Department of Biology
Latest Publications

List of current publications.

Rustom Antia
September 2015
Masking of antigenic epitopes by antibodies shapes the humoral immune response to influenza.
Zarnitsyna VI, Ellebedy AH, Davis C, Jacob J, Ahmed R, Antia R. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140248. doi: 10.1098/rstb.2014.0248.

March 2015
Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccination.
Akondy RS, Johnson PL, Nakaya HI, Edupuganti S, Mulligan MJ, Lawson B, Miller JD, Pulendran B, Antia R, Ahmed R. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3050-5. doi: 10.1073/pnas.1500475112. Epub 2015 Feb 23.

January 2014
How sticky should a virus be? The impact of virus binding and release on transmission fitness using influenza as an example.
Handel A, Akin V, Pilyugin SS, Zarnitsyna V, Antia R. J R Soc Interface. 2014 Jan 15;11(92):20131083. doi: 10.1098/rsif.2013.1083. Print 2014 Mar 6.

December 2013
Estimating the Diversity, Completeness, and Cross-Reactivity of the T Cell Repertoire
Zarnitsyna VI, Evavold BD, Schoettle LN, Blattman JN, Antia R. Front Immunol. 2013 Dec 26;4:485. eCollection 2013. Review.

December 2003
The role of evolution in the emergence of infectious diseases.
Antia R, Regoes RR, Koella JC, Bergstrom CT. Nature. 2003 Dec 11;426(6967):658-61.

Chris Beck
December 2016
Alternative Realities: Faculty and Student Perceptions of Instructional Practices in Laboratory Courses.
Beck CW, Blumer LS. CBE Life Sci Educ. 2016 winter;15(4). pii: ar52.

June 2016
Bridging the Divide Between Biology Educators and Disciplinary Researchers. CUR
Spell, R.M. and C.W. Beck. (2016). Quarterly, 36, 46

January 2016
Course-based Science Research Helps Students from Diverse Institutions.
Staub, N.L., L.S. Blumer, C.W. Beck, V.A. Delesalle, G.D. Griffin, R.B. Merritt, B.S. Hennington, W.H. Grillo, G.P. Hollowell, S.L. White, and C.M. Mader (2016). CUR Quarterly, 37, 36-46

Gordon Berman
February 2017
An unsupervised method for quantifying the behavior of paired animals.
Klibaite U, Berman GJ, Cande J, Stern DL, Shaevitz JW. Phys Biol. 2017 Feb 16;14(1):015006. doi: 10.1088/1478-3975/aa5c50.

February 2017
Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.
Tabler JM, Rigney MM, Berman GJ, Gopalakrishnan S, Heude E, Al-Lami HA, Yannakoudiadkis BZ, Fitch RD, Carter C, Vokes S, Liu KJ, Tajbakhsh S, Egnor SR, Wallingford JB. Elife. 2017 Feb 13;6. pii: e19153. doi: 10.7554/eLife.19153.

November 2016
Functional connectivity metrics for wavelet clustering of rs-fMRI data
Billings, J.C., Medda, A., Berman, G.J. and Keilholz, S.D. (2016). 2016 50th Asilomar Conference on Signals, Systems and Computers, 2016, 1295-1299.

October 2016
Predictability and hierarchy in Drosophila behavior.
Berman GJ, Bialek W, Shaevitz JW. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11943-11948. Epub 2016 Oct 4.

October 2014
Mapping the stereotyped behaviour of freely moving fruit flies.
Berman GJ, Choi DM, Bialek W, Shaevitz JW. J R Soc Interface. 2014 Oct 6;11(99). pii: 20140672. doi: 10.1098/rsif.2014.0672.

Ronald Calabrese, Senior Associate Dean for Research
July 2014
Variation in motor output and motor performance in a centrally generated motor pattern.
Wenning A, Norris BJ, Doloc-Mihu A, Calabrese RL. J Neurophysiol. 2014 Jul 1;112(1):95-109. doi: 10.1152/jn.00856.2013. Epub 2014 Apr 9.

June 2014
Identifying crucial parameter correlations maintaining bursting activity.
Doloc-Mihu A, Calabrese RL. PLoS Comput Biol. 2014 Jun 19;10(6):e1003678. doi: 10.1371/journal.pcbi.1003678. eCollection 2014 Jun.

November 2013
Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation.
Lamb DG, Calabrese RL. PLoS One. 2013 Nov 18;8(11):e79267. doi: 10.1371/journal.pone.0079267. eCollection 2013.

March 2012
Animal-to-animal variability of connection strength in the leech heartbeat central pattern generator.
Roffman RC, Norris BJ, Calabrese RL. J Neurophysiol. 2012 Mar;107(6):1681-93. doi: 10.1152/jn.00903.2011. Epub 2011 Dec 21.

November 2011
Patterns of presynaptic activity and synaptic strength interact to produce motor output.
Wright TM Jr, Calabrese RL. J Neurosci. 2011 Nov 30;31(48):17555-71. doi: 10.1523/JNEUROSCI.4723-11.2011.

