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, https://doi.org/10.1093/gbe/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  https://doi.org/10.1093/sysbio/syab060

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) https://doi.org/10.1093/gbe/evab166

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. https://doi.org/10.3390/ijms22157912

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,
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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. https://doi.org/10.3390/genes12060817
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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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8117757/

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. https://doi.org/10.1371/journal.pgen.1009512

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). https://doi.org/10.3847/25c2cfeb.cb78fd8a

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). https://doi.org/10.3847/25c2cfeb.2e749fbd

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. https://doi.org/10.1002/pro.4066

Green EA, Smedley SR, and Klassen JL. 2021. North American fireflies host low bacterial diversity Microb Ecol https://link.springer.com/article/10.1007%2Fs00248-021-01718-7.

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. https://doi.org/10.1128/mBio.03656-20

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. https://pubmed.ncbi.nlm.nih.gov/33593974/https://doi.org/10.1093/molbev/msab043

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). https://doi.org/10.1128/MRA.00922-20

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. 
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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.
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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 https://doi.org/10.1210/clinem/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. https://doi.org/10.1093/gbe/evaa055

Lee, Juneyoung, John d'Aigle, Louise Atadja, Victoria Quaicoe, Pedram Honarpisheh, Bhanu P Ganesh, Ahmad Hassan, Joerg Graf, Joseph F Petrosino, Nagireddy Putluri, Liang Zhu, David J Durgan, Robert M Bryan, Jr, Louise D McCullough, Venugopal Reddy Venna. 2020. Gut Microbiota-Derived Short-Chain Fatty Acids Promote Post-Stroke Recovery in Aged Mice. Circulation Research.127:453. https://doi.org/10.1161/CIRCRESAHA.119.316448

Pirhanov, A.; Bridges, CM; Goodwin, RA; Gao, Y; Furrer, J; Shor, LM; Gage, DJ and Cho, YK. (2021) Optogenetics in Sinorhizobium melilotienables spatial control of exopolysaccharide production and biofilm structure. ACS Synthetic Biology: https://pubs.acs.org/doi/pdf/10.1021/acssynbio.0c00498

Bridges, C.M., Nelson, M.C., Graf, J. and Daniel. J. Gage (2021). Draft Genome Sequences of Dysgonomonas sp. Strains BGC7and HGC4, Isolated from the Hindgut of a Lower Termite. Microbiol. Resour. Announc. 10:e01427-20. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7844080/

Bridges, C.M. and Daniel. J. Gage (2021). Development and application of aerobic, chemically defined media for Dysgonomonas. Anaerobe 67:102302. https://doi.org/10.1016/j.anaerobe.2020.102302

Stephen J. Taerum, Blaire Steven, Daniel J. Gage, and Lindsay R. Triplett (2020). Validation of a PNA clamping method for Reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies. https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-05-20-0040-TA

Stephens ME, Gage DJ (2020) Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host. PLOS ONE 15(5): e0233065. https://doi.org/10.1371/journal.pone.0233065

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 https://pubs.acs.org/doi/full/10.1021/acs.chemrev.0c00921

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, https://doi.org/10.1016/j.jmb.2020.166793.

Goldstein SL and Klassen JL. 2020. Pseudonocardia symbionts of fungus-growing ants and the evolution of defensive secondary metabolism Front. Microbiol. 11:621041 https://www.frontiersin.org/articles/10.3389/fmicb.2020.621041/full

Huiliang Zhang, Nathan N Alder, Wang Wang, Hazel Szeto, David J Marcinek, Peter S Rabinovitch, Reduction of elevated proton leak rejuvenates mitochondria in the aged cardiomyocyte.  eLife 2020;9:e60827 DOI: 10.7554/eLife.60827

Donal Sheets, Jamie Shaw, Michael Baldwin, David Daggett, Ibrahim Elali, Erin B. Curry, Ilya Sochnikov, Jason N. Hancock, An apparatus for rapid and nondestructive comparison of masks and respirators. Rev. Sci. Instrum. 91, 114101 (2020) https://doi.org/10.1063/5.0015983

Tomizawa Y, Dixit K, Daggett D, Hoshino K. Biocompatible Cantilevers for Mechanical Characterization of Zebrafish Embryos using Image Analysis. Sensors (Basel). 2019 Mar 28;19(7):1506. doi: 10.3390/s19071506. PMID: 30925721; PMCID: PMC6479902. https://pubmed.ncbi.nlm.nih.gov/30925721/

