MCB Publications

Israela Turgeman-Grott, Danielle Arsenault, Dekel Yahav, Yutian Feng, Guy Miezner, Doron Naki, Omri Peri, R Thane Papke, Johann Peter Gogarten, Uri Gophna, Neighboring inteins interfere with one another's homing capacity, PNAS Nexus, Volume 2, Issue 11, November 2023, pgad354,

Clare K. Melchiorre, Matthew D. Lynes, Sadikshya Bhandari, Sheng-Chiang Su, Christian M. Potts, Amy V. Thees, Carol E. Norris, Lucy Liaw, Yu-Hua Tseng and Michael A. Lynes, Extracellular metallothionein as a therapeutic target in the early progression of Type 1 Diabetes, Cell Stress and Chaperones, (2024)

Clare K. Melchiorre, Matthew D. Lynes, Sadikshya Bhandari, Sheng-Chiang Su, Christian M. Potts, Amy V. Thees, Carol E. Norris, Lucy Liaw, Yu-Hua Tseng and Michael A. Lynes, Extracellular metallothionein as a therapeutic target in the early progression of Type 1 Diabetes, Cell Stress and Chaperones, (2024)

Leavitt JC, Woodbury BM, Gilcrease EB, Bridges CM, Teschke CM, Casjens SR. Bacteriophage P22 SieA-mediated superinfection exclusion. mBio. 2024 Feb 14;15(2):e0216923. doi: 10.1128/mbio.02169-23. Epub 2024 Jan 18. PMID: 38236051.

Burdick, L. N., DelVichio, A. H., Hanson, L. R., Griffith, B. B., Bouchard, K. R., Hunter, J. W., and Goldhamer, D. J. (2024). Sex as a critical variable in basic and pre-clinical studies of fibrodysplasia ossificans progressiva. Biomolecules 14, 177.

Golla, V.K., Boyd, K.J. & May, E.R. Curvature sensing lipid dynamics in a mitochondrial inner membrane model. Commun Biol 7, 29 (2024).

Devarakonda PM, Sarmiento V, Heaslip AT. F-actin and myosin F control apicoplast elongation dynamics which drive apicoplast-centrosome association in Toxoplasma gondii. mBio. 2023 Oct 31;14(5):e0164023. doi: 10.1128/mbio.01640-23. Epub 2023 Sep 21. PMID: 37732764; PMCID: PMC10653800.

Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Protocol for an agent-based model of recombination in bacteria playing a public goods game. STAR Protoc. 2023 Nov 18;4(4):102733. doi: 10.1016/j.xpro.2023.102733. Epub ahead of print. PMID: 37980566.

Jeffrey D. Tamucci, Nathan N. Alder, and Eric R. May, Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations, Mol. Pharmaceutics, 2023 Oct 30,

Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E, Novel Metagenome Protein Families Consortium*, Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A & Kyrpides NC *Klassen JL is a member of the Novel Metagenome Protein Families Consortium. 2023. Unraveling the functional dark matter through global metagenomics Nature 622:594-602

Seo, D., Kammerer, R.A., & Alexandrescu, A.T. (2023) “Solution NMR assignments and structure for the dimeric kinesin neck domain”, Biomol NMR Assign, online ahead of print

Devarakonda PM, Sarmiento V, Heaslip AT. F-actin and myosin F control apicoplast elongation dynamics which drive apicoplast-centrosome association in Toxoplasma gondii. mBio. 2023 Sep 21:e0164023. doi: 10.1128/mbio.01640-23. Epub ahead of print. PMID: 37732764.

Klassen JL. 2023. Resistance waxes for mutualists protected by wasp secretions PNAS 120(36):e2311815120

Rua, A.J., Whitehead, R. 3rd,  & Alexandrescu, A.T (2023) “NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750”, J Struct Biol X 8, article 100093.

Devisscher L, Van Campenhout S, Lefere S, Raevens S, Tilleman L, Van Nieuwerburgh F, Van Eeckhoutte HP, Hoorens A, Lynes MA, Geerts A, Laukens D, Van Vlierberghe H. (2022) Metallothioneins alter macrophage phenotype and represent novel therapeutic targets for acetaminophen-induced liver injury. J Leukoc Biol. 111(1):123-133.

Maltz-Matyschsyk M, Melchiorre CK, Herbst KW, Hogan AH, Dibble K, O'Sullivan B, Graf J, Jadhav A, Lawrence DA, Lee WT, Carson KJ, Radolf JD, Salazar JC, Lynes MA; Connecticut Children’s COVID Collaborative. Development of a biomarker signature using grating-coupled fluorescence plasmonic microarray for diagnosis of MIS-C. Front Bioeng Biotechnol. 2023 Mar 31;11:1066391. doi: 10.3389/fbioe.2023.1066391. PMID: 37064248; PMCID: PMC10102909.

Lee, I.P.A., Eldakar, O.T., Gogarten, J.P., and Andam, C.P. (2023): Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. 
iScience 26. 

Koga A, Nishihara H, Tanabe H, Tanaka R, Kayano R, Matsumoto S, Endo T, Srikulnath K, O'Neill RJ. Kangaroo endogenous retrovirus (KERV) forms megasatellite DNA with a simple repetition pattern in which the provirus structure is retained. Virology. 2023 Jul 19;586:56-66. doi: 10.1016/j.virol.2023.07.005. Epub ahead of print. PMID: 37487326.

Lisa Rouressol, John Briseno, Nidhi Vijayan, Grischa Y. Chen, Elena A. Ritschard, Gustavo Sanchez, Spencer V. Nyholm, Margaret J. McFall-Ngai, Oleg Simakov, Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid, iScience, Volume 26, Issue 7, 2023, 107091, ISSN 2589-0042,

Ng EL, Reed AL, O'Connell CB, Alder NN. Using Live Cell STED Imaging to Visualize Mitochondrial Inner Membrane Ultrastructure in Neuronal Cell Models. J Vis Exp. 2023 Jun 30;(196). doi: 10.3791/65561. PMID: 37458423.

Feregrino-Mondragón RD, Santiago-Martínez MG, Silva-Flores M, Encalada R, Reyes-Prieto A, Rodríguez-Zavala JS, Peña-Ocaña BA, Moreno-Sánchez R, Saavedra E, Jasso-Chávez R. Lactate oxidation is linked to energy conservation and to oxygen detoxification via a putative terminal cytochrome oxidase in Methanosarcina acetivorans. Arch Biochem Biophys. 2023 Jul 15;743:109667. doi: 10.1016/ Epub 2023 Jun 14. PMID: 37327962.

Asis K. Jana, Mahmoud Sharawy, Eric R. May, Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions, Journal of Structural Biology, Volume 215, Issue 2, 2023, 107964, ISSN 1047-8477,

Hosseini M, Palmer A, Manka W, Grady PGS, Patchigolla V, Bi J, O'Neill RJ, Chi Z, Aguiar D. Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures. Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i242-i251. doi: 10.1093/bioinformatics/btad220. PMID: 37387144; PMCID: PMC10311326.

Kyle KE*, Puckett SP*, Caraballo-Rodríguez AM, Rivera-Chávez J, Samples RM, Earp CE, Rajad HA, Pearce CJ, Ernst M, van der Hooft JJJ, Adams ME, Oberlies NH, Dorrestein PC, Klassen JL#, and Balunas MJ#. 2023. Trachymyrmex septentrionalis ants promote fungus garden hygiene using Trichoderma-derived metabolite cues PNAS 120(25):e2219373120

Hanlon S. L., and R. S. Hawley, 2023 B chromosomes reveal a female meiotic drive suppression system in Drosophila melanogaster. Curr Biol.

Alexandrescu, A.T., Dregni, A.J. & Teschke, C.M. NMR detection and conformational dependence of two, three, and four-bond isotope shifts due to deuteration of backbone amides. J Biomol NMR (2023).

Herder EA, Skeen HR, Lutz HL, Hird SM. Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds. Microbiol Spectr. 2023 Apr 11:e0374922. doi: 10.1128/spectrum.03749-22. Epub ahead of print. PMID: 37039681.

Santiago-Martínez MG, Ferry JG. Methods for Culturing Anaerobic Microorganisms. Methods Mol Biol. 2023;2648:231-238. doi: 10.1007/978-1-0716-3080-8_14. PMID: 37039994.

King VL and Campellone KG.  2023.  F-actin-rich territories coordinate apoptosome assembly and caspase activation during DNA damage-induced intrinsic apoptosis.  Mol Biol Cell.  34(5):ar41.  doi: 10.1091/mbc.E22-04-0119. Cover

Escalona M, VanCampen J, Maurer NW, Haukness M, Okhovat M, Harris RS, Watwood A, Hartley GA, O'Neill RJ, Medvedev P, Makova KD, Vollmers C, Carbone L, Green RE. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered. 2023 Mar 16;114(1):35-43. doi: 10.1093/jhered/esac043. PMID: 36146896; PMCID: PMC10019027.

Sladewski TE, Campbell PC, Billington N, D'Ordine A, Cole JL, de Graffenried CL. Cytokinesis in Trypanosoma brucei relies on an orphan kinesin that dynamically crosslinks microtubules. Curr Biol. 2023 Mar 13;33(5):899-911.e5. doi: 10.1016/j.cub.2023.01.035. Epub 2023 Feb 13. PMID: 36787745; PMCID: PMC10023446.

King VL, Campellone KG. F-actin-rich territories coordinate apoptosome assembly and caspase activation during DNA damage-induced intrinsic apoptosis. Mol Biol Cell. 2023 Mar 15:mbcE22040119. doi: 10.1091/mbc.E22-04-0119. Epub ahead of print. PMID: 36920061.

Markert J, Luger K, Lee H, Hu H, Taylor NMI, Fernandez-Martinez J, Rout M, Alder N. Depicting protein structures as schematics. Trends Biochem Sci. 2023 Apr;48(4):307-310. doi: 10.1016/j.tibs.2023.01.006. PMID: 36931235.

Truchon, A. N., Dalsing, B. L., Khokhani, D., MacIntyre, A., McDonald, B. R., Ailloud, F., Klassen, J., Gonzalez-Orta, E. T., Currie, C., Prior, P., Power, T. M., Allen, C. 2023. Plant pathogenic Ralstonia phylotypes evolved divergent respiratory strategies and behaviors to thrive in xylem. mBio 14:e03188-22

Kenneth G. Campellone, Nadine M. Lebek, Virginia L. King, Branching out in different directions: Emerging cellular functions for the Arp2/3 complex and WASP-family actin nucleation factors, European Journal of Cell Biology, Volume 102, Issue 2, 2023, 151301, ISSN 0171-9335,

Podgorski JM, Freeman K, Gosselin S, Huet A, Conway JF, Bird M, Grecco J, Patel S, Jacobs-Sera D, Hatfull G, Gogarten JP, Ravantti J, White SJ. A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability. Structure. 2023 Mar 2;31(3):282-294.e5. doi: 10.1016/j.str.2022.12.012. Epub 2023 Jan 16. PMID: 36649709.