Dave Civitello
June 2016
Spatial scale modulates the strength of ecological processes driving disease distributions.
Cohen JM, Civitello DJ, Brace AJ, Feichtinger EM, Ortega CN, Richardson JC, Sauer EL, Liu X, Rohr JR. Proc Natl Acad Sci U S A. 2016 Jun 14;113(24):E3359-64. doi: 10.1073/pnas.1521657113. Epub 2016 May 31.

September 2015
Success, failure and ambiguity of the dilution effect among competitors.
Strauss AT, Civitello DJ, Cáceres CE, Hall SR. Ecol Lett. 2015 Sep;18(9):916-26. doi: 10.1111/ele.12468. Epub 2015 Jun 25.

July 2015
Biodiversity inhibits parasites: Broad evidence for the dilution effect.
Civitello DJ, Cohen J, Fatima H, Halstead NT, Liriano J, McMahon TA, Ortega CN, Sauer EL, Sehgal T, Young S, Rohr JR. Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8667-71. doi: 10.1073/pnas.1506279112. Epub 2015 Jun 11.

July 2015
Resources, key traits and the size of fungal epidemics in Daphnia populations.
Civitello DJ, Penczykowski RM, Smith AN, Shocket MS, Duffy MA, Hall SR. J Anim Ecol. 2015 Jul;84(4):1010-7. doi: 10.1111/1365-2656.12363. Epub 2015 Mar 21.

May 2013
Parasite consumption and host interference can inhibit disease spread in dense populations.
Civitello DJ, Pearsall S, Duffy MA, Hall SR. Ecol Lett. 2013 May;16(5):626-34. doi: 10.1111/ele.12089. Epub 2013 Mar 3.

Megan Cole
April 2017
Using Facebook groups to encourage science discussions in a large enrollment biology class.
Pai A, McGinnis G, Bryant D, Cole MF, Stovall K, Kovacs J, Lee M and Bryant D. 2017. J Ed. Techn. Sys. April 24th.

January 2016
Choosy Worms to Teach Experimental Design.
Cole MF, de Roode JC and Gerardo NM. Tested Studies for Laboratory Teaching. 2016 Proceedings of the Association for Biology Lab Educators. 37:Article 5.

January 2016
Using the Game of Mastermind to Teach Critical Thinking.
Cole MF. Tested Studies for Laboratory Teaching. 2016 Proceedings of the Association for Biology Lab Educators. 38.

January 2013
Reconstructing evolutionary adaptive paths for protein engineering.
Cole MF, Cox VE, Gratton KL, Gaucher EA. Methods Mol Biol. 2013;978:115-25. doi: 10.1007/978-1-62703-293-3_8.

June 2011
Utilizing natural diversity to evolve protein function: applications towards thermostability.
Cole MF, Gaucher EA. Curr Opin Chem Biol. 2011 Jun;15(3):399-406. doi: 10.1016/j.cbpa.2011.03.005. Epub 2011 Apr 4. Review.

Anita Corbett
May 2017
Novel mouse models of oculopharyngeal muscular dystrophy (OPMD) reveal early onset mitochondrial defects and suggest loss of PABPN1 may contribute to pathology.
Vest KE, Phillips BL, Banerjee A, Apponi LH, Dammer EB, Xu W, Zheng D, Yu J, Tian B, Pavlath GK, Corbett AH. Hum Mol Genet. 2017 May 29. doi: 10.1093/hmg/ddx206. [Epub ahead of print]

January 2017
Insight into the RNA Exosome Complex Through Modeling Pontocerebellar Hypoplasia Type 1b Disease Mutations in Yeast.
Fasken MB, Losh JS, Leung SW, Brutus S, Avin B, Vaught JC, Potter-Birriel J, Craig T, Conn GL, Mills-Lujan K, Corbett AH, van Hoof A. Genetics. 2017 Jan;205(1):221-237. doi: 10.1534/genetics.116.195917. Epub 2016 Oct 24.

November 2016
Links between mRNA splicing, mRNA quality control, and intellectual disability.
Fasken MB, Corbett AH. RNA Dis. 2016;3(4). pii: e1448. Epub 2016 Nov 7.

October 2016
The Polyadenosine RNA-binding Protein, Zinc Finger Cys3His Protein 14 (ZC3H14), Regulates the Pre-mRNA Processing of a Key ATP Synthase Subunit mRNA.
Wigington CP, Morris KJ, Newman LE, Corbett AH. J Biol Chem. 2016 Oct 21;291(43):22442-22459. Epub 2016 Aug 25.

July 2016
Use of a Grant Writing Class in Training PhD Students.
Kahn RA, Conn GL, Pavlath GK, Corbett AH. Traffic. 2016 Jul;17(7):803-14. doi: 10.1111/tra.12398. Epub 2016 May 3.

Victor Corces
February 2016
The three-dimensional cancer genome.
Corces MR, Corces VG. Curr Opin Genet Dev. 2016 Feb 5;36:1-7. doi: 10.1016/j.gde.2016.01.002. [Epub ahead of print] Review.

