10.1080/07391102.2021.1953604.

Parthasarathy, A**, Borrego, EJ, Savka, MA, Dobson, RCJ, Hudson, AO. (2021). Amino acid-derived secondary metabolites from plants: A potential source to facilitate antimicrobial development. J Biol Chem. 2021 Feb 18:100438. doi: 10.1016/j.jbc.2021.100438.

Wengert, PC*, Wong, NH, Barton, HA, Hudson, AO, Savka MA (2021). Genomic characterization of underground lake bacteria from Wind Cave National Park: Insight into the archetypical LuxI/LuxR and identification of novel LuxR solos. BMC Res Notes. 8; 14(1):175. doi: 10.1186/s13104-021-05589-6.

Gaeth, VA*, Domodon, CJ*, Podbielski, PA*, Aswad, VX*, Wrightstone, EA*, Wong, NH, Burke, WH*, Melita, J*, Murray, KM*, Hudson, AO. (2021). Whole genome sequencing and annotation of 10 endophytic and epiphytic bacteria isolated from Lolium arundinaceum.  Microbiol Resour Announc. 10(19):e00317-21. doi: 10.1128/MRA.00317-21.

Cavanaugh, NT*, Parthasarathy, A**, Wong, NH, Steiner, KK*, Chu, J*, Adjei, J*, Hudson, AO. (2021). Exiguobacterium sp. RIT 452 is endowed with antibiotic properties against Gram positive/negative bacteria. BMC Res Notes. 14, 230.

Thomas, SE, Abajorga, M*, Glover, MA*, Wengert, PC*, Parthasarathy, A**, Savka ,MA, Wadsworth, CB, Shipman PA, Hudson AO. (2020). Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669 – potential zoonotic pathogens isolated from spotted turtles. Microorganisms:17;8(11):E1805. doi: 10.3390/microorganisms8111805.   

Fiore, MA*, Raisman, JC*, Wong, NH, Hudson, AO, Wadsworth, CB. (2020). Exploration of the Neisseria resistome reveals resistance mechanisms in commensals that may be acquired by N. gonorrhea through horizontal gene transfer. Antibiotics (Basel); 9 (10):E656. doi: 10.3390/antibiotics9100656. PMID: 33007823.

Muyiwa, AS, Olanrewaju, MB, Borrego, EJ, Hudson, AO, Thomas, BN. (2020). Differential evolution of α-glucan water dikinase (GWD) in plants. Plants (Basel). 9(9):E1101 doi:10.3390/plants9091101.

Steiner, KK*, Parthasarathy, A**, Wong, NH*, Cavanaugh, NT*, Chu, J*, Hudson AO. (2020). Isolation, Whole-Genome Sequencing and Antibiotic of Pseudomonas sp RIT 623, a slow-growing bacterium endowed with antibiotic properties. BMC Res Notes 13, 370.

Babbitt, GA, ML, Lynch, McCoy, M, Fokoue, EP, Hudson, AO. (2020). Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition J. Biomol Struct Dyn. 1-16. doi:10.1080/07391102.2020.1815578. 

Thomas SE, Glover MA*, Parthasarathy, P**, Wong, NH, Shipman PA, Hudson AO. (2020). Expression of a Shiga-like toxin during plastic colonization by two multidrug resistant bacteria, Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669, isolated from endangered turtles (Clemmys guttata). Microorganisms:8, 1172. doi: 10.3390/microorganisms8081172.

Reilly, E*, Abajorga, M*, Kiser, C*, Redzuan, NHM*, Haidar, Z*, Adams, L*, Diaz, R,* Pinzon, J*, Hudson, AO, Black, L Hsia, R, Weintraub, S, Thomas J. (2020). A Cut Above The Rest: Characterization of Assembly Mechanisms of a Large Viral Icosahedral Capsid. Viruses. 12, 725.

Thomas, SG, Glover, MA*, Parthasarathy, A**, Hudson, AO. (2020). The Close-Call in Microbiology-Understanding Microbes. Advances in Biology Laboratory Education: 41 Article 85.