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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679083/

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 https://www.nature.com/articles/s41587-020-0718-6

Wood, W. M., Otis, C., Etemad, S., and Goldhamer, D. J. (2020). Development and patterning of rib primordia are dependent on associated musculature. Dev. Biol. 468, 133-145

Mitchell, W., Ng, E.A., Tamucci, J.D., Boyd, K.J., Sathappa, M., Coscia, A., Pan, M., Xan, X., Eddy, N.A., May, E.R., Szeto, H.H., and Alder, N.N. (2020) The mitochondria-targeted peptide SS-31 binds lipid bilayers and modulates surface electrostatics as a key component of its mechanism of action. Journal of Biological Chemistry 295: 7452-7469. doi: 10.1074/jbc.RA119.012094

Dedeo, C.L., Teschke, C.M., & Alexandrescu, A.T (2020) “Keeping it together: structures, functions, and applications of viral decoration proteins”, Viruses 12, 1163. https://doi.org/10.3390/v12101163

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, https://doi.org/10.1016/j.tim.2020.08.004

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

Fortin, J., Tian, R., Zarrabi, I., Hill, G., Williams, E., Sanchez-Duffhues, G., Thorikay, M., Ramachandran, P., Siddaway, R., Wong, J. F., Wu,  A., Apuzzo, L. N., Haight, J., You-Ten, A., Snow, B., Wakeham, A., Goldhamer, D. J., Schramek, D., Bullock, A. N., Dijke, P. T., Hawkins, C., and Mak, T. W.^. (2020). Mutant ACVR1 arrests glial cell differentiation to drive tumorigenesis in pediatric gliomas. Cancer Cell 37, 308-323. e12

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: https://doi.org/10.1083/jcb.202002086

Asis K Jana, Eric R May. Structural and dynamic asymmetry in icosahedrally symmetric virus capsids. Current Opinion in Virology, Volume 45, December 2020, Pages 8-16 https://doi.org/10.1016/j.coviro.2020.06.002

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),  https://doi.org/10.1016/j.str.2020.03.002

Kabrawala S, Zimmer MD, Campellone KG (2020) WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility. PLoS Genet 16(3): e1008694. https://doi.org/10.1371/journal.pgen.1008694

Zerbe, Cassie M, and Cole, James L. "Regulation of PKR by Epstein-Barr Virus EBER1 RNA." Biochemistry.Ja (2020): Biochemistry. , 2020, (ja). Web. DOI: 10.1021/acs.biochem.0c00088

Capunitan D, Johnson O, Terrill RS, Hird SM. Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea. Molecular Ecology, 29(4):829-847. https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15354

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, https://doi.org/10.1016/j.devcel.2020.01.005

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, https://doi.org/10.1093/femsec/fiz182

Grond Kirsten, Guilani Hannah and Hird Sarah M. Spatial heterogeneity of the shorebird gastrointestinal microbiome7 Soc. open sci.http://doi.org/10.1098/rsos.191609

Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N and Dorrestein PC. 2020. Mass spectrometry searches using MASST Nature Biotechnology 38(1):23-26 PMID(31894142) https://www.ncbi.nlm.nih.gov/pubmed/31894142

Klassen, J.L. Ecology helps bound causal explanations in microbiology. Biol Philos (2020) 35: 3. doi.org/10.1007/s10539-019-9728-5 https://link.springer.com/article/10.1007/s10539-019-9728-5

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 https://www.nature.com/articles/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 https://www.sciencedirect.com/science/article/pii/S0005273619302482

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) https://www.ncbi.nlm.nih.gov/pubmed/31662458

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.