April 2015
Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing.
Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Ong CT, Cubeñas-Potts C, Hu M, Lei EP, Bosco G, Qin ZS, Corces VG. Mol Cell. 2015 Apr 16;58(2):216-31. doi: 10.1016/j.molcel.2015.02.023. Epub 2015 Mar 26.

June 2014
Insulator function and topological domain border strength scale with architectural protein occupancy.
Van Bortle K, Nichols MH, Li L, Ong CT, Takenaka N, Qin ZS, Corces VG. Genome Biol. 2014 Jun 30;15(6):R82. doi: 10.1186/gb-2014-15-5-r82.

September 2013
Poly(ADP-ribosyl)ation regulates insulator function and intrachromosomal interactions in Drosophila.
Ong CT, Van Bortle K, Ramos E, Corces VG. Cell. 2013 Sep 26;155(1):148-59. doi: 10.1016/j.cell.2013.08.052. Epub 2013 Sep 19.

June 2013
Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG. Cell. 2013 Jun 6;153(6):1281-95. doi: 10.1016/j.cell.2013.04.053. Epub 2013 May 23.

Gray Crouse
February 2016
Non-canonical actions of mismatch repair.
Crouse GF. DNA Repair (Amst). 2016 Feb;38:102-9. doi: 10.1016/j.dnarep.2015.11.020. Epub 2015 Dec 2. Review.

March 2015
Replicative DNA polymerase ¿ but not ¿ proofreads errors in Cis and in Trans.
Flood CL, Rodriguez GP, Bao G, Shockley AH, Kow YW, Crouse GF. PLoS Genet. 2015 Mar 5;11(3):e1005049. doi: 10.1371/journal.pgen.1005049. eCollection 2015 Mar.

October 2013
Oxidative damage and mutagenesis in Saccharomyces cerevisiae: genetic studies of pathways affecting replication fidelity of 8-oxoguanine.
Shockley AH, Doo DW, Rodriguez GP, Crouse GF. Genetics. 2013 Oct;195(2):359-67. doi: 10.1534/genetics.113.153874. Epub 2013 Jul 26.

October 2013
Different roles of eukaryotic MutS and MutL complexes in repair of small insertion and deletion loops in yeast.
Romanova NV, Crouse GF. PLoS Genet. 2013 Oct;9(10):e1003920. doi: 10.1371/journal.pgen.1003920. Epub 2013 Oct 31.

August 2013
In Vivo bypass of 8-oxodG.
Rodriguez GP, Song JB, Crouse GF. PLoS Genet. 2013;9(8):e1003682. doi: 10.1371/journal.pgen.1003682. Epub 2013 Aug 1.

Jaap De Roode
March 2016
Within-host competition and drug resistance in the human malaria parasite Plasmodium falciparum.
Bushman M, Morton L, Duah N, Quashie N, Abuaku B, Koram KA, Dimbu PR, Plucinski M, Gutman J, Lyaruu P, Kachur SP, de Roode JC, Udhayakumar V. Proc Biol Sci. 2016 Mar 16;283(1826). pii: 20153038. doi: 10.1098/rspb.2015.3038.

October 2015
Disease ecology across soil boundaries: effects of below-ground fungi on above-ground host-parasite interactions.
Tao L, Gowler CD, Ahmad A, Hunter MD, de Roode JC. Proc Biol Sci. 2015 Oct 22;282(1817):20151993. doi: 10.1098/rspb.2015.1993.

September 2015
Why infectious disease research needs community ecology.
Johnson PT, de Roode JC, Fenton A. Science. 2015 Sep 4;349(6252):1259504. doi: 10.1126/science.1259504. Review.

October 2014
The genetics of monarch butterfly migration and warning colouration.
Zhan S, Zhang W, Niitepõld K, Hsu J, Haeger JF, Zalucki MP, Altizer S, de Roode JC, Reppert SM, Kronforst MR. Nature. 2014 Oct 16;514(7522):317-21. doi: 10.1038/nature13812. Epub 2014 Oct 1.

April 2013
Self-medication in animals.
de Roode JC, Lefèvre T, Hunter MD. Science. 2013 Apr 12;340(6129):150-1. doi: 10.1126/science.1235824. No abstract available.

Roger Deal
April 2017
A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate.
Foley SW, Gosai SJ, Wang D, Selamoglu N, Sollitti AC, Köster T, Steffen A, Lyons E, Daldal F, Garcia BA, Staiger D, Deal RB, Gregory BD. Dev Cell. 2017 Apr 24;41(2):204-220.e5. doi: 10.1016/j.devcel.2017.03.018.

January 2015
Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus.
Gosai SJ, Foley SW, Wang D, Silverman IM, Selamoglu N, Nelson AD, Beilstein MA, Daldal F, Deal RB, Gregory BD. Mol Cell. 2015 Jan 22;57(2):376-88. doi: 10.1016/j.molcel.2014.12.004. Epub 2014 Dec 31.