Weatherhead, AW, Crowther, JM, Horne, CR, Meng, Y, Coombes, D, Currie, MJ, Watkin, SAJ, Adams, LE*, Parthasarathy, A**, Dobson, RCJ, Hudson AO. (2020). Structural-functional studies of the antibiotic target L,L-diaminopimelate aminotransferase from Verrucomicrobium spinosum reveal and an unusual oligomeric structure. Biochemistry 59: 2274-2288. Featured Cover Article

Adams, LE*, Rynkiewicz, P*, Babbitt, GA, Mortensen, JA*, North, RA, Dobson, RCJ, Hudson, AO. (2020). Comparative molecular dynamics simulations provide insight into antibiotic interactions: A case study using the enzyme L,L-diaminopimelate aminotransferase (DapL). Front. Mol. Biosci. | doi: 10.3389/fmolb.2020.00046.

Coll De Peña, A, Miller, A, Lentz, C, Hill, N, Parthasarathy, A**, Hudson, AO, Lapizco-Encinas, B. (2020). Creation of an electrokinetic characterization library for the detection and identification of biological cells. Anal Bioanal Chem. doi.org/10.1007/s00216-020-02621-9. (Co-corresponding author).

Wong, NH, Rosato, AJ*, Rose, YM*, Penix, TS*, Fung, JB*, Vanitski, AL*, Goossen, CJ*, Bradshaw, SG*, Lopp, SM*, Pennington, AD*, Darmohray, VM*, Steiner KK*, Kersey, GE*, Brylow, KB*, Pridmore, MV,* Hedges, JS*, Rynkiewicz, P*, Hudson AO (2020). Isolation and whole-genome sequencing of 12 mushroom associated bacterial strains: an inquiry based laboratory exercise in a genomics course at the Rochester Institute of Technology. Microbiol Resour Announc. doi: 10.1128/MRA.01457-19.

Gan, HM, Parthasarathy, A**, Henry, KR*, Savka, MA, Thomas, BN, Hudson, AO. (2020). Whole-genome sequencing of Pantoea sp strain RIT388, a potential oral opportunistic pathogen isolated from a chewing stick (Distemonanthus benthamianus).  Microbiol Resour Announc. doi: 10.1128/MRA.01468-19.

Gan, HM, Wengert, PC*, Barton, HA, Hudson, AO, Savka, MA. (2020). Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from an untouched site of the Lechuguilla Cave. Access Microbiology 2020;2 doi: 10.1099/acmi.0.000089.

Gan, HM, Wengert, PC*, Barton, HA, Hudson, AO, Savka, MA. (2019). Whole-genome sequencing of five proteobacteria isolated from Lechuquilla Cave, New Mexico, USA: Insights into taxonomy and quorum sensing.  Microbiol Resour Announc. e00913-19. doi: 10.1128/MRA.00913-19.

Parthasarathy, A**, Adams, LE*, Savka, FC*, Hudson AO. (2019). The Arabidopsis thaliana gene annotated by the locus tag At3g08860 encodes alanine aminotransferase. Plant Direct. 3:1–10.

Morenikeji, OB, Hawkes, ME, Hudson, AO, Thomas, BN. (2019). Computational analysis identifies evolutionary conserved miRNA-gene interaction potentially regulating immune response in bovine trypanosomosis. Front. Microbiol 10:2010. doi: 10.3389/fmicb.2019.02010.

Gan, HM, Szegedi, E, Fersi, R, Chebil, S, Kovacs, I, Kawaguchi, A, Hudson, AO, Burr, T, Savka, MA. (2019). Insight into the microbial co-occurrence and diversity of 73 grapevine (Vitis vinefera) crown galls collected across the northern hemisphere. Front. Microbiol. 10:1896. doi:10.3389/fmicb.2019.01896.

Parthasarathy, A**, Savka, MA, Hudson, AO (2019). The synthesis and role of β-Alanine in plants. Front. Plan Sci. 10:921. doi: 10.3389/fpls.2019.00921.

Parthasarathy A**, Wong NH, Burns ND, Aziz-Dickerson AH, Dweh J, Buchanan D, Savka MA, Hudson AO. (2019). Isolation, whole-genome sequencing and annotation of Yimella sp. RIT 621, a strain that produces antibiotic compounds against Escherichia coli ATCC 25922 and Bacillus subtilis BGSC 168. Microbiol Resour Announc. 2019 Apr 25; 8(17). pii: e00329-19. doi: 10.1128/MRA.00329-19.

Crowther, JC, Cross, PJ, Oliver, MR, Leeman, MM*, Bartl, AJ*, Weatherhead, AW, North, RA, Donovan, KA, Griffin, MDW, Suzuki, H, Hudson, AO, Kassanmascheff, M, Dobson, RCJ. (2019). Structure function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereo chemical control. J. Biol. Chem: 294:8505-8515. Co-corresponding author.