Christopher J. Hawxhurst, Jamie L. Micciulla, Charles M. Bridges, Mikhael Shor, Daniel J. Gage, Leslie M. Shor and Irina S. Druzhinina. Soil Protists Can Actively Redistribute Beneficial Bacteria along Medicago truncatula Roots. Environmental Microbiology. 6 March 2023. doi:

Gosselin SP, Arsenault DR, Jennings CA, Gogarten JP. The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination. Genes (Basel). 2023 Jan 21;14(2):288. doi: 10.3390/genes14020288. PMID: 36833214; PMCID: PMC9957025.

Griffith, M.B.Pearce, C.S. & Heaslip, A.T. (2022Dense granule biogenesis, secretion, and function in Toxoplasma gondiiJournal of Eukaryotic Microbiology69, e12904. Available from:

Sladewski TE, Campbell PC, Billington N, D'Ordine A, Cole JL, de Graffenried CL. Cytokinesis in Trypanosoma brucei relies on an orphan kinesin that dynamically crosslinks microtubules. Curr Biol. 2023 Feb 10:S0960-9822(23)00069-6. doi: 10.1016/j.cub.2023.01.035. Epub ahead of print. PMID: 36787745.

Grond K, Louyakis AS, Hird SM. Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover. mSystems. 2023 Feb 14:e0112822. doi: 10.1128/msystems.01128-22. Epub ahead of print. PMID: 36786579.

Genomic instability caused by Arp2/3 complex inactivation results in micronucleus biogenesis and cellular senescence. Haarer EL, Theodore CJ, Guo S, Frier RB, and Campellone KG. PLoS Genetics 2023. 19(1):e1010045. doi: 10.1371/journal.pgen.1010045.

McAnulty SJ, Kerwin AH, Koch E, Nuttall B, Suria AM, Collins AJ, Schleicher TR, Rader BA, Nyholm SV. "Failure To Launch": Development of a Reproductive Organ Linked to Symbiotic Bacteria. mBio. 2023 Jan 19:e0213122. doi: 10.1128/mbio.02131-22. Epub ahead of print. PMID: 36656023.

Bleiler M, Cyr A, Wright DL, Giardina C. Incorporation of 53BP1 into phase-separated bodies in cancer cells during aberrant mitosis. J Cell Sci. 2023 Jan 1;136(1):jcs260027. doi: 10.1242/jcs.260027. Epub 2023 Jan 6. PMID: 36606487.

Gil JC, Hird SM. Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes. Microbiol Spectr. 2022 Dec 21;10(6):e0238422. doi: 10.1128/spectrum.02384-22. Epub 2022 Nov 1. PMID: 36318011; PMCID: PMC9769641.

Hanlon, S.L., Larracuente, A.M. When it comes to genetics, cheaters do prosper. Chromosome Res 30, 137–139 (2022). Part of the Special Issue on "Non-Mendelian Inheritance and Meiotic Drive" co-edited by S.L. Hanlon and A.M. Larracuente.

Casale A, Maldonado CA, Taropawala O, O'Sullivan B, Graf J. Draft Genome Sequence of Plesiomonas shigelloides MD22D9, Isolated from the Digestive Tract of Macrobdella decora. Microbiol Resour Announc. 2022 Dec 14:e0093922. doi: 10.1128/mra.00939-22. Epub ahead of print. PMID: 36515507.

Li F, Hou CD, Yang R, Whitehead R 3rd, Teschke CM, Cingolani G. High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine. Sci Adv. 2022 Dec 9;8(49):eadc9641. doi: 10.1126/sciadv.adc9641

Milligan-McClellan KC, Dundore-Arias JP, Klassen JL, Shade A, Kinkel LL, and Wolfe BE. Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science. 2022 mSystems

Green EA and Klassen JL. Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes. mSphere 7:00989-21

Zhao T, Alder N, N, Starkweather A, R, Chen M, -H, Matson A, P, Xu W, Balsbaugh J, L, Cong X: Associations of Mitochondrial Function, Stress, and Neurodevelopmental Outcomes in Early Life: A systematic review. Dev Neurosci 2022. doi: 10.1159/000526491

Fleck K, Raj R and Erceg J (2022), The 3D genome landscape: Diverse chromosomal interactions and their functional implications. Front. Cell Dev. Biol. 10:968145. doi: 10.3389/fcell.2022.968145

Wayne Mitchell, Jeffrey D Tamucci, Emery L Ng, Shaoyi Liu, Alexander V Birk, Hazel H Szeto, Eric R May, Andrei T Alexandrescu, Nathan N Alder (2022) Structure-activity relationships of mitochondria-targeted tetrapeptide pharmacological compounds eLife 11:e75531

Yamamoto, M., Stoessel, S. J., Yamamoto, S., and Goldhamer, D. J. (2022). Over-expression of wild-type ACVR1 in fibrodysplasia ossificans progressiva mice rescues perinatal lethality and inhibits heterotopic ossification. J. Bone Miner. Res.

Venkata S.P. Patchigolla, Barbara G. Mellone, Enrichment of Non-B-Form DNA at D. melanogaster Centromeres, Genome Biology and Evolution, Volume 14, Issue 5, May 2022, evac054,

Fremin BJ, Bhatt AS, Kyrpides NC, Global Phage Small Open Reading Frame (GP-SmORF) Consortium* (*JL Klassen is a member of the GP-SmORF Consortium). 2022. Thousands of small, novel genes predicted in global phage genomes Cell Reports 39:110984

Yagi, M., Ji, F., Charlton J., Cristea S., Messemer, K., Horwitz, N., Di Stefano, B., Tsopoulidis N., Hoetker, M., Huebner, A., Almada A., Yamamoto, M., Patelunas A., Goldhamer, D. J., Wagers, A., Michor, F., Meissner, A., Sadreyev, R., and Hochedlinger, K. (2021). Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes & Development 35, 1-20.

Harris A. Lewin, Stephen Richards and The Earth Biogenome Project Working Group (alphabetical): Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklós Bálint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla‐Rubio, Shu‐Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Federigo, Paul Flicek, Guilio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer A.M. Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J.M. Jones, Elinor K. Karlsson, Paul Kersey, Jin‐Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K.N. Lawniczak, James Leebens‐Mack, Xueyan Li, Kerstin Lindblad‐Toh, Xin Liu, Jose Lopez, Tomas Marques‐Bonet, Sophie Mazard, Jonna A.K. Mazet, Camila J. Mazzoni, Gene Myers, Rachel J. O’Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S.M. Sabir, H. Bradley, Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano‐Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, and Guojie Zhang. The Earth BioGenome Project 2020: Starting the Clock. Proceedings of the National Academy of Sciences Jan 2022119 (4) e2115635118; DOI:10.1073/pnas.2115635118.COVER

Lees-Shepard, J. B*., Stoessel, S. J.*, Chandler, J., Bouchard, K., Bento, P., Apuzzo, L. N., Devarakonda, P. M., Hunter, J. W., Goldhamer, D. J. (2022). An anti-ACVR1 antibody exacerbates heterotopic ossification by fibro-adipogenic progenitors in fibrodysplasia ossificans progressiva mice. J. Clin. Invest. 132(12):e153795.  *co-first authors

Whitehead, R. D. III, Teschke, C.M.,Alexandrescu, A.T (2022) “Pulse-field gradient nuclear magnetic resonance of protein translational diffusion from native to non-native states”, Protein Sci, in press.

Michael E. Stephens, Jacquelynn Benjamino, Joerg Graf, Daniel J. Gage (2022). Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts. mSphere:

Abdellatif Gueddou, Indrani Sarker, Arnab Sen, Faten Ghodhbane-Gtari, David R. Benson, Jean Armengaud, Maher Gtari.  2022.  Effect of actinorhizal root exudates on the proteomes of Frankia soli NRRL B-16219, a strain colonizing the root tissues of its actinorhizal host via intercellular pathway. Research in Microbiology 173:103900

Sharawy, MPigni, NBMay, ERGascón, JAA favorable path to domain separation in the orange carotenoid proteinProtein Science20221– 14

Stephen J. Taerum, Jamie Micciulla, Gabrielle Corso, Blaire Steven, Daniel J. Gage and Lindsay R. Triplett (2021). 18S rRNA gene amplicon sequencing combined with culture-based surveys of maize rhizosphere protists reveal dominant, plant-enriched and culturable community members. Environmental Microbiology Reports. doi:10.1111/1758-2229.13038 

Erlandsen, H., Jecrois, A.M., Nichols, J.C., Cole, J.L. and Royer, W.E., Jr (2022), NADH/NAD+ binding and linked tetrameric assembly of the oncogenic transcription factors CtBP1 and CtBP2. FEBS Letters. Accepted Author Manuscript.

Lee IPA, Eldakar OT, Gogarten JP, Andam CP (2021): Bacterial cooperation through horizontal gene transfer.  Trends in Ecology & Evolution

Presley, SJ, J Graf, AF Hassan, AR Sjodin,  and MR Willig. 2021. Effects of host species identity and diet on biodiversity of oral and rectal microbiomes of Puerto Rican bats. Curr. Microbio. 78:3526-40.

Testerman, T., S. Reichley, S. King, J. Graf. 2021. Draft Genome of Aeromonas popoffii ID682, isolated from a natural water source in Idaho. Microbiology Resource Announcements 10 (29)

Allison H. KerwinSarah J. McAnulty, and Spencer V. Nyholm Development of the Accessory Nidamental Gland and Associated Bacterial Community in the Hawaiian Bobtail Squid, Euprymna scolopes. The Biological Bulletin Volume 240, Number 3, 2021,

Nyholm, S.V., McFall-Ngai, M.J. A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner. Nat Rev Microbiol 19, 666–679 (2021).

Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP (2021): An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets. Genome Biology and Evolution, 2021, evab187,

Gosselin S.   Fullmer MS,   Feng Y,   Gogarten JP (2021) Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support Systematic Biology, syab060, Currently being typeset but available as submitted version at

Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP (2021): The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biology and Evolution 13 (8)

Caraballo-Rodríguez AM, Pucket SP, Kyle KE, Petras D, da Silva RR, Nothias L-F, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC. 2021. Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden mSystems 6(4):e00601-21

Shamilov, R.; Robinson, V.L.; Aneskievich, B.J. Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder. Int. J. Mol. Sci. 2021, 22, 7912.

Harris A. Lewin, Stephen Richards and The Earth Biogenome Project Working Group (R. O’Neill, Member): 2021. The Earth BioGenome Project 2020: Starting the Clock. Cell Genomics in press

Joseph C. Iovine, Steven M. Claypool, Nathan N. Alder. (2021) Mitochondrial compartmentalization: emerging themes in structure and function, Trends in Biochemical Sciences, ISSN 0968-0004,

Peterson, S. C.**; K. B. Samuelson**, and S.L. Hanlon*. (2021) Multi-Scale Organization of the Drosophila melanogaster Genome. Special issue on "Chromosome-Centric View of the Genome Organization and Evolution" in Genes 12, no. 6: 817.
* corresponding author  ** equal contribution

EA McClure, EA, MC Nelson, A Lin, J Graf. Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech. Appl. Env. Microbiol. 87:e02082-20.

King VL, Leclair NK, Coulter AM, Campellone KG (2021) The actin nucleation factors JMY and WHAMM enable a rapid Arp2/3 complex-mediated intrinsic pathway of apoptosis. PLoS Genet 17(4): e1009512.

Stephen Hesler, Matthew Angeliadis, Bushra Husain, and James L. Cole. 2021. Contribution of dsRBD2 to PKR Activation. ACS Omega DOI: 10.1021/acsomega.1c00343

Asis K. Jana, Eric May. 2021. Atomistic dynamics of a viral infection process: Release of membrane lytic peptides from a non-enveloped virus. Science Advances. Vol. 7, no. 16, eabe1761 DOI: 10.1126/sciadv.abe1761

Goldman, A., Fournier, G., Gogarten, J. P., Petrov, A. S., Rothschild, L., Segrè, D., Smith, E., Williams, L. (2021). Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life. Bulletin of the AAS, 53(4).

Fournier, G., Gogarten, J. P., Goldman, A. D., Petrov, A. S., Rothschild, L., Segrè, D., Smith, E., Williams, L. (2021). Understanding the Early Major Transitions in Evolutionary History Part 2: Ancient Evolution of Biological Systems and the Biosphere. Bulletin of the AAS, 53(4).

Kaplan, A.R., Olson, R. & Alexandrescu, A.T (2021) “Protein yoga: conformational versatility of the hemolysin II C-terminal domain detailed by NMR structures for multiple states”, Protein Sci, in press.

Green EA, Smedley SR, and Klassen JL. 2021. North American fireflies host low bacterial diversity Microb Ecol

Graf, J., N. Ledala, M.J. Caimano, E. Jackson, D. Gratalo, D. Fasulo, M.D. Driscoll, S. Coleman, A. Matson. 2021. High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon. mBio 12:e03656-20.

Klub, L., Gosselin, S., Fullmer, M., Graf, J. Gogarten, J.P. and M. Bansal. 2021. Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes. Mol. Biol. Evol. in press.

Graf, J., M.C. Nelson, and S.M. Colston. 2020. Closed Genome Sequence of Aeromonas veronii Strain Hm21, an Isolate from the Medicinal Leech Hirudo verbana. Microbiology Resource Announcements 9 (42).

Makkay AM, Louyakis AS, Ram‐Mohan N, Gophna U, Gogarten JP, Papke T (2020) Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon. 
Sci Rep 10, 22297 (2020).

Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV (2020) Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum.
MicrobiologyOpen. 2020; 9:e1047.

Kravetz, A.M., T. Testerman, B. Galuppo, J. Graf, B. Pierpont, S. Siebel, R. Feinn, N. Santoro. 2020. Effect of Gut Microbiota and PNPLA3 rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth. J. Clin Endocrinol Metabol. 105:dgaa382

Talagrand-Reboul, E., SM Colston, J Graf, B Lamy, E Jumas-Bilak. 2020. Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas. Genome biology and evolution 12: 535-552.

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Jasmin Portelinha, Searle S. Duay, Seung I. Yu, Kara Heilemann, M. Daben J. Libardo, Samuel A. Juliano, Jonathan L. Klassen*, and Alfredo M. Angeles-Boza* Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities Chem. Rev. 2021

Sujit Basak, Nabanita Sakia, Laura Dougherty, Zhuojun Guo, Fang Wu, Frank Mindlin, Jeffrey W. Lary, James L. Cole, Feng Ding, Mark E. Bowen, Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer, Journal of Molecular Biology, Volume 433, Issue 5, 2021, 166793, ISSN 0022-2836,

Goldstein SL and Klassen JL. 2020. Pseudonocardia symbionts of fungus-growing ants and the evolution of defensive secondary metabolism Front. Microbiol. 11:621041

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Green EA and Klassen JL. 2020. Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748,isolated from a Dragonfly. Microbiology Resource Announcments 9(47):e00422-20

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen I-M, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe S, Visel A, IMG/M Data Consortium*, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EM (*JL Klassen is a member of the IGM/M Data Consortium). 2020. A Genomic Catalog of Earth’s Microbiomes Nature Biotechnology

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Michael R.Fulcher, Marian L.Bolton, Michael D.Millican, José PabloDundore-Arias, JoHandelsman, Jonathan L.Klassen, Kathryn C.Milligan-Myhre, Benjamin E.Wolfe, Linda L.Kinkel, Broadening Participation in Scientific Conferences during the Era of Social Distancing, Trends in Microbiology, September 2020,

Grubbs KJ, Surup F, Biedermann PHW, McDonald BR, Klassen JL, Carlson CM, Clardy J and Currie CR (2020) Cycloheximide-Producing Streptomyces Associated With Xyleborinus saxesenii and Xyleborus affinis Fungus-Farming Ambrosia Beetles. Front. Microbiol. 11:562140. doi: 10.3389/fmicb.2020.562140

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Nadine M. Lebek, Kenneth G. Campellone; Adding SNX to the mix: SNX9 drives filopodia biogenesis. J Cell Biol 6 April 2020; 219 (4): e202002086. doi:

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Trumbo, S., and Klassen, J. 2020. Editorial overview: Hidden players: microbes reshape the insect niche. Curr. Opin. Insect Sci. 39: vi-viii

Jason G. Pattis and Eric R. May, Markov State Model of Lassa Virus Nucleoprotein Reveals Large Structural Changes during the Trimer to Monomer Transition, Structure (2020),

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Jason Palladino, Ankita Chavan, Anthony Sposato, Timothy D. Mason, Barbara G. Mellone, Targeted De Novo Centromere Formation in Drosophila Reveals Plasticity and Maintenance Potential of CENP-A Chromatin, Developmental Cell, Volume 52, Issue 3, 10 February 2020, Pages 379-394.e7,

Kirsten Grond, Kayce C Bell, John R Demboski, Malia Santos, Jack M Sullivan, Sarah M Hird, No evidence for phylosymbiosis in western chipmunk species, FEMS Microbiology Ecology, Volume 96, Issue 1, February 2020, fiz182,

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Klassen, J.L. Ecology helps bound causal explanations in microbiology. Biol Philos (2020) 35: 3.

Jolanta Krucinska, Michael N. Lombardo, Heidi Erlandsen, Akram Hazeen, Searle S. Duay, Jason G. Pattis, Victoria L. Robinson, Eric R. May & Dennis L. Wright. Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate. Sci Rep 9, 17106 (2019) doi:10.1038/s41598-019-53301-3

Shivangi Nangia, Kevin J. Boyd, Eric R. May, Molecular dynamics study of membrane permeabilization by wild-type and mutant lytic peptides from the non-enveloped Flock House virus, Biochimica et Biophysica Acta (BBA) - Biomembranes, 2019,183102, ISSN 0005-2736, doi:10.1016/j.bbamem.2019.183102

Kerwin AH*, Gromek SM*, Suria AM, Samples RM, Deoss DJ, O’Donnell K, Frasca Jr. S, Sutton DA, Wiederhold NP, Balunas MJ#, Nyholm SV# (2019) Shielding the next generation: symbiotic bacteria from a reproductive organ protect bobtail squid eggs from fungal fouling. mBio 10(5). pii: e02376-19. doi: 10.1128/mBio.02376-19. (*contributed equally; #corresponding)

Joseph, G. A., Hung, M., Goel, A. J., Hong, M., Rieder, M-K., Beckmann, N. D., Serasinghe, M. N., Chipuk, J. E., Devarakonda, P. M., Goldhamer, D. J., Aldana-Hernandez, P., Curtis, J., Jacobs, R. L., Krauss, R. S. (2019). Late-onset megaconial myopathy in mice lacking group I Paks. Skeletal Muscle 9, 5.

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Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA (2019) Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. Elife Oct 1;8. pii: e47606. doi: 10.7554/eLife.47606

Lynch JB, Schwartzman JA, Bennett BD, McAnulty SJ, Knop M, Nyholm SV, Ruby EG (2019) Ambient pH alters the protein content of outer membrane vesicles, driving host development in a beneficial symbiosis. J. Bacteriol. 201 (20) pii:e00319-19. doi: 10.1128/JB.00319-19

Rader BA, McAnulty SJ, Nyholm SV (2019) Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna scolopes/Vibrio fischeri symbiosis. Microbiology Open Jun 13:e858. doi: 10.1002/mbo3.858

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Minkyung Bae, Yoojin Lee, Young-Ki Park, Dong-Guk Shin, Pujan Joshi, Seung-Hyun Hong, Nathan Alder, Sung I. Koo, Ji-Young Lee (2019) Astaxanthin attenuates the increase in mitochondrial respiration during the activation of hepatic stellate cells. The Journal of Nutritional Biochemistry 71 (2019) 82-89

JL Klassen, SR Lee, M Thomas-Poulsen, C Beemelmanns, KH Kim. (2019) Efomycins K and L from a Termite-associated Streptomyces sp. M56 and Their Putative Biosynthetic Origin. Frontiers in Microbiology 10:1739

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Fullmer MS, Ouellette M, Louyakis AS, Papke RT, Gogarten JP (2019) The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. Genes (Special Issue on Genetics of Halophilic Microorganisms) 10(3), 233

Brian Maniaci, Colin H. Lipper, Lalitha Deepthi Anipindi, Heidi Erlandsen, James L. Cole, Boguslaw Stec, Tom Huxford, and John J. Love (2019) Design of High-Affinity Metal-Controlled Protein Dimers. Biochemistry DOI: 10.1021/acs.biochem.9b00055

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Mahdi Belcaid, Giorgio Casaburi, Sarah J. McAnulty, Hannah Schmidbaur, Andrea M. Suria, Silvia Moriano-Gutierrez, M. Sabrina Pankey, Todd H. Oakley, Natacha Kremer, Eric J. Koch, Andrew J. Collins, Hoan Nguyen, Sai Lek, Irina Goncharenko-Foster, Patrick Minx, Erica Sodergren, George Weinstock, Daniel S. Rokhsar, Margaret McFall-Ngai, Oleg Simakov, Jamie S. Foster, and Spencer V. Nyholm. 2018. Symbiotic Organs Shaped by Distinct Modes of Genome Evolution in Cephalopods. PNAS

Sarah Goldstein, Lidia Bekah, Joerg Graf and Jonathan L. Klassen. 2018. Evaluation of Strategies for the Assembly of Diverse Bacterial Genomes Using MinION Long-Read Sequencing. BMC Genomics

Kevin J. Boyd and Eric R. May (2018). BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition. Journal of Chemical Theory and Computation. DOI: 10.1021/acs.jctc.8b00765.