January 2015
Epigenome profiling of specific plant cell types using a streamlined INTACT protocol and ChIP-seq.
Wang D, Deal RB. Methods Mol Biol. 2015;1284:3-25. doi: 10.1007/978-1-4939-2444-8_1.

October 2014
Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model.
Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM. Plant Physiol. 2014 Oct;166(2):455-69. doi: 10.1104/pp.114.239392. Epub 2014 May 27.

Arri Eisen
May 2017
Parental Perspectives on Pharmacological Clinical Trials: a Qualitative Study in Down Syndrome and Fragile X Syndrome.
Reines V, Charen K, Rosser T, Eisen A, Sherman SL, Visootsak J. J Genet Couns. 2017 May 24. doi: 10.1007/s10897-017-0111-x. [Epub ahead of print]

April 2017
The Enlightened Gene: Biology, Buddhism, and the Convergence that Explains the World.
Arri Eisen and Yungdrung Konchok (2017). Lebanon, NH, University Press of New England, ForeEdge

January 2014
Learning Science by Engaging Religion: A Novel Two-Course Approach for Biology Majors.
Arri Eisen, Junjian Huang. (2014). College Teaching 62:1, 25-31

January 2013
My take: an American Jew finds MLK-and a new understanding-on the West Bank

January 2013
Ethical perspectives on knowledge translation in rehabilitation.
Banja JD, Eisen A. Arch Phys Med Rehabil. 2013 Jan;94(1 Suppl):S55-60. doi: 10.1016/j.apmr.2012.08.218. Epub 2012 Nov 17.

Alexander Escobar
September 2016
QVA: A massively parallel model for vision.
Psychology of Consciousness: Theory, Research, and Practice, Vol 3(3), Sep 2016, 222-238.

September 2014
Breaking down experiences into millions of parts may help explain consciousness
The Conversation

November 2013
Quantized visual awareness.
Escobar WA. Front Psychol. 2013 Nov 22;4:869. doi: 10.3389/fpsyg.2013.00869. eCollection 2013.

June 2011
Qualia as the fundamental nature of visual awareness.
Escobar A. J Theor Biol. 2011 Jun 21;279(1):172-6. Epub 2011 Mar 29.

Andreas Fritz
September 2012
A novel microtubule-modulating agent EM011 inhibits angiogenesis by repressing the HIF-1¿ axis and disrupting cell polarity and migration.
Prasanthi Karna, Padmashree C.G. Rida, Ravi Chakra Turaga, Jinmin Gao, Meenakshi Gupta, Andreas Fritz, Erica Werner, Clayton Yates, Jun Zhou, and Ritu Aneja (2012). Carcinogenesis 33(9): 1769-1781. PMCID: PMC3514903

February 2011
Rack1 is required for Vangl2 membrane localization and planar cell polarity signaling while attenuating canonical Wnt activity.
Li S, Esterberg R, Lachance V, Ren D, Radde-Gallwitz K, Chi F, Parent JL, Fritz A, Chen P. Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2264-9. Epub 2011 Jan 24.

November 2010
Core fucosylation is required for midline patterning during zebrafish development.
Seth A, Machingo QJ, Fritz A, Shur BD. Dev Dyn. 2010 Dec;239(12):3380-90.

Nicole Gerardo
April 2017
Life-history strategy determines constraints on immune function.
Parker BJ, Barribeau SM, Laughton AM, Griffin LH, Gerardo NM. J Anim Ecol. 2017 May;86(3):473-483. doi: 10.1111/1365-2656.12657. Epub 2017 Apr 3.

March 2016
Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture.
de Man TJ, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM. Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3567-72. doi: 10.1073/pnas.1518501113. Epub 2016 Mar 14.

March 2014
Partner associations across sympatric broad-headed bug species and their environmentally acquired bacterial symbionts.
Garcia JR, Laughton AM, Malik Z, Parker BJ, Trincot C, S L Chiang S, Chung E, Gerardo NM. Mol Ecol. 2014 Mar;23(6):1333-47. doi: 10.1111/mec.12655. Epub 2014 Feb 7.

April 2013
Symbiont-mediated protection against fungal pathogens in pea aphids: a role for pathogen specificity?
Parker BJ, Spragg CJ, Altincicek B, Gerardo NM. Appl Environ Microbiol. 2013 Apr;79(7):2455-8. doi: 10.1128/AEM.03193-12. Epub 2013 Jan 25.

February 2010
Immunity and other defenses in pea aphids, Acyrthosiphon pisum.
Gerardo NM, Altincicek B, Anselme C, Atamian H, Barribeau SM, de Vos M, Duncan EJ, Evans JD, Gabaldón T, Ghanim M, Heddi A, Kaloshian I, Latorre A, Moya A, Nakabachi A, Parker BJ, Pérez-Brocal V, Pignatelli M, Rahbé Y, Ramsey JS, Spragg CJ, Tamames J, Tamarit D, Tamborindeguy C, Vincent-Monegat C, Vilcinskas A. Genome Biol. 2010;11(2):R21. Epub 2010 Feb 23.