Parthasarathy, A**, Wong, NH, Weiss, AN*, Tian, S*, Ali, SE*, Cavanaugh, NT*, Chinsky,TM*, Cramer, CE*, Gupta, A*, Jha, R*, Johnson, LK*, Tuason, ED*, Khafehn, LM*, Krishnadas, V*, Musich, RJ*, Pfaff, JM*, Richman, SC*, Shumway, AJ*, Hudson, AO. (2019). SELfies and CELLfies: Whole genome sequencing and annotation of five antibiotic resistant bacteria isolated from the surfaces of smartphones, an inquiry based laboratory exercise in a genomics undergraduate course at the Rochester Institute of Technology. J. Genomics 7: 26-30.

Parthasarathy, A**, Tyler, AC, Hoffman, MJ, Savka, MA, Hudson, AO. (2019). Is plastic pollution in aquatic and terrestrial environments a driver for the evolution and transmission of antibiotic resistant pathogenic bacteria? Envrion Sci Technol. 53 (4) 1744-1745.

Mantravadi, PK, Kalesh, KA, Dodson, RCJ, Hudson, AO, Parthasarathy A** (2019). The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies Antibiotics and antimicrobial technologies: novel molecules and emerging trends. Antibiotics. 8 (1). doi: 10.3390/antibiotics8010008. Corresponding author-Featured Cover Article

Parthasarathy**, A, Wong NH, Cavanaugh, NT*, Steiner, KK*, Wengert, PC*, Savka, MA, Hudson, AO (2018). Whole genome sequencing and annotation of Exiguobacterium sp. RIT 452, an antibiotic producing strain isolated from a pond located on the campus of the Rochester Institute of Technology. Microbiol Resour Announc 7:e01342-18.

Parthasarathy, A**, Gan HM, Wong, NH, Savka, MA, Steiner, KK*, Henry, KR*, Hudson, AO. (2018). Isolation and genomic characterization of six endophytic bacteria isolated from Saccharum sp (sugarcane): Insights into antibiotic, secondary metabolite and quorum sensing metabolism. Journal of Genomics. 6: 117-121.

Parthasarathy, A**, Cross, PJ, Dobson, RCJ, Adams LE*, Savka, MA, Hudson, AO. (2018). A three-ring circus: Metabolism of the three proteogenic aromatic amino acids and their role in the health of plants and animals. Front Mol Biosci. DOI: 10.3389/fmolb.2018.00029.

Babbitt, GA, Coppola, EE*, Mortensen, JS*, Ekeren PX, Viola, C, Goldblatt, D, Hudson, AO. (2018). Synonymous codon organization reduces the impact of mutation on nucleic acid molecular dynamics. J. Mol. Evo. (doi: 10.1007/s00239-018-9828).

Gan, HM, Thomas, BN, Cavanaugh, NT*, Morales, GH*, Mayers, AN*, Savka, MA, Hudson, AO. (2017). Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis. Peer J. 5:e4050; DOI 10.7717/peerJ.4030.

Gan, HM, Eng, WWH, Barton, M*, Adams, LE*, Samsudin, N*, Bartl, AJ*, Hudson, AO, Savka, MA, Thomas, J. (2017).  Whole genome of Salmonella enterica subsp. enterica serovar Typhimurium strains TT6675 and TT9097 employed in the isolation and characterization of a novel giant phage mutant collection. Genome Announc. 5(34): e00857-17. doi: 10.1128/genomeA.00857-17.

Kumar, HKS, Gan, HM, Tan, MH, Eng, WWH, Barton, HA, Hudson, AO, Savka, MA. (2017). Genomic characterization of eight Ensifer strain isolated from pristine caves and a whole genome phylogeny of Ensifer (Sinorhizobium).  Journal of Genomics. 5:12-15.

Cala, AR*, Nadeau, MT*, Anthony W. Weatherhead*, Staker, BL, Dobson, RCJ, Abendroth, J, Myler, PJ, Hudson, AO. (2016).The crystal structure of dihydrodipicolinate reductase at 2.3A Å from the human pathogenic bacterium Bartonella henselae str. Houston-1. Acta Cryst F72, 885-891. Featured Cover Article.