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Lees-Shepard, J. B*., Yamamoto, M*., Biswas, A. A., Stoessel, S. J., Nicholas, S-A. E., Cogswell, C. A., Devarakonda, P. M., Schneider Jr., M. J., Cummins, S. M., Legendre, N. P., Yamamoto, S., Kaartinen, V., Hunter, J. W., and Goldhamer, D. J.  (2018). Activin-dependent signaling in fibro/adipogenic progenitors causes fibrodysplasia ossificans progressiva, Nature Communications, 9, 471. *co-first authors

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Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S (2018) Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire. ISME J. 2018 Jun 28. doi 10.1038/s41396-018-0166-1.

Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT (2018) Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing. Gene- Section: Microbial Genetics and Genomics, Genetic and Genomics Extremophiles 9(3), 129; doi: 10.3390/genes9030129.

Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U (2018) Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax. Gene- Section: Microbial Genetics and Genomics, Genetic and Genomics Extremophiles9 (3), 172;

Sarah Kopac, Hannah Beatty, Philip Gialopsos, Marcel Huntemann, Alicia Clum, Alexander Spunde, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Chris Daum, Vivian Ng, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Jonathan L. Klassen. 2018. High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. Microbiology Resource Announcements DOI: 10.1128/MRA.00871-18.

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Spychala, M.S., V.R. Venna, M. Jandzinski, S.J. Doran, D.J. Durgan, B.P. Ganesh, N.J. Ajami, N. Putluri, J. Graf, R.M. Bryan, L.D. McCullough. 2018. Age‐related changes in the gut microbiota influence systemic inflammation and stroke outcome. Ann. Neurol

Colston, S.M., A. Navarro, A.J. Martinez-Murcia, and J. Graf. 2018. Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474T, Isolated from a Cavern Brook in the Moravia Region of the Czech Republic. Genome announcements 6: e00227-18.

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O’Neill, M.J. and O’Neill, R.J. 2018. Sex chromosome repeats tip the balance towards speciation. Molecular Ecology Apr 6. doi: 10.1111/mec.14577.

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Kerwin AH, Nyholm SV (2018) Reproductive system symbiotic bacteria are conserved between two distinct populations of Euprymna scolopes from Oahu, HI. mSphere doi: 10.1128/mSphere.00531-17. eCollection 2018 Mar-Apr. PMID: 29600280 (cover image March/April 2018)

Kevin J. Boyd, Nathan N. Alder, Eric R. May. (2018)  Molecular Dynamics Analysis of Cardiolipin and Monolysocardiolipin on Bilayer Properties. Biophysical Journal,

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Rizzo, A.A., Suhanovsky, M.M., Baker, M.L., Fraser, L.C.R., Jones, L.M., Rempel, D.L., Gross, M.L., Chiu, W., Alexandrescu, A.T. & Teschke, C.M. (2014) “Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and cryoEM modeling”. Structure 22, 830-841.

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y (2014): AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees. PLos One 9(6):e98844. doi: 10.1371/journal.pone.0098844.

Cortines JR, Motwani T, Vyas AA, Teschke CMJ Virol. (2014) Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein. May;88(10):5287-97. doi: 10.1128/JVI.00036-14. Epub 2014 Mar 5.

Kaus, K., Lary, J.W., Cole, J.L. and Olson, R. (2014) Glycan specificity of the Vibrio vulnificus hemolysin lectin outlines evolutionary history of membrane targeting by a toxin family. J. Mol. Biol., in press, DOI:10.1016/j.jmb.2014.05.021

Devisscher L, H.P., Lynes M, Waeytens A, Cuvelier C, De Vos F, Vanhove C, De Vos M, Laukens D.(2014) Role of metallothioneins as danger signals in the pathogenesis of colitis. J. Pathol 233:89-100 DOI: 10.1002/path.4330

Lynes, M.A., Hidalgo, J., Manso, Y., Devisscher, L., Laukens, D., and Lawrence, D.A. (2014) Metallothionein and stress combine to affect multiple organ systems. Cell Stress and Chaperones. In press. PMID: 24584987

Wowor, A.J., Yan, Y., Auclair, S.M., Yu, D., Zhang, J., May, E.R., Gross, M.L., Kendall, D.A. and Cole, J.L. (2014) Analysis of SecA Dimerization in Solution. Biochemistry, in press, DOI:10.1021/bi500348p

E.R. May (2014) Recent developments in molecular simulation approaches to study spherical virus
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Chung KM, Kolling IV F, Gajdosik M, Burger S, Russell A, Nelson C (2014) Single Cell Analysis Reveals the Stochastic Phase of Reprogramming to Pluripotency Is an Ordered Probabilistic Process. POLS One DOI: 10.1371/journal.pone.0095304

Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, et al. (2014) DNA as a Phosphate Storage Polymer and the Alternative Advantages of Polyploidy for Growth or Survival. PLoS ONE 9(4): e94819. doi:10.1371/journal.pone.0094819 

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT:
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Nelson, M.C.,, H.G. Morrison, J. Benjamino, S.L. Grim, J. Graf. 2014. Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys. PLOS One 9(4): e94249. doi:10.1371/journal.pone.0094249.

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Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP and Papke RT (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front. Microbiol. 5:143. doi: 10.3389/fmicb.2014.00143

Amanda K. Dupuy, Marika S. David, Lu Li, Thomas N. Heider, Jason D. Peterson, Elizabeth A. Montano, Anna Dongari-Bagtzoglou, Patricia I. Diaz, Linda D. Strausbaugh (2014) Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal. PLoS ONE, DOI: 10.1371/journal.pone.0090899

Chimileski S, Dolas K, Naor A, Gophna U and Papke RT (2014) Extracellular DNA metabolism in Haloferax volcanii. Frontiers in Microbiology 5:57. doi:10.3389/fmicb.2014.00057

Veltman DM, Lemieux MG, Knecht DA, Insall RH (2014) PIP(3)-dependent macropinocytosis is incompatible with chemotaxis. J Cell Biol 204: 497-505.

E.R. May, K. Arora, C.L. Brooks, III (2014) pH Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway. J. Am. Chem. Soc.

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David R. Benson and Roger K. Kjelgren. 2014. Tacit diplomacy in the life sciences. A foundation for science diplomacy. Science and Diplomacy (AAAS). 3(1):Jan. 13

Chin-Chi Chen, Mekonnen Lemma Dechassa, Emily Bettini, Mary B. Ledoux, Christian Belisario, Patrick Heun, Karolin Luger, and Barbara G. Mellone. 2014. CAL1 is the Drosophila CENP-A assembly factor. J. Cell Biol. 10.1083/jcb.201305036, highlighted in JCB

Jha, S., Snell, J.M., Sheftic, S.R., Patil S.M., Daniels, S.B., Kolling, F.W., & Alexandrescu, A.T. (2014) “pH dependence of amylin fibrillization”. [Epub ahead of print ]

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Katherine Launer-Felty and James L. Cole (2014) Domain interactions in Adenovirus VAI RNA mediate high affinity PKR binding J. Mol. Biol., DOI: 10.1016/j.jmb.2013.12.019

Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM (2013). Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS One 8(12):e84300. doi: 10.1371/journal.pone.0084300.

Marcellino, N. and D. R. Benson. 2013. The good, the bad and the ugly: Tales of mold-ripened cheese. Microbiology Spectrum ASM 1:doi:10.1128/microbiolspec.CM-0005-2012.

Anne R. Kaplan, Mark W. Maciejewski, Rich Olson, Andrei T. Alexandrescu (2013). NMR assignments for the cis and trans forms of the hemolysin II C-terminal domain. Biomol NMR Assign [Epub ahead of print] . doi: 10.1007/s12104-013-9530-2

Marcellino, N. and D. R. Benson. 2013. The good, the bad and the ugly: Tales of mold-ripened cheese. Microbiology Spectrum ASM 1:doi:10.1128/microbiolspec.CM-0005-2012.

Matthew Ouellette, Andrea M. Makkay, and R. Thane Papke (2013) Dihydroxyacetone metabolism in Haloferax volcanii. Front. Microbiol. doi: 10.3389/fmicb.2013.00376

J. S. Yuk, E. F. Guignon, M. A. Lynes (2013) Sensitivity enhancement of a grating-based surface plasmon-coupled emission (SPCE) biosensor chip by optimizing gold thickness Chemical Physics Letters [Advance Access. Author’s preprint version]

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Wanczyk, H., Barker, T., Rood, D., Zapata, D.I., Howell, A.R., Richardson, S.K., J., Marusov, G.P., Lynes, M.A., Silbart, L.K. (2013) Cloning and Characterization of a Hybridoma Secreting a 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-Specific Monoclonal Antibody and Recombinant F(ab).Toxins 5(3):568-89. DOI:10.3390/toxins5030568.

Kristen S. Swithers, Shannon M. Soucy, Erica Lasek-Nesselquist, Pascal Lapierre and Johann Peter Gogarten (2013) Distribution and Evolution of the Mobile vma-1b Intein Molecular Biology and Evolution Advance Access doi: 10.1093/molbev/mst164

Lemieux MG, Janzen D, Hwang R, Roldan J, Jarchum I et al. (2013) Visualization of the actin cytoskeleton: Different F-actin-binding probes tell different stories. Cytoskeleton (Hoboken)

Joshi GN, Knecht DA (2013) Silica phagocytosis causes apoptosis and necrosis by different temporal and molecular pathways in alveolar macrophages. Apoptosis 18: 271-285.