Dieter Jaeger
June 2017
Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice.
Abbasi S, Hudson AE, Maran SK, Cao Y, Abbasi A, Heck DH, Jaeger D. PLoS Comput Biol. 2017 Jun 15;13(6):e1005578. doi: 10.1371/journal.pcbi.1005578. [Epub ahead of print]

March 2016
Cerebellar Nuclei Neurons Show Only Small Excitatory Responses to Optogenetic Olivary Stimulation in Transgenic Mice: In Vivo and In Vitro Studies.
Lu H, Yang B, Jaeger D. Front Neural Circuits. 2016 Mar 24;10:21. doi: 10.3389/fncir.2016.00021. eCollection 2016.

March 2015
Bursting activity of substantia nigra pars reticulata neurons in mouse parkinsonism in awake and anesthetized states.
Lobb CJ, Jaeger D. Neurobiol Dis. 2015 Mar;75:177-85. doi: 10.1016/j.nbd.2014.12.026. Epub 2015 Jan 6.

February 2014
Optogenetic activation of nigral inhibitory inputs to motor thalamus in the mouse reveals classic inhibition with little potential for rebound activation.
Edgerton JR, Jaeger D. Front Cell Neurosci. 2014 Feb 11;8:36. doi: 10.3389/fncel.2014.00036. eCollection 2014.

December 2013
In vivo electrophysiology of nigral and thalamic neurons in alpha-synuclein-overexpressing mice highlights differences from toxin-based models of parkinsonism.
Lobb CJ, Zaheer AK, Smith Y, Jaeger D. J Neurophysiol. 2013 Dec;110(12):2792-805. doi: 10.1152/jn.00441.2013. Epub 2013 Sep 25.

George H. Jones, Emeritus
March 2014
SCO5745, A bifunctional RNase J ortholog affects antibiotic production in Streptomyces coelicolor.
Bralley P, Aseem M, Jones GH. J Bacteriol. 2014 Mar;196(6):1197-205. doi: 10.1128/JB.01422-13. Epub 2014 Jan 10.

November 2013
Transcription of the rpsO-pnp operon of Streptomyces coelicolor involves four temporally regulated, stress responsive promoters.
Jones GH, Mackie GA. J Bacteriol. 2013 Nov;195(22):5151-9. doi: 10.1128/JB.00936-13. Epub 2013 Sep 13.

November 2013
Streptomyces coelicolor polynucleotide phosphorylase can polymerize nucleoside diphosphates under phosphorolysis conditions-implications for the degradation of structured RNAs.
Jones GH, Mackie GA. J Bacteriol. 2013 Nov;195(22):5151-9. doi: 10.1128/JB.00936-13. Epub 2013 Sep 13.

October 2013
RNase III is required for actinomycin production in Streptomyces antibioticus.
Lee JH, Gatewood ML, Jones GH. Appl Environ Microbiol. 2013 Oct;79(20):6447-51. doi: 10.1128/AEM.02272-13. Epub 2013 Aug 16.

William Kelly
February 2017
Establishment and Maintenance of Heritable Chromatin in C. elegans.
Gangishetti U, Kelly WG (2017). JSM Genet Genomics 4(1): 1022

August 2016
A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans.
Ahn JH, Rechsteiner A, Strome S, Kelly WG. PLoS Genet. 2016 Aug 19;12(8):e1006227. doi: 10.1371/journal.pgen.1006227. eCollection 2016 Aug. Erratum in: PLoS Genet. 2017 May 31;13(5):e1006821.

May 2014
RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases.
Bowman EA, Kelly WG. Nucleus. 2014 May-Jun;5(3):224-36. doi: 10.4161/nucl.29347. Epub 2014 May 30. Review.

May 2014
A role for WDR5 in TRA-1/Gli mediated transcriptional control of the sperm/oocyte switch in C. elegans.
Li T, Kelly WG. Nucleic Acids Res. 2014 May;42(9):5567-81. doi: 10.1093/nar/gku221. Epub 2014 Mar 20.

March 2014
Transgenerational epigenetics in the germline cycle of Caenorhabditis elegans.
Kelly WG. Epigenetics Chromatin. 2014 Mar 29;7(1):6. doi: 10.1186/1756-8935-7-6.

Steven L'Hernault, Chairman
June 2016
Gamete interactions require transmembranous immunoglobulin-like proteins with conserved roles during evolution.
Nishimura H, L'Hernault SW. Worm. 2016 Jun 9;5(3):e1197485. eCollection 2016.

December 2015
The Immunoglobulin-like Gene spe-45 Acts during Fertilization in Caenorhabditis elegans like the Mouse Izumo1 Gene.
Nishimura H, Tajima T, Comstra HS, Gleason EJ, L'Hernault SW. Curr Biol. 2015 Dec 21;25(24):3225-31. doi: 10.1016/j.cub.2015.10.056. Epub 2015 Dec 6.