Thomas, J, Benitez-Quintana, AD*, Bosch, M, Coll De Pena*, A, Aguilera, E, Coulibaly, A, Wu, W, Osier, M, Hudson, AO, Wintraub, S, and Black, L. (2016). Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly. J. Virol. 90:10284-10298.

Gan, HM, Dailey, LK*, Halliday, N, Williams, P, Hudson, AO and Savka, MA. (2016). Genome sequencing-assisted identification and the first validation of N-acyl-homoserine-lactone synthases from the Sphingomonadaceae family. Peer J. 4:e2332.

Hudson, AO, Harkness TCM* and Savka, MA. (2016). Functional complementation analysis (FCA): A laboratory exercise designed and implemented to supplement the teaching of biochemical pathways. J. Vis. Exp. (112), e53850, doi:10.3791/53850.

Naqvi, KF*, Patin, P, Wheatley, MS*, Savka, MA, Dobson, RC, Gan, HM, Barreteau, H, Blanot, D, Mengin-Lecreulx, D and Hudson, AO. (2016). Identification and partial characterization of a novel UDP-N-acetylenolpyruvoylglucosamine reductase/UDP-N-acetylmuramate:l-alanine ligase fusion enzyme from Verrucomicrobium spinosum DSM 4136T.  Front. Microbiol. 7:362. doi: 10.3389/fmicb.2016.00362.

Wai, Lai, Gan, HM, Hudson, AO and Savka MA. Whole genome sequencing reveals a new genospecies of Methylobacterium sp. GXS13, isolated from Vitis vinifera L. xylem sap. Genome Announc. 4(1).e01695-15. doi: 10.1128/genomeA.01695-15.

Babbitt, GA, Coppola, EE*, Alawad, MA* and Hudson, AO. (2016). Can all heritable biology really be reduced to a single dimension? Gene. 578: 162-168.

Naqvi, KF*, Staker, B, Dobson, RC, Sankaran, B, Myler, P and Hudson, AO. (2016). Cloning, expression, purification, crystallization and x-ray diffraction analysis of dihydrodipicolinate synthase (DapA) from the human pathogenic bacterium Bartonella henselae str. Houston-1 at 2.1 Åresolution. Acta Cryst F72, 2-9.

Tran, P, Tan, N, Lee, Y, Gan, HM, Polter SJ*, Dailey L*, Hudson, AO, Savka, MA. (2015). Whole genome sequence and classification of eleven endophytic bacteria from poison ivy (Toxicodendron radicans).  Genome Announc 3(6):e01319-15. doi:10.1128/genomeA.01319-15.

Polter, SJ*, Caraballo, AA*, Lee, YP, Eng, WWH, Gan, HM, Wheatley*, MS, Savka, MA, Thomas, BN, Hudson, AO. (2015). Isolation, identification, whole genome sequencing and annotation of four Bacillus species: B. anthracis RIT375, B. circulans RIT379, B. alttiudinis RIT380 and B. megateriumRIT381 from internal stem tissue of “the insulin plant” Costus igneus. Genome Announc. 3:e00847-15; doi:10.1128/genomeA.00847-15.

Eng W, Gan, HM, Huah HY, Hudson, AO, Pseudomonas kilonensis Savka, MA. (2015) Whole genome sequence and annotation of octopine-utilizingPseudomonas kilonensis (previously P. fluorescens) strain 1855-344. Genome Announc. 3(3) e00463-15. doi: 10.1128/genomeA.00463-15.

Gan HY, Gan HM, Savka, MA, Triassi AJ*, Wheatley, MS*, Naqvi, KF*, Foxhall TE*, Anauo MJ*, Baldwin MK*, Burkhardt, RN*,, O’Bryon, IG*, Dailey LK*, Busairi NI*, Keith, RC*, Mazhar  Khair, MH*, Modh Rasul, MZ*, Mohd Rosdi, NA*, Moutzourous JR*, Rhoads, AC*, Selcohan, MA*, Tautanov TB*, Polter, SJ*, Marks, KD*, Caraballo, AA*, Hudson, AO. (2015). Whole genome sequencing and annotation of Bacillus safensis RIT372 andPseudomonas oryzihabitans RIT370 from Capsicum annuum (bird’s eye chili) and Capsicum chinese (yellow lantern chili) respectively. Genome Announc. 3(2):e00288-15. doi:10.1128/genomeA.00288-15.