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Butzin N, Secinaro M, Swithers KS, Gogarten JP, and Noll K (2013) Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12 Applied and Environmental Microbiology Published ahead of print 6 September 2013,  doi: 10.1128/AEM.01800-13

Lee, K.K., Fujimoto, K., Zhang, C., Schwall, C.T., Alder, N.N. , Pinkert, C.A., Krueger, W., Rasmussen, T., and Boelsterli, U.A. (2013). Isoniazid-induced cell death is precipitated by underlying mitochondrial complex I dysfunction in mouse hepatocytes. [Epub ahead of print]

Anna G. Green, Kristen S. Swithers, Jan F. Gogarten and J. Peter Gogarten (2013) Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum. Molecular Biology and Evolution Advance Access doi:10.1093/molbev/mst145, authors' pre-print version

de al Haba, R.R., Sánchez-Porro, C., León, M.J., Papke, R.T., . and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Pseudoalteromonas ruthenica strain CP76. Genome Announcements. 1:e00268-13

Papke, R.T., de al Haba, R.R., Infante, C., Perez, D., Sánchez-Porro, C., Lapierre, P, and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Marinobacter lipolyticus strain SM19. Genome Announcements 1:e00379-13.

Malhotra, K., Sathappa, M., Landin, J.S., Johnson, A.E. and Alder, N.N. (2013) Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force. Nat. Struct. Mol. Biol. Epub ahead of print

Malhotra, K., Sathappa, M., Landin, J.S., Johnson, A.E. and Alder, N.N. (2013) Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force. Nat. Struct. Mol. Biol. Epub

Long, A.R., OBrien, C.C., Malhotra, K., Schwall, C.T., Albert, A.D., Watts, A., and Alder, N.N. (2013) A detergent-free strategy for the reconstitution of active enzyme complexes from native biological membranes into nanoscale discs. BMC Biotechnol. May 11; 13:41.

Ross, B.D., Rosin, L., Thomae A.W., Hiatt, M.A., Vermaak, D., de la Cruz A.F., Imhof A., Mellone, B.G., Malik, H.S. Stepwise evolution of essential centromere function in a Drosophila neogene. Science, 2013 Vol. 340 no. 6137 pp. 1211-1214.

Lasek-Nesselquist E, Gogarten JP.:The effects of model choice and mitigating bias on the ribosomal tree of life. Mol Phylogenet Evol. 2013 May 22;. [Epub ahead of print]

Yu, D., Wowor, A.J., Cole, J.L. and Kendall, D.A. (2013). Defining the Escherichia coli SecA Dimer Interface Residues through in Vivo Site-specific Photo-crosslinking. J. Bacteriol., in press

Aaron Ehlinger, Soyeon Park, Amr Fahmy, Jeffrey W. Lary, James L. Cole, Daniel Finley, and Kylie J. Walters (2013) Conformational Dynamics of the Rpt6 ATPase in Proteasome Assembly and Rpn14 Binding Structure., in press

Brit Winnen, Eric Anderson, James L. Cole, Glenn F. King, and Susan L. Rowland (2013). Role of the PAS sensor domains in the Bacillus subtilis sporulation kinase KinA. J. Bacteriol., in press

Daniel F. Lyons, Jeffrey W. Lary, Bushra Husain, John J. Correia and James L. Cole (2013) Are fluorescence-detected sedimentation velocity data reliable? Analytical Biochemistry, in press

Carone, D.M. Ferreri, G.C., J.D. Brown, C. Obergfell, B.R. Carone, M.J. O’Neill, R.J. O’Neill. 2013. Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading. Chromosome Research DOI 10.1007/s10577-013-9337-0

McFall-Ngai M, MHadfield, T Bosch, H Carey, T Domazet-Loso, A Douglas, N Dubilier, G Eber, T Fukami, S Gilbert, U Hentschel, N King, S Kjelleberg, AH Knoll, N Kremer, S Mazmanian, J Metcalf, K Nealson, N Pierce, J Rawls, A Reid, E Ruby, M Rumpho, J Sanders, D Tautz and J Wernegreen (2013) Animals in a bacterial world: A new imperative for the life sciences. Proceedings of the National Academy of Sciences USA 110 (9): 3229-3236; doi:10.1073/pnas.1218525110

J Snijder, VS Reddy, ER May, WH Roos, GR Nemerow, GJL Wuite (2013) Integrin and Definsin Modulate the Mechanical Properties of Adenovirus. Journal of Virology 87 (5), 2756-2766 doi:10.1128/JVI.02516-12

Andrei T. Alexandrescu (2013) Amide proton protection in amylin fibrils probed by quenched hydrogen exchange NMR PLoS ONE, doi:10.1371/journal.pone.005646

Olga Zhaxybayeva, Ramunas Stepanauskas, Nikhil Ram Mohan, R. Thane Papke (2013) Cell Sorting Analysis of Geographically Separated Hypersaline Environments. Extremophiles, doi:10.1007/s00792-013-0514-z

Bansal MS, Banay, G, Harlow TJ, Gogarten JP, Shamir R
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Christopher Wostenberg, Jeffrey W. Lary, Debashish Sahu, Roderico Acevedo, Kaycee A. Quarles, James L. Cole, Scott A. Showalter (2012) The Role of Human Dicer-dsRBD in Processing Small Regulatory RNAs PLoS ONE, doi:10.1371/journal.pone.0051829

Williams, D., Gogarten, J.P., and Papke, R.T. (2012) Quantifying homologous replacement of loci between haloarchaeal species. Genome Biology and Evolution 4:1223-1244

Nyholm SV, Graf J. Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nat Rev Microbiol. 2012 Dec;10(12):815-27. doi: 10.1038/nrmicro2894. Epub 2012 Nov 13. PMID: 23147708; PMCID: PMC3870473. Nature Reviews Microbiology

Yang and Burkhard: Encapsulation of gold nanoparticles into self-assembling protein nanoparticles. Journal of Nanobiotechnology 2012 10:42.

Ngunjiri JM, Mohni KN, Sekellick MJ, Schultz-Cherry S, Webster RG, Marcus PI. (2012). Lethal H5N1 influenza viruses are not resistant to interferon action in human, simian, porcine, or chicken cells. Nature Medicine 18:1456­1457 (2012) DOI:10.1038/nm.2879

Ashley R. Long, Catherine C. O¹Brien, and Nathan N. Alder (2012). The Cell-Free Integration of a Polytopic Mitochondrial Membrane Protein into Liposomes Occurs Cotranslationally and in a Lipid-Dependent Manner. PLoS ONE 7(9): e46332. doi:10.1371/journal.pone.0046332

Shen QT, Hsiue PP, Sindelar CV, Welch MD, Campellone KG, and Wang HW (2012). Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling. J Cell Biol. 199:111-124. Cover, Preview, Pape

Bushra Husain, Ishita Mukerji and James L. Cole (2012) Analysis of high affinity binding of PKR to dsRNA Biochemistry, DOI:10.1021/bi301226h

Long AR, O'Brien CC, Alder NN (2012) The Cell-Free Integration of a Polytopic Mitochondrial Membrane Protein into Liposomes Occurs Cotranslationally and in a Lipid-Dependent Manner. PLoS ONE 7(9): e46332. doi:10.1371/journal.pone.0046332

Nelson, M.C. and J. Graf. 2012. Bacterial symbioses of the medicinal leech Hirudo verbena. Gut Microbes 4(3)

Bomar, L. and J. Graf. 2012. Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq. Biol. Bull. 223:155-66

Rizzo, A.A., Fraser, L.C.R., Sheftic, S.R., Suhanovsky, M.S., Teschke, C.M., Alexandrescu, A.A. (2012) NMR assignments for the telokin-like domain of P22 coat protein. Biomol. NMR Assign.

Chin-Chi Chen, Elizabeth Greene, Sarion R. Bowers, Barbara G. Mellone. A Role for the CAL1-Partner Modulo in Centromere Integrity and Accurate Chromosome doi:10.1371/journal.pone.0045094PLoS ONE 7(9): e45094. Segregation in Drosophila. (2012).

Sheftic, S.R., Garcia, P.P., White, E., Robinson, V.L., Gage, D. & Alexandrescu, A.T. (2012) “NMR Structure and Dynamics of the Response Regulator Sma0114 from Sinorhizobium meliloti”. Biochemistry 51, 6932-6941.DOI: 10.1021/bi300922z

Sheftic, S.R., Snell, J. M., Jha, S. & Alexandrescu, A.T. (2012) “Inhibition of Semen-derived Enhancer of Virus Infection (SEVI) fibrillogenesis by physiological zinc and copper concentrations”, European Biophysics Journal, in press. DOI: 10.1007/s00249-012-0846-0

Lapierre P, Lasek-Nesselquist E, and Gogarten JP (2012) The impact of HGT on phylogenomic reconstruction methods Brief Bioinform [first published online August 20, 2012] doi:10.1093/bib/bbs050 [Fulltext]

Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM: Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 33(22):5628-37, 2012; doi:j.biomaterials.2012.04.026

Padilla-Meier GP, Gilcrease EB, Weigele PR, Cortines JR, Siegel M, Leavitt JC, Teschke CM, Casjens SR. (2012) Unraveling the Role of the C-terminal Helix-Turn-Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein. J Biol Chem. 2012 Aug 9. [Epub ahead of print] doi:10.1074/jbc.M112.393132

Campellone KG, Siripala AD, Leong JM, and Welch MD (2012). Membrane-deforming proteins play distinct roles in actin pedestal biogenesis by enterohemorrhagic Escherichia coli. J Biol Chem 287: 20613-20624

Bateman,JR, Larschan, E., D’Souza, R., Marshall,L.S, Dempsey, K.E., Johnson, J.E., Mellone, B.G. and Kuroda, M.I. Genome-Wide Screen Identifies Genes That Affect Somatic Homolog Pairing in Drosophila. G3: Genes, Genomes, Genetics. doi: 10.1534/g3.112.002840 G3 July 1, 2012 vol. 2 no. 7 731-740

Ragini Phansalkar, Pascal Lapierre and Barbara G. Mellone. Evolutionary insights into the role of the essential centromere protein CAL1 in Drosophila. Chromosome Research 2012, DOI: 10.1007/s10577-012-9299-

Swithers KS, Petrus AK, Secinaro MA, Nesbo; CL, Gogarten JP, Noll KM and Butzin NC (2012). Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales. Genome Biology and Evolution [Epub before print] doi:10.1093/gbe/evs057

Andam CP, Harlow TJ, Papke RT, Gogarten JP (2012) Ancient origin of the divergent forms of leucyl-tRNA synthetases in the halobacteriales Journal: BMC Evolutionary Biology 12:85 doi:10.1186/1471-2148-12-85

Swithers KS, Soucy SM, Gogarten JP (2012) The Role of Reticulate Evolution in Creating Innovation and Complexity. International Journal of Evolutionary Biology 2012, ID 418964, 10 pages, doi:10.1155/2012/418964

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y (2012) Quartet decomposition server: a platform for analyzing phylogenetic trees BMC Bioinformatics 13:123 doi:10.1186/1471-2105-13-123

Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM (2012) Genes for the Major Structural Components of Thermotogales Species' Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs. PLoS One 7(6):e40236 doi:10.1371/journal.pone.0040236

Pietrosimone, K. M., Yin, X., Knecht, D. A., Lynes, M. A. Measurement of Cellular Chemotaxis with ECIS/Taxis. J. Vis. Exp. (62), e3840; DOI: 10.3791/3840

Yuk*, J., Gibson*, G., Rice, J., Guignon, E., and Lynes, M.A. (* co-first authors) (2012) Analysis of immunoarrays using a gold grating-based dual mode surface plasmon-coupled emission (SPCE) sensor chip, Analyst, 2012,137, 2574-2581; DOI: 10.1039/C2AN35143A.

Collins AJ*, Schleicher TR*, Rader BA, Nyholm SV. (2012) Understanding the role of host hemocytes in a squid/Vibrio symbiosis using transcriptomics and proteomics. Frontiers Immunol. 3: 91. *co-primary authors

Collins AJ, LaBarre BA, Wong Won BS, Shah MV, Heng S, Choudhury MH, Haydar SA, Santiago J, Nyholm SV (2012) Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes. Appl. Environ. Microbiol. 78: 4200-4208

Fidopiastis P, Rader BA, Gerling D, Gutierrez N, Watkins K, Frey M, Nyholm SV, Whistler CA. (2012) Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early state of squid colonization. J. Bacteriol. (Epub ahead of print)

Ngunjiri, J. M., C-W Lee, A. Ali, and P.I. Marcus (2012). "Influenza virus interferon-inducing particle efficiency is reversed in avian and mammalian cells, and enhanced in cells co-infected with defective-interfering particles." J. Interferon & Cytokine Res. 32(6):In press. (doi:10.1089/jir.2011.0102)

Malinoski, C.P., and P.I. Marcus (2012). "Influenza virus: A single noninfectious interferon-suppressing particle blocks expression of interferon-inducing particles." J. Interferon & Cytokine Res. 32(3):121-126. (doi:10.1089/jir.2011.0078)

Schwall, C.T., Greenwood, V.L., and Alder, N.N. (2012) The stability and activity of respiratory Complex II is cardiolipin-dependent. Biochimica et Biophysica Acta – Bioenergetics. doi:10.1016/j.bbabio.2012.04.015

Wosczyna, M. N., Biswas, A., Cogswell, C., and Goldhamer, D. J. (2012). Multipotent progenitors resident in the skeletal muscle interstitium exhibit robust BMP-dependent osteogenic activity and mediate heterotopic ossification. J. Bone Miner. Res. 27, 1004-1017

Nelson, M. and J. Graf. 2012. Bacterial Symbioses of Hirudo verbana. Gut Microbes 3:1-10

B. R. Menzies, M. B. Renfree, T. Heider, F. Mayer, T. B. Hildebrandt and A. J. Pask. 2012. Limited genetic diversity preceded extinction of the Tasmanian Tiger. PlosOne 7(4): e35433. doi:10.1371/journal.pone.0035433

Laufer H, Baclaski B, Koehn U (2012) Alkylphenols affect lobster (Homarus americanus) larval survival, molting and metamorphosis. Invertebrate Reproduction & Development, March 2012

Papke RT, Gogarten JP (2012) How Bacterial Lineages Emerge. Science 336: 45-46 10.1126/science.1219241

Fournier GP, Andam CP, Alm EJ, Gogarten JP Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life. Origins of Life and Evolution of Biospheres [Epub ahead of print]

Rice, J.M., Stern, L.J., Guignon, E.F., Lawrence, D.A., and Lynes, M.A. (2012) T cell phenotyping microarrays using Grating Coupled Surface Plasmon Resonance Imaging and Surface Plasmon Coupled Emission. Biosensors and Bioelectronics, 31(1) 264-269

Kuratnik A, Senapati VE, Verma R, Mellone BG, Vella AT, Giardina C. 2012. Acute sensitization of colon cancer cells to inflammatory cytokines by prophase arrest. Biochem Pharmacol. 2012 Jan 25. [Epub ahead of print]

Rohit Ghai, Lejla Pašić, Ana Beatriz Fernández, Ana-Belen Martin-Cuadrado, Carolina Megumi Mizuno , Katherine D. McMahon, R. Thane Papke, Ramunas Stepanauskas, Beltran Rodriguez-Brito, Forest Rohwer, Cristina Sánchez-Porro, Antonio Ventosa, & Francisco Rodríguez-Valera (2011) New Abundant Microbial Groups in Aquatic Hypersaline Environments. Scientific Reports. 1:135

Marusov, G. P., A J Sweatt, K Pietrosimone, D R Benson, S J Geary, L K Silbart, S Challa, J Lagoy, D A Lawrence, and M Lynes. 2011. A Microarray Biosensor for Multiplexed Detection of Microbes Using Grating-Coupled Surface Plasmon Resonance Imaging. Environmental Science and Technology DOI: 10.1021/es201239

Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP and Gogarten JP (2011) A Rooted Net of Life Biology Direct 6:45 doi:10.1186/1745-6150-6-45

Schleicher TS, Nyholm SV (2011) Characterizing the host and symbiont proteomes in the association between the bobtail squid Euprymna scolopes and the bacterium Vibrio fischeri. PLoS ONE 6(10) e25649

Andam CP, Gogarten JP (2011) Biased gene transfer and its implications for the concept of lineage. (Research) Biology Direct 6:47 doi:10.1186/1745-6150-6-47

Eric Anderson, Willythssa S. Pierre-Louis, C. Jason Wong, Jeffrey W. Lary and James L. Cole (2011) Heparin Activates PKR by Inducing Dimerization J. Mol. Biol., doi:0.1016/j.jmb.2011.09.025

Deshmukh L, Meller N, Alder NN, Byzova T, and Vinogradova O (2011) Tyrosine Phosphorylation as a Conformational Switch: A Case Study of Integrin Beta3 Cytoplasmic Tail. J. Biol. Chem. doi:10.1074/jbc.M111.231951

Ranaghan MJ, Schwall CT, Alder NN and Birge RR (2011) Green Proteorhodopsin Reconstituted into Nanoscale Phospholipid Bilayers (Nanodiscs) as Photoactive Monomers. J. Am. Chem. Soc. DOI: 10.1021/ja2070957

Swithers KS, Dipippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbø CL, Gogarten JP, Noll KM (2011) Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea. J Bacteriol 193(19):5566-7 pubmed

Bansal MS, Banay G, Gogarten JP, Shamir R (2011) Detecting highways of horizontal gene transfer. J Comput Biol 18(9): 1087-1114. pubmed

Sarion R Bowers and Barbara G Mellone: Starting from scratch: de novo kinetochore assembly in vertebrates. The EMBO Journal 6 September 2011; doi:10.1038/emboj.2011.329

Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P: Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria. PLoS One. 2011;6(8):e23774. doi:10.1371/journal.pone.0023774

Derek M. Bickhart and David R. Benson. 2011. Transcriptomes of Frankia sp. strain CcI3 in growth transitions. BMC Microbiology 11:192 [doi:10.1186/1471-2180-11-192]

Papke, R.T. and Chimileski, S. (2011) Gene Transfer Mechanisms, Population Genetics/Genomics and the Evolution of Haloarchaea, in Advances in Understanding the Biology of Halophilc Bacteria and Archaea (Vreeland, R., ed). Springer (in press)

Ying Huang and D. R. Benson. 2011. Growth and development of Frankia sp. strain CcI3 at the single-hypha level in liquid culture. Archives of Microbiology DOI: 10.1007/s00203-011-0734-5

Rafael Ruiz de la Haba, M. del Carmen Marquez, R. Thane Papke and Antonio Ventosa (2011) Multilocus sequence analysis (MLSA) of the family Halomonadaceae. Structure. 2010 Mar 10;18(3):390-401

Cheryl P. Andam, David Williams, and J. Peter Gogarten (2010) Biased gene transfer mimics patterns created through shared ancestry. PNAS published ahead of print May 21, doi:10.1073/pnas.1001418107

Cole, James L. (2010) Analysis of PKR activation using analytical ultracentrifugation. Macromol. Biosci. DOI: 10.1002/mabi.20100006

Fournier GP, Gogarten JP (2010) Rooting the Ribosomal Tree of Life. Molecular Biology and Evolution [Epub ahead of print]

Poptsova MS, Gogarten JP. Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology. 2010 Apr 29;. [Epub ahead of print]

Teschke CM, Parent KN.'Let the phage do the work': Using the phage P22 coat protein structures as a framework to understand its folding and assembly mutants. Virology. 2010 Mar 15. [Epub ahead of print]

Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker TS. P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Structure. 2010 Mar 10;18(3):390-401. On the Cover.

Fournier GP, Neumann JE, Gogarten JP (2010) Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders. PLoS ONE 5(3): e9437. doi:10.1371/journal.pone.0009437

Messina G, Biressi S, Monteverde S, Magli A, Pistocchi A, Gargioli C, Campbell CE, Tagliafico E, Grossi M, Cotelli F, Goldhamer DJ, Gronostajski RM, Cossu G (2010). NFIX regulates fetal specific transcription in developing skeletal muscle. Cell 140, 554-566.

Williams D, Gogarten JP, Lapierre P (2010) Filling the gaps in the genomic landscape. Genome Biology 11:103

McFall-Ngai, MJ, Nyholm SV, Castillo MG (2009) The role of the immune system in the initiation and persistence of the Euprymna scolopes-Vibrio fischeri symbiosis. Semin. Immunol. (in press) published online Dec. 2009

Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ. (2010) Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc. Nat. Acad. Sci., USA, 107, 2259-64

Collins AJ, Nyholm SV (2010). Obtaining Hemocytes from the Hawaiian Bobtail Squid Euprymna scolopes and Observing their Adherence to Symbiotic and Non-Symbiotic Bacteria. JoVE. 36.

Sheftic, S.R., Croke, R.L., LaRochelle, J.R., & Alexandrescu, A.T. (2009) “Electrostatic contributions to the stabilities of native proteins and amyloid complexes.” Methods in Enzymology 466, 233-258.

Anderson, E., Quartararo, C., Brown, R.S., Shi, Y., Yao, X. and Cole, J.L (2010) Analysis of monomeric and dimeric phosphorylated forms of protein kinase R. Biochemistry 10.1021/bi901873p

P. M. Herron, D. J. Gage, and Z. G. Cardon (2010) Microscale water potential gradients visualized in soil around plant root tips using microbiosensors. Plant, Cell and Environment 33:199-210

Auclair SM, Moses JP, Musial-Siwek M, Kendall DA, Oliver DB, Mukerji I. Mapping of the Signal Peptide-Binding Domain of Escherichia coli SecA Using Forster Resonance Energy Transfer. Biochemistry. 2010 Jan 8. [Epub ahead of print] PubMed PMID: 20025247

Gage, D. J. (2009) Architecture of infection thread networks in nitrogen-fixing root nodules. In Plant Cell Monographs Volume 12, Root Hairs, A. M. C. Emons and T. Ketelaar (ed.), Springer, Heidelberg, German

Gage, D. J. (2009) Legume Nodule Formation. In D. W. Emerich and H. B. Krishnan (ed.), Nitrogen Fixation in Crop Production. American Society of Agronomy, Madison, WI, US

Arango-Pinedo and D. J. Gage. (2009) Plasmids that insert into the rhamnose utilization locus, rha: a versatile tool for genetic studies in Sinorhizobium meliloti. Journal of Molecular Biology and Biotechnology 17:201-21

Alekseev, A. E, Reyes, S., Yamada. S., Hodgson-Zingman, D. M., Sattiraju, S., Zhu, Z., Sierra, A., Gerbin, M., Coetzee, W. A., Goldhamer, D. J., Terzic, A., and Zingman, L. V. (2010). Sarcolemmal ATP-sensitive K+ channels control energy expenditure determining body weight. Cell Metabolism 11, 58-69

Kaba SA, Brando C, Guo Q, Mittelholzer C, Raman SK, Tropel D, Aebi U, Burkhard P, Lanar DE. (2009). A non-adjuvanted polypeptide nanoparticle vaccine confers long-lasting protection against rodent malaria. J Immunol. 183(11):7268-77

Rio, R.V.M., M. Maltz, B. McCormick, A. Reiss and J. Graf. 2009. Symbiont Succession during the Embryonic Development of the European Medicinal Leech, Hirudo verbana. Appl. Environ. Microbiol. 75:6890-6895

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009) Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution 2009: doi:10.1093/gbe/evp032

Swithers KS, Senejani AG, Fournier GP, Gogarten JP (2009) Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements. BMC Evolutionary Biology 2009, 9:303 doi:10.1186/1471-2148-9-303

Mastronunzio, J. E & D. R. Benson. 2010. Wild nodules can be broken: proteomics of Frankia in field-collected root nodules. Symbiosis 49:10.1007/s13199-009-0030-1.

J. E. Mastronunzio, Y. Huang, and D. R. Benson. 2009. Diminished Exoproteome of Frankia spp. in Culture and Symbiosis. Appl. Environ. Microbiol. 75: 6721-6728.

Williamson A*, Wickliffe KE*, Mellone BG, Song L, Karpen GH, Rape M. Identification of a physiological E2 module for the human anaphase-promoting complex. PNAS epub ahead of print.

Kikuchi, Y. L. Bomar and J. Graf. (2009) Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana. Environ. Microbiol. 11:2758-2770. Cover article

Pores-Fernando AT, Zweifach A. Calcium influx and signaling in cytotoxic T-lymphocyte lytic granule exocytosis. Immunol Rev. 2009 Sep;231(1):160-73. PMID: 19592494

Pores-Fernando AT, Ranaghan MY, Zweifach A. No specific subcellular localization of protein kinase C is required for cytotoxic T cell granule exocytosis. J Biol Chem. 2009 Sep 11;284(37):25107-15. Epub 2009 Jul 10. PMID: 1975489

Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009) Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genomics. 2009 Oct 12;10(1):468

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct. 2009 Sep 29;4:34.

Olendzenski L, Gogarten JP (2009) Evolution of Genes and Organisms: The Tree/Web of Life in Light of Horizontal Gene Transfer. Annals of the New York Academy of Sciences 1178: 137-145 doi: 10.1111/j.1749-6632.2009.04998.x

Pores-Fernando, A. T., S. Gaur, M. J. Grybko, and A Zweifach. 2008. ERK activation is only one role of PKC in TCR-independent cytotoxic T cell granule exocytosis. Biochem Biophys Res Commun. 371: 630–634.

Tang, L., J. Franca-Koh, Y. Xiong, M. Y. Chen, Y. Long, R. M. Bickford, D. A. Knecht, P. A. Iglesias and P. N. Devreotes. 2008. tsunami, the Dictyostelium homolog of the Fused kinase, is required for polarization and chemotaxis. Genes Dev. 22:2278-2290.

Musial-Siwek, M., P. Y. Yeagle and D. A. Kendall. 2008. A small set of signal peptidase residues are perturbe by signal peptide binding. Chem. Biol. Drug Des. 72:140-146

Sallum, U. W., W. Ulysses and T. Chen. 2008. Inducible resistance of fish bacterial pathogens to the antimicrobial peptide cecropin B. Antimicrobial Agents Chemotherapy 53:3006-3012

Pimentel, T.A., Z. Yan, S. A. Jeffers, K. V. Holmes, R. S. Hodges, P. Burkhard. 2009. Peptide nanoparticles as novel immunogens: design and analysis of a prototypic severe acute respiratory syndrome vaccine. Chem. Biol. Drug Des. 73:53-61.

Longo, M.S., Carone, D.M., Marzelli, M., M.J. O’Neill, E. Green, NISC Sequencing Consortium, R.J. O’Neill. 2009. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10:334.

Brown J.D. and R.J. O’Neill. 2009. The Mysteries of Chromosome Evolution in Gibbons: Methylation Is a Prime Suspect. PLoS Genet 5(6): e1000501. doi:10.1371/journal.pgen.1000501.

O’Neill, R.J. and D.M. Carone. 2009. Chapter 4: The role of ncRNA in centromeres: lessons from marsupials. in: Centromere: structure and evolution ed: D. Ugarkovic, Springer Press. Pp77-101.

Gage, D. J., Herron, P. M., Arango-Pinedo, C., and Z. G. Cardon (2008). Live reports from the soil grain--the promise and challenge of microbiosensors. Functional Ecology 22:983.

C. Arango-Pinedo and D. J. Gage (2009) HPrK regulates succinate- mediated catabolite repression in the Gram negative symbiont Sinorhizobium meliloti. J. Bacteriol. 191:298-309

Zhang, N., Wang, Q. Ehlinger, A., Randles, L., Lary, J. W., Kang, Y., Haririnia, A., Storaska, A. J., Cole, J. L., Fushman, D., Walters, K. J. (2009) Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13. Mol. Cell 35, 280-290.

Silver, A.C. and J. Graf. 2009. Prevalence of genes encoding type three secretion system and the effectors AexT and AexU in the Aeromonas veronii group. DNA Cell Biol. 28:383-388

Swithers KS, Gogarten JP, Fournier GP (2009) Trees in the Web of Life, Journal of Biology 2009, 8:54 doi:10.1186/jbiol160

Fournier GP, Huang JL, Gogarten JP (2009) Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci. 364 (1527):2229-39.

Kanisicak, O., Mendez, J. J., Yamamoto, S., Yamamoto, M., and Goldhamer, D. J. (2009). Progenitors of skeletal muscle satellite cells express the muscle determination gene, MyoD. Dev. Biol. 332, 131 141.

R.T. Emeny, G. Marusov, D.A. Lawrence, J. Pederson-Lane, X. Yin, M.A. Lynes, Manipulations of metallothionein gene dose accelerate the response to Listeria monocytogenes, Chemico-Biological Interactions (2009), doi:10.1016/j.cbi.2009.06.01

Marcus P.I., Ngunjiri J.M. and M.J. Sekellick. 2009. Dynamics of Biologically Active Subpopulations of Influenza Virus: Plaque-Forming, Noninfectious Cell-Killing, and Defective-Interfering Particles. J. Virol. doi:10.1128/JVI.02680-08

Guardino, K.M., Sheftic, S.R., Slattery, R.E., & Alexandrescu, A.T. (2009) “Hallmarks of conserved and non-conserved structures in the OB-fold superfamily”. Int. J. Mol. Sci. 10, 2412-2430

Patil, S.M., Xu, S., Sheftic, S.R., & Alexandrescu, A.T. (2009) “Dynamic alpha-helix structure of micelle-bound human amylin”, J Biol Chem, 284, 11982-1199

Heinicke, L.A., Wong, C.J., Lary, J., Nallagatla, S.R., Deigelman-Parente, A., Zheng, X., Cole, J.L. and Bevilacqua, P.C. (2009) RNA Dimerization promotes PKR dimerization and activation. J. Mol. Biol. doi:10.1016/j.jmb.2009.05.005

Whitaker, I. S., C. Kamya, E. A. Azzopardi, J. Graf, M. Kon, W. C. Lineaweaver. 2009. Preventing infective complications following leech therapy: is practice keeping pace with current research? Microsurgery in press.

Papke RT (2009) A critique of prokaryotic species concepts. Methods Mol Biol 532:379-95.

Noll KM, Thirangoon K (2009) Interdomain transfers of sugar transporters overcome barriers to gene expression. Methods Mol Biol 532:309-22.

Huang J, Gogarten JP (2009) Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol. 2009; 532:127-39.

Olendzenski L, Gogarten JP (2009) Gene transfer: who benefits? Methods Mol Biol. 2009;532:3-9.

Poptsova M (Gogarten Lab)(2009) Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol. 2009;532:227-40.

Fournier G (Gogarten Lab) (2009) Horizontal gene transfer and the evolution of methanogenic pathways. Methods Mol Biol. 2009;532:163-79.

Gogarten, M.B., Gogarten, J.P., Olendzenski, L.C. (editors), (2009) Horizontal Gene Transfer: Genomes in Flux. Humana Press - Springer ISBN-13: 978-1603278522

Alexandrescu, A. T. & Croke, R.L. (2008) “NMR of Amyloidogenic proteins”, in Protein Misfolding ISBN 978-1-60456-881-3

Croke, R.L., Sallum, C.O., Watson, E., Watt, E.D. & Alexandrescu, A. T. (2008) “Hydrogen exchange of monomeric a-synuclein shows unfolded structure persists at physiological temperature and is independent of molecular crowding in Escherichia coli”. Protein Science 17, 1434-1445.

Lounev, V. Y., Ramachandran, R., Wosczyna, M. N., Yamamoto, M., Maidment, A. D. A., Shore, E. M., Glaser, D. L., Goldhamer, D. J., and Kaplan, F. S. (2009). Identification of progenitor cells that contribute to heterotopic skeletogenesis. J Bone Joint Surg 91:652-663.

Mellone, B.G. (2009). Structural and temporal regulation of centromeric chromatin. Biochem Cell Biol. 87(1):255-64.

Yamamoto, M., Shook, N. A., Kanisicak, O., Yamamoto, S., Wosczyna, M. N., Camp, J. R., and Goldhamer, D. J. (2009). A multifunctional reporter mouse line for Cre- and FLP-dependent lineage analysis. Genesis 47, 107-114

VanOudenhove, J., Anderson, E., Krueger, S. and Cole, J.L. (2009) Analysis of PKR structure by small angle scattering. J. Mol. Biol. doi:10.1016/j.jmb.2009.02.019

Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome Trends in Genetics, doi:10.1016/j.tig.2008.12.004

Carone DM, Longo MS, Ferreri GC, Hall L, Harris M, Shook N, Bulazel KV, Carone BR, Obergfell C, O'Neill MJ, O'Neill RJ. 2008. A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres. Chromosoma. 2008 Oct 7. [Epub ahead of print]

Erhardt, S., Mellone B. G., Betts, C. M. et al. 2008. Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation. The Journal of Cell Biology. Vol. 183 No. 5: 805-818

Nyholm, S. V. et al. 2008. Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ. Microbiol. 9:1462-2920.

Nukaga, M., C. R. Bethel, J. M. Thomson, A. M. Hujer, A. Distler, V. E. Anderson, J. R. Knox and R. A. Bonomo. 2008. Inhibition of class A ß-lactamases by carbapenems: Crystallographic observation of two conformations of meropenem in SHV-1. J. Am. Chem. Soc. 130: 12656–12662.

Laufer, A., M. Siddall and J. Graf. 2008. Characterization of the Digestive-Tract Microbiota of Hirudo orientalis, a European Medicinal Leech. Appl. Environ. Microbiol. 74:6151-6154

Edrington TC, Bennett MP, Albert AD. 2008. Calorimetric Studies of Bovine Rod Outer Segment Disk Membranes Support a Monomeric Unit for Both Rhodopsin and Opsin. Biophys J. Jun 27. Epub ahead of print.

deLivron, M.A. and Robinson, V.L. (2008) Salmonella enterica sv. Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes J. Bacteriol. E-Publ. ahead of print.

Jinling Huang and J. Peter Gogarten (2008) Concerted gene recruitment in early plant evolution Genome Biology 9(7): R10

Lemaire, P.A., Anderson, E., Lary, J. and Cole, J.L. (2008) Mechanism of PKR activation by dsRNA. J. Mol. Biol. 381, 351-360.

Hou JM, D'Lima NG, Rigel NW, Gibbons HS, McCann JR, Braunstein M, Teschke CM. (2008) ATPase activity of Mycobacterium tuberculosis SecA1 and SecA2 proteins and its importance for SecA2 function in macrophages. J Bacteriol. 190:4880-7.

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. 2008. Unsupervised Learning in Detection of Gene Transfer. Journal of Biomedicine and Biotechnology [Epub ahead of print] doi: 10.1155/2008/472719.

Santos CL, Vieira J, Tavares F, Benson DR, Tisa LS, Berry AM, Moradas-Ferreira P, Normand P. 2008. On the nature of fur evolution: a phylogenetic approach in Actinobacteria. BMC Evol Biol. 25:8:185. [Epub ahead of print];PMID: 18578876.

Sudi J, Zhang S, Intrieri G, Hao X, Zhang P. Coincidence of p-insertion sites and breakpoints of deletions induced by activating p elements in Drosophila. Genetics. 2008. 179:227-35.

Eric Anderson and James L. Cole 2008. Domain stabilities in PKR: evidence for weak interdomain interactions. Biochemistry 47: 4887-4897.

Arango-Pinedo, C., Bringhurst, R.M. and D. J. Gage (2008). Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production. J. Bacteriol. 190:2947

Noll KM, Lapierre P, Gogarten JP and Nanavati DM (2008) Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
BMC Evolutionary Biology 2008, 8:7

Metcalfe, C.J., K.V. Bulazel, G. C. Ferreri, W. Rens, E. Schroeder-Reiter, G. Wanner, M. D. B. Eldridge, and R. J. O'Neill. 2007. Genomic instability within centromeres of interspecific marsupial hybrids. Genetics 177: 2507-2517.

Brown, J.D., D. Golden, R.J.O’Neill. 2008. Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91: 267-273

Sen, A., S. Sur, A. K. Bothra, D. R. Benson, P. Normand and L. S. Tisa. 2008. The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie van Leeuwenhoek Published on-line, Feb.

Robertson, P.D., Warren, E.M., Zhang, H., Friedman, D.B., Lary, J.W., Cole, J.L., Tutter, A.V., Walter, J.C., Fanning, E., Eichman, B.F. (2008) Domain architecture and biochemical characterization of vertebrate MCM10. J. Biol. Chem. 83, 3338-3348.

Fournier, Gregory P., and Gogarten, J. Peter (2008) Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia J. Bacteriol. 190(3): 1124-7 

Sharma, AK, Zhaxybayeva, O., Papke, RT, Doolittle, WF. 2008. Actinorhodopsins: proteorhodopsin-like gene sequence found predominantly in non-marine environments. Environmental Microbiology (OnlineEarly Articles). doi:10.1111/j.1462-2920.2007.01525.

Juliana E Mastronunzio , L S Tisa , P. Normand and D R Benson. 2008. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbiont. BMC Genomics 2008, 9:47

Ngunjiri, J. M., M. J. Sekellick and P. I. Marcus. 2008. Clonogenic Assay of Type A Influenza Viruses Reveals Noninfectious Cell-Killing (Apoptosis-Inducing) Particles. J. Virol. 0: JVI.02221-07 [published online ahead of print]

Spurling CC, Godman CA, Noonan EJ, Rasmussen TP, Rosenberg DW, Giardina C. 2007. HDAC3 overexpression and colon cancer cell proliferation and differentiation. Mol Carcinogenesis [EPub ahead of print, September].

J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva (2007) Gene transfer and the reconstruction of life's early history from the molecular record. Space Science Reviews [Epub ahead of print] DOI: 10.1007 /s11214-007-9253-8

Hadjout, N., X. Yin, D. A. Knecht, and M. A. Lynes. 2007. Automated real-time measurements of leukocyte chemotaxis. J Immunol Methods. 2007 320:70-80

Sun, C., S. L. Rusch, J. Kim and D. A. Kendall. 2007. Chloroplast SecA and Escherichia coli SecA have distinct lipid and signal peptide preferences. J. Bacteriol. 189:1171-1175.

M. Willian, Dagan, T., Koonin, E. B., Dipippo, J. L., Gogarten, J. P. and Lake, J. A. 2007. The Evolution of Eukaryotes, Letter on "Genomics and the irreducible nature of eukaryotic cells" Science 316:542-543

Huang, Jinling and J. Peter Gogarten (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biology 8(6): R99

Laufer, H., Demir, N., Capulong, C, Pan, X., Biggers, W.J. 2006. Hormonal Responses to Lobsters of Long Island Sound. Long Island Sound Research Conference Proceedings. 7:41-43.

Zhaxybayeva O, Gogarten JP, Doolittle WF (2007) A hyperconserved protein in Prochlorococcus and marine Synechococcus. FEMS Microbiol Lett. 274 (1): 30-4.

Silver, A.C., N. M. Rabinowitz, S. Küffer and J. Graf. 2007. Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana. J Bacteriol. 189:6763-72.

Fournier, G. P. and J. P. Gogarten. 2007. Signature of a primitive genetic code in ancient protein lineages. J. Mol. Evol. 65:425-36.

R.T. Papke, O. Zhaxybayeva, E. Feil, K. Sommerfeld, D. Muise and W.F. Doolittle. 2007. Searching for species in haloarchaea. PNAS 104:14092-14097.

Q. Yan., V.N. Malashkevich, A. Fedorov, E. Fedorov, E. Cao, J.W. Lary, J.L. Cole, S.G. Nathenson and S.C. Almo. 2007. Structure of CD84 provides insight into SLAM family function. PNAS 104: 10583-10588

E. Watson, W.M. Matousek, E.L. Irimies, A.T. Alexandrescu 2007. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 46:9484-9494.

M. A. Lynes, J. Kang, S. L. Sensi, G. A. Perdrizet, and L. E. Hightower. 2007. Heavy metal ions in normal physiology, toxic stress and cytoprotection. Ann N Y Acad Sci. May 4 e-pu

A. C. Silver, Y. Kikuchi, A. A. Fadl, J. Sha, A. K. Chopra, and J. Graf. 2007. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations. PNAS 104:9481-9486.

Normand, P., P. Lapierre, L. S. Tisa, J. P. Gogarten, N. Alloisio, E.Bagnarol, C.A. Bassi, A.M. Berry, D. M. Bickhart, N. Choisne,, A. Couloux, B. Cournoyer, S. Cruveiller, V. Daubin, N. Demange, M. P. Francino, E. Goltsman, Y. Huang, O.R. Kopp, L. Labarre, A. Lapidus, C. Lavire, J. Marechal, M. Martinez, J. E. Mastronunzio, B. C. Mullin, J. Niemann, P. Pujic, T. Rawnsley, Z. Rouy, C. Schenowitz, A. Sellstedt, F. Tavares, J. P. Tomkins, D.Vallenet, C. Valverde, L.G. Wall, Y.Wang, C. Medigue, & D. R. Benson. 2007. Genome sizes of facultatively symbiotic Frankia sp. strains reflect host plant biogeography. Genome Res. 17:7-15