January 2014
Role of posttranslational modifications in C. elegans and ascaris spermatogenesis and sperm function.
Miao L, L'Hernault SW. Adv Exp Med Biol. 2014;759:215-39. doi: 10.1007/978-1-4939-0817-2_10. Review.

January 2014
Functional roles of spe genes in the male germline during reproduction of Caenorhabditis elegans.
Nishimura, H., T. Tajima, S. Comstra and S. W. L¿Hernault 2014 Chapter 18, pp 199-213 in "Sexual Reproduction in Animals and Plants" ed by Sawada, H., N. Inoue and M. Iwano, Springer Open, Tokyo, DOI 10.1007/978-4-431-54589-7_18

December 2013
Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes.
Tornieri K, Zlatic SA, Mullin AP, Werner E, Harrison R, L'hernault SW, Faundez V. Hum Mol Genet. 2013 Dec 20;22(25):5215-28. doi: 10.1093/hmg/ddt378. Epub 2013 Aug 4.

Bruce Levin
August 2017
Phagocytes, Antibiotics, and Self-Limiting Bacterial Infections.
Levin BR, Baquero F, Ankomah PP, McCall IC. Trends Microbiol. 2017 Aug 23. pii: S0966-842X(17)30175-0. doi: 10.1016/j.tim.2017.07.005. [Epub ahead of print] Review.

July 2017
Growth of bacteria in 3-d colonies.
Shao X, Mugler A, Kim J, Jeong HJ, Levin BR, Nemenman I. PLoS Comput Biol. 2017 Jul 27;13(7):e1005679. doi: 10.1371/journal.pcbi.1005679. eCollection 2017 Jul.

February 2017
A Numbers Game: Ribosome Densities, Bacterial Growth, and Antibiotic-Mediated Stasis and Death.
Levin BR, McCall IC, Perrot V, Weiss H, Ovesepian A, Baquero F. MBio. 2017 Feb 7;8(1). pii: e02253-16. doi: 10.1128/mBio.02253-16.

January 2017
Synergy and Order Effects of Antibiotics and Phages in Killing Pseudomonas aeruginosa Biofilms.
Chaudhry WN, Concepción-Acevedo J, Park T, Andleeb S, Bull JJ, Levin BR. PLoS One. 2017 Jan 11;12(1):e0168615. doi: 10.1371/journal.pone.0168615. eCollection 2017.

January 2017
Single variant bottleneck in the early dynamics of bacteremia in neonatal rats questions the theory of independent action.
Shao, X, B. R. Levin and I. Nemenman (2017) Physical Biology. 14: 045004

Robert Liu
July 2017
Perineuronal Nets in the Adult Sensory Cortex Are Necessary for Fear Learning.
Banerjee SB, Gutzeit VA, Baman J, Aoued HS, Doshi NK, Liu RC, Ressler KJ. Neuron. 2017 Jul 5;95(1):169-179.e3. doi: 10.1016/j.neuron.2017.06.007. Epub 2017 Jun 22.

June 2017
Dynamic corticostriatal activity biases social bonding in monogamous female prairie voles.
Amadei EA, Johnson ZV, Jun Kwon Y, Shpiner AC, Saravanan V, Mays WD, Ryan SJ, Walum H, Rainnie DG, Young LJ, Liu RC.

February 2015
Behavioral relevance helps untangle natural vocal categories in a specific subset of core auditory cortical pyramidal neurons.
Shepard KN, Lin FG, Zhao CL, Chong KK, Liu RC. J Neurosci. 2015 Feb 11;35(6):2636-45. doi: 10.1523/JNEUROSCI.3803-14.2015.

February 2015
Norepinephrine is necessary for experience-dependent plasticity in the developing mouse auditory cortex.
Shepard KN, Liles LC, Weinshenker D, Liu RC. J Neurosci. 2015 Feb 11;35(6):2432-7. doi: 10.1523/JNEUROSCI.0532-14.2015.

June 2009
Inhibitory plasticity in a lateral band improves cortical detection of natural vocalizations.
Galindo-Leon EE, Lin FG, Liu RC. Neuron. 2009 Jun 11;62(5):705-16. doi: 10.1016/j.neuron.2009.05.001.

John Lucchesi, Emeritus
August 2013
Topoisomerase II plays a role in dosage compensation in Drosophila.
Cugusi S, Ramos E, Ling H, Yokoyama R, Luk KM, Lucchesi JC. Transcription. 2013 Aug 23;4(5). [Epub ahead of print]

May 2013
Expression, purification and proteomic analysis of recombinant histone H4 acetylated at lysine 16.
Kallappagoudar S, Dammer EB, Duong DM, Seyfried NT, Lucchesi JC. Proteomics. 2013 May;13(10-11):1687-91. doi: 10.1002/pmic.201300025. Epub 2013 Apr 26.

December 2012
Distinct contributions of MSL complex subunits to the transcriptional enhancement responsible for dosage compensation in Drosophila.
Dunlap D, Yokoyama R, Ling H, Sun HY, McGill K, Cugusi S, Lucchesi JC. Nucleic Acids Res. 2012 Dec;40(22):11281-91. doi: 10.1093/nar/gks890. Epub 2012 Oct 9.

February 2012
The role of MOF in the ionizing radiation response is conserved in Drosophila melanogaster.
Bhadra MP, Horikoshi N, Pushpavallipvalli SN, Sarkar A, Bag I, Krishnan A, Lucchesi JC et al. Chromosoma. 2012 Feb;121(1):79-90. doi: 10.1007/s00412-011-0344-7. Epub 2011 Nov 10.

April 2011
Role of the ATPase/helicase maleless (MLE) in the assembly, targeting, spreading and function of the male-specific lethal.
Morra R, Yokoyama R, Ling H, Lucchesi JC. Epigenetics Chromatin. 2011 Apr 12;4:6. doi: 10.1186/1756-8935-4-6.

David Lynn
July 2014
Neurofibrillar tangle surrogates: histone H1 binding to patterned phosphotyrosine peptide nanotubes.
Li S, Sidorov AN, Mehta AK, Bisignano AJ, Das D, Childers WS, Schuler E, Jiang Z, Orlando TM, Berland K, Lynn DG. Biochemistry. 2014 Jul 8;53(26):4225-7. doi: 10.1021/bi500599a. Epub 2014 Jun 23.

June 2014
Mapping amyloid-ß(16-22) nucleation pathways using fluorescence lifetime imaging microscopy.
Anthony NR, Mehta AK, Lynn DG, Berland KM. Soft Matter. 2014 Jun 21;10(23):4162-72. doi: 10.1039/c4sm00361f.

January 2014
Liberal Arts Education and the Complexity of Human Society.
Goodwin, JT; Lynn, DG. 2014. Angew. Chem. International Edition, vol 53: pp 6832¿6833, early view DOI: 10.1002/anie.201400597.

January 2014
Alternative Chemistries of Life ¿ Empirical Approaches.
Goodwin JT; Lynn DG. 2014. Emory University, ISBN: 978-0-692-24992-5.

Levi Morran
November 2016
Coevolutionary interactions with parasites constrain the spread of self-fertilization into outcrossing host populations.
Slowinski SP, Morran LT, Parrish RC 2nd, Cui ER, Bhattacharya A, Lively CM, Phillips PC. Evolution. 2016 Nov;70(11):2632-2639. doi: 10.1111/evo.13048. Epub 2016 Sep 15.

September 2016
Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal-Microbe Interactions.
Hoang KL, Morran LT, Gerardo NM. Front Microbiol. 2016 Sep 13;7:1444. doi: 10.3389/fmicb.2016.01444. eCollection 2016. Review.

March 2016
Nematode-bacteria mutualism: Selection within the mutualism supersedes selection outside of the mutualism.
Morran LT, Penley MJ, Byrd VS, Meyer AJ, O'Sullivan TS, Bashey F, Goodrich-Blair H, Lively CM. Evolution. 2016 Mar;70(3):687-95. doi: 10.1111/evo.12878. Epub 2016 Mar 2.

November 2015
The evolution of reduced antagonism--A role for host-parasite coevolution.
Gibson AK, Stoy KS, Gelarden IA, Penley MJ, Lively CM, Morran LT. Evolution. 2015 Nov;69(11):2820-30. doi: 10.1111/evo.12785. Epub 2015 Oct 13.

August 2014
Experimental coevolution: rapid local adaptation by parasites depends on host mating system.
Morran LT, Parrish RC 2nd, Gelarden IA, Allen MB, Lively CM. Am Nat. 2014 Aug;184 Suppl 1:S91-100. doi: 10.1086/676930. Epub 2014 Jul 17.

Ilya Nemenman
January 2017
Motor control by precisely timed spike patterns.
Srivastava KH, Holmes CM, Vellema M, Pack AR, Elemans CP, Nemenman I, Sober SJ. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1171-1176. doi: 10.1073/pnas.1611734114. Epub 2017 Jan 18.

December 2016
Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level.
Leung K, Mohammadi A, Ryu WS, Nemenman I. PLoS Comput Biol. 2016 Dec 27;12(12):e1005262. doi: 10.1371/journal.pcbi.1005262. eCollection 2016 Dec.

January 2016
Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis.
Ellison D, Mugler A, Brennan MD, Lee SH, Huebner RJ, Shamir ER, Woo LA, Kim J, Amar P, Nemenman I, Ewald AJ, Levchenko A. Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E679-88. doi: 10.1073/pnas.1516503113. Epub 2016 Jan 20.

August 2015
Automated adaptive inference of phenomenological dynamical models.
Daniels BC, Nemenman I. Nat Commun. 2015 Aug 21;6:8133. doi: 10.1038/ncomms9133.

October 2011
Information transduction capacity of noisy biochemical signaling networks.
R Cheong, A Rhee, CJ Wang, I Nemenman, and A Levchenko. Science 334, 354¿358, 2011.