Savka, MA, Dailey, L*, Popova, Mihaylova, R M, Merritt, B*, Masek, M*, Le, P, Radziah Mat Nor*, S, Ahmad, M*, Hudson, AO, Bankova, V. (2015) Analyses of propolis extracts from seven states in the United States: Chemical composition and disruption in geographically diverse United States propolis. Evid Based Complement Alternat Med. Volume 2015, Article ID 472593.

Gan, HM, Gan, HY, Ahmad, NH*, Aziz, NA*, Hudson, AO, Savka, MA. (2015). Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging the Sphingomonadaceae family. Front. Cell. Infect. Microbiol. 4:188. doi: 10.3389/fcimb.2014.00188.

Babbitt, GA, Alawad, MA*, Schulze, KV*, Hudson, AO. (2014). Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucl. Acids Res doi:10.1093/nar/gku811.

Gan, HY, Gan, HM, Tarasco, AM*, Busairi, NI*, Barton, HA, Hudson, AO, Savka, MA. (2014). Whole genome sequences of four oligotrophic bacteria isolated from deep within a cave (>400 m): Lechuguilla Cave, New Mexico, USA. 2(6):e01133-14. doi:10.1128/genomeA.01133-14.

Triassi, AJ*, Wheatley, MS*, Savka, MA, Gan, HM, Dobson, RCJ, Hudson, AO. (2014) L,L-diaminopimelate aminotransferase (DapL): A putative target for the development of narrow –spectrum antibacterial compounds. Front. Microbiol 5:509. doi: 10.3389/fmicb.2014.00509.

Gan, HY, Gan, HM, Savka, MA, Triassi, AJ*, Wheatley, MS*, Smart, LB, Fabio, ES, Hudson, AO. Whole genome sequences of thirteen endophytic bacteria isolated from shrub willow (Salix) grown in Geneva, New York. (2014) Genome Announc. 2(3):e00288-14. doi:10.1128/genomeA.00288-14.

Oliver, MR, Crowther, JM, Leeman, MM*, Kessans, SA, North, RA, Donovan KA, Griffin, MDW, Suzuki, H, Hudson, AO, Kassanmascheff, M, Dobson, RCJ. (2014).The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase fromArabidopsis thaliana.  Acta Cryst (F70) 663-668.

Gan, HM, Triassi, AJ*, Wheatley, MS*, Savka, MA, Hudson, AO. (2014) High quality whole genome sequences of three strains of Enterobacter sp. Isolated from Jamaican Dioscorea cayenensis (Yellow Yam). Genome Announc: 13;2(2) doi:10.1128/genomeA.00170-14.

Mckinnie, SM, Rodriquez-Lopex, EM, Vederas, JC, Crowther, JM, Suzuki, H, Dobson, RC, Leustek, T, Triassi, AJ*, Wheatley, MS*, Hudson, AO. (2014) Differential response of orthologous L,L-diaminopimelate aminotransferase (DapL) to enzyme inhibitory antibiotic lead compounds.  Bioorganic and Medicinal Chemistry. 22 (1) 523-530.

Gan, HM, Hudson, AO, Rahman, A, Chan KG and Savka MA. (2013) Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: Insights into host interactions, marine adaptation and bioremediation. BMC Genomics: 14:431 doi:10.1186/1471-2164-14-431.

McGroty, SE*, Pattaniyil, DT*, Patin, D, Blanot, D, Ravichandran, AC, Suzuki, H, Dobson RCJ, Savka, MA and Hudson, AO. (2013) Biochemical Characterization of UDP-N-acetylmuramoyl-l-alanyl-d-glutamyl:meso-2,6-diaminopimelate ligase (MurE) from Verrucomicrobium spinosum DSM 4136^T PLoS ONE 8(6):e66458.doi:10.1371/journal.pone.0066458.

North, R*, Kessans, S*, Atkinson, S*, Suzuki, H, Watson, A, Burgess, B, Angley, L, Hudson, AO, Varsani, A, Griffin, M, Fairbanks, A, Dobson, RCJ. (2013). Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetyl neuraminate lyase from methicillin resistantStaphylococcus aureus. Acta Cryst (F69) 306-312.

Gan, HM, McGroty, SE*, Chew, TH, Chan, KG, Buckley, LJ, Savka, MA, Hudson, AO. (2012). Whole genome sequence of Enterobacter sp. SST3, an endophyte isolated from Jamaica sugarcane (Saccharum sp) stalk tissue. Journal of Bacteriol.194: 5981-5982.