Goldhamer, D. J. and Lees-Shepard, J. B. (2019). Response to comment on 'Palovarotene reduces heterotopic ossification in juvenile FOP mice but exhibits pronounced skeletal toxicity.” eLife 8. doi:10.7554/eLife.43928

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 https://www.ncbi.nlm.nih.gov/pubmed/31571583

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 https://www.ncbi.nlm.nih.gov/pubmed/31331976

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 https://www.ncbi.nlm.nih.gov/pubmed/31197972

Zerbe, C.M., Mouser, D.J. and Cole, J.L. (2019) Oligomerization of RIG-I and MDA5 2CARD Domains.  Protein Science URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.3776

Whitehead, R. D. III, Teschke, C.M., & Alexandrescu, A.T (2019) “NMR mapping of disordered segments for a viral scaffolding protein enclosed in a 23 MDa procapsid”, Biophysical J. 117: 1387-1392. DOI: 1016/j.bpj.2019.08.038

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 https://doi.org/10.1016/j.jnutbio.2019.06.001

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 https://www.frontiersin.org/articles/10.3389/fmicb.2019.01739/abstract

Wizeman, J.W., Guo, Q., Wilion, E.M., Li, J.Y.H. (2019). Specification of diverse cell types during early neurogenesis of the mouse cerebellum. eLife 8. doi: 10.7554/eLife.42388

Christopher B. Mayo, Heidi Erlandsen, David J. Mouser, Aaron G. Feinstein, Victoria L. Robinson, Eric R. May, James L. Cole (2019)  Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry, DOI: 10.1021/acs.biochem.9b00161 https://pubs.acs.org/doi/10.1021/acs.biochem.9b00161

Klassen JL. 2019. Keeping it fresh eLife 8:e48268 https://elifesciences.org/articles/48268.

Asija K, Teschke CM (2019): Of capsid structure and stability: The partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein.
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Asija K, Teschke CM (2019): A hydrophobic network: Intersubunit and intercapsomer interactions stabilizing the bacteriophage P22 capsid. J Virol. 2019 May 8. pii: JVI.00727-19. doi: 10.1128/JVI.00727-19. [Epub ahead of print] https://www.ncbi.nlm.nih.gov/pubmed/31068429

Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP (2019): Identification and characterization of putative Aeromonas spp. T3SS effectors
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Chang C-H, Chavan A, Palladino J, Wei X, Martins NMC, Santinello B, et al. (2019) Islands of retroelements are major components of Drosophila centromeres. PLoS Biol 17(5): e3000241. https://doi.org/10.1371/journal.pbio.3000241

Newcomer, R.L., Schrad, J.R., Gilcrease, E.B., Casjens, S.R., Feig, M., Teschke, C.M., Alexandrescu, A.T, & Parent K.N. (2019) “The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy”, eLife 8, e45345. https://doi.org/10.7554/eLife.45345

Maher Gtari, David R. Benson, Imen Nouioui, Jeffery O. Dawson, Faten Ghodhbane-Gtari (eds.). 2019.  19th International Meeting on Frankia and Actinorhizal Plants. Antonie van Leeuwenhoek 112:1-4. https://doi.org/10.1007/s10482-018-1202-x

Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP (2019) Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21
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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 http://dx.doi.org/10.3390/genes10030233

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 https://pubs.acs.org/doi/10.1021/acs.biochem.9b00055

Motwani, T., and Teschke, CM. “The Architect of Virus Assembly: Portal Protein Nucleates Procapsid Assembly in Bacteriophage P22.” Current Neurology and Neuroscience Reports., U.S. National Library of Medicine, 20 Feb. 2019, www.ncbi.nlm.nih.gov/pubmed/30787152.

Tripler, T.N., Kaplan, A.R., Alexandrescu, A.T, & Teschke, C.M. (2019) “Conservation and divergence of the I-domain inserted into the ubiquitous HK97 coat protein fold in the P22-like bacteriophages”, Journal of Virology 93, e0007-19. DOI: 1128/JVI.00007-19

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 https://doi.org/10.1073/pnas.1817322116

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 bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5381-7

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.

Friedman, R., Khalid, S., Aponte-Santamaría, C. et al. 2018. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. J Membrane Biol. DOI:10.1007/s00232-018-0050-y

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Samantha M. Gromek, Anne A. Sung, Jonathan L. Klassen, Marcy J. Balunas (2016). Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate. Genome Announc. September/October 2016 vol. 4 no. 5 e00856-16. doi: 10.1128/genomeA.00856-16.

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Adit Naor, Neta Altman-Price, Shannon M. Soucy, Anna G. Green (UConn undergrad), Yulia Mitiagin, Israela Turgeman-Grott, Noam Davidovich, Johann Peter Gogarten*, Uri Gophna*  (2016). Impact of a homing intein on recombination frequency and organismal fitness. PNAS 2016; published ahead of print July 26, 2016, doi:10.1073/pnas.1606416113.

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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