Astrid Prinz
August 2015
Degradation of extracellular chondroitin sulfate delays recovery of network activity after perturbation.
Hudson AE, Gollnick C, Gourdine JP, Prinz AA. J Neurophysiol. 2015 Aug;114(2):1346-52. doi: 10.1152/jn.00455.2015. Epub 2015 Jun 24.

June 2015
Differential effects of conductances on the phase resetting curve of a bursting neuronal oscillator.
Soofi W, Prinz AA. J Comput Neurosci. 2015 Jun;38(3):539-58. doi: 10.1007/s10827-015-0553-9. Epub 2015 Apr 3.

May 2015
Distal spike initiation zone location estimation by morphological simulation of ionic current filtering demonstrated in a novel model of an identified Drosophila motoneuron.
Günay C, Sieling FH, Dharmar L, Lin WH, Wolfram V, Marley R, Baines RA, Prinz AA. PLoS Comput Biol. 2015 May 15;11(5):e1004189. doi: 10.1371/journal.pcbi.1004189. eCollection 2015 May.

June 2014
Phase maintenance in a rhythmic motor pattern during temperature changes in vivo.
Soofi W, Goeritz ML, Kispersky TJ, Prinz AA, Marder E, Stein W. J Neurophysiol. 2014 Jun 15;111(12):2603-13. doi: 10.1152/jn.00906.2013. Epub 2014 Mar 26.

May 2014
Differential roles of nonsynaptic and synaptic plasticity in operant reward learning-induced compulsive behavior.
Sieling F, Bédécarrats A, Simmers J, Prinz AA, Nargeot R. Curr Biol. 2014 May 5;24(9):941-50. doi: 10.1016/j.cub.2014.03.004. Epub 2014 Apr 3

Leslie Real
June 2015
The Role of Human Transportation Networks in Mediating the Genetic Structure of Seasonal Influenza in the United States.
Bozick BA, Real LA. PLoS Pathog. 2015 Jun 18;11(6):e1004898. doi: 10.1371/journal.ppat.1004898. eCollection 2015 Jun.

July 2013
Structuring targeted surveillance for monitoring disease emergence by mapping observational data onto ecological process.
Gerardo-Giorda L, Puggioni G, Rudd RJ, Waller LA, Real LA. J R Soc Interface. 2013 Jul 17;10(86):20130418. doi: 10.1098/rsif.2013.0418. Print 2013 Sep 6.

June 2011
Strong seasonality produces spatial asynchrony in the outbreak of infectious diseases.
Duke-Sylvester SM, Bolzoni L, Real LA. J R Soc Interface. 2011 Jun 6;8(59):817-25. Epub 2010 Oct 20. [PubMed - in process]

January 2011
Mathematical models for rabies.
Panjeti VG, Real LA. Adv Virus Res. 2011;79:377-95. doi: 10.1016/B978-0-12-387040-7.00018-4. Review.

May 2007
A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus.
Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA. Proc Natl Acad Sci U S A. 2007 May 8;104(19):7993-8. Epub 2007 Apr 30.

Iain Shepherd
October 2016
Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes.

September 2016
Enteric Nervous System Development in Avian and Zebrafish Models.
Tiffany Haenue, Iain Shepherd and Alan Burns (2016). Developmental Biology 417(2):129-138

December 2015
The zebrafish mutant, lessen, an appropriate experimental model for human pediatric ENS motility disorders.
Leen Uyttebroek, Iain T. Shepherd, Guy Hubens, Jean-Pierre Timmermans and Luc Van Nassauw (2015). Neurogastroenterology and Motility 28: 345-57

December 2014
In vivo visualization of the development of the enteric nervous system using a Tg(-8.3bphox2b:Kaede) transgenic zebrafish.
Harrison C, Wabbersen T, Shepherd IT. Genesis. 2014 Dec;52(12):985-90. doi: 10.1002/dvg.22826. Epub 2014 Nov 4.

November 2013
Expression of neuropeptides and anoctamin 1 in the embryonic and adult zebrafish intestine, revealing neuronal subpopulations and ICC-like cells.
Uyttebroek, Leen; Shepherd, Iain; Hubens, Guy; Timmermans, Jean-Pierre; Van Nassauw, Luc (2013). Cell and Tissue Research 354(2): 355-70.

Sam Sober
February 2017
Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.
Tabler JM, Rigney MM, Berman GJ, Gopalakrishnan S, Heude E, Al-Lami HA, Yannakoudiadkis BZ, Fitch RD, Carter C, Vokes S, Liu KJ, Tajbakhsh S, Egnor SR, Wallingford JB. Elife. 2017 Feb 13;6. pii: e19153. doi: 10.7554/eLife.19153.

January 2017
Motor control by precisely timed spike patterns.
Srivastava KH, Holmes CM, Vellema M, Pack AR, Elemans CP, Nemenman I, Sober SJ. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1171-1176. doi: 10.1073/pnas.1611734114. Epub 2017 Jan 18