Gan, HM, Chew, TH, Hudson, AO, Savka, MA. (2012). Genome sequence of Novosphingobium sp. Strain Rr02-17, a nopaline crown gall associated bacterium isolated from Vitis vinifera L. Grapevine.  Journal of Bacteriol. 194: 5137-5138.

Gan, HM, Chew, TH, Hudson, AO, Savka, MA. (2012). Genome sequence of Methylobacterium sp. Strain GXF4, a xylem associated bacterium isolated from Vitis vinifera L. Grapevine.  Journal of Bacteriol. 194: 5157-5158.

Nachar, VR*, Savka, FC*, McGroty, SE*, Donovan, KA*, North, RA*, Dobson, RC, Buckley, LJ, Hudson, AO (2012). Genomic and biochemical analysis of the diaminopimelate and lysine biosynthesis pathway in Verrucomicrobium spinosum: Identification and partial characterization of L,L-diaminopimelate aminotransferase and UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-meso-diaminopimelate ligase. Front. Microbio. 3:183. doi: 10.3389/fmicb.2012.00183.

Bulman,Z*,  Le,P, Hudson, AO, Savka, MA (2011). A novel property of propolis (bee glue): Anti-pathogenic activity by inhibition of N-acyl-homoserine lactone mediated signaling in bacteria. Journal of Ethanopharmacology. 138. 788-797.

Dobson, RCJ, Giron, I*, Hudson, AO (2011) L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development. PLoS ONE 6(5): e20439. doi:10.1371/journal.pone.0020439.

Hudson, AO, Klartag, A, Gilvarg, C, Dobson, RC, Marques, FG, Leustek T (2011) Dual diaminopimelate biosynthesis pathways in Bacteroides fragilisand Clostridium thermocellum. BBA proteins and proteomics (1814):1162-1168.

Hudson, AO, Giron, I*, Dobson, R. (2011) Crystallization and preliminary X-ray diffraction analysis of L,L-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii.  Acta Cryst (F67) 140-143.

Hudson, AO, Ahmad, NH*, Van Buren, R*, Savka, MA. (2010) Sugarcane and Grapevine endophytic bacteria: Isolation, detection of quorum sensing signals and identification by 16 v3 rDNA sequence analysis. Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology Volume 2 ISBN (13): 978-84-614-6195-0 Pg. 801-806.

Prabhu, P*, Hudson, AO. (2010) Identification and partial characterization of an L-Tyrosine aminotransferase from Arabidopsis thaliana. Biochemistry Research International (2010) Article ID 549572.

Gan, HM*, Buckley, L, Szegedi, E, Hudson, AO, Savka, MA. (2009).   Identification of an rsh gene from Novosphingobium sp. Necessary for quorum sensing signal accumulation. Journal of Bacteriology (191) 2551-2560.

Hudson, AO, Gilvarg C and Leustek T. (2008) Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of L,L-diaminopimelate aminotransferase. Journal of Bacteriol (190) 3256-3263.

Martin M, Saladores P*, Lambert E*, Hudson AO, Leustek T (2007). Localization of members of the γ-glutamyl transpepdidase family identifies sites of glutathione and glutathione S-conjugate hydrolysis. Plant Physiol (144) 1742-1752.

McCoy A, Adams N, Hudson AO, Gilvarg C, Leustek T, Maurelli A (2006) Chlamydia trachomatis CT390 is a transkingdom L,L-diaminopimelate aminotransferase variant of the meso-diaminopimelate/lysine biosynthetic pathway. PNAS (47) 17909-17914.

Hudson, AO, Singh BK, Leustek T and Gilvarg C (2006) An L,L- diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiol (140) 292-301.

Hudson, AO, Bless, C*. Macedo, P*. Chatterjee SP. Singh, BK. Gilvarg, C. Leustek, T. (2005). Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochemica et Biophysica Acta. (1721) 27-36.

Lee, M., Martin M., Hudson AO., Lee, J., Muhitch, M., Leustek, T. (2005) Methionine and threonine synthesis are limited by homoserine availability and not the activity of homoserine kinase in Arabidopsis thaliana. The Plant Journal. (41) 685-696.

Morgan, CA., Hudson, AO., Konopka A, Nakatsu CH. (2002) Analyses of  microbial activity in biomass-recycle reactors using denaturing gradient gel electrophoresis of 16S rDNA and 16S rRNA PCR products. Can. J. Microbiol. (48) 333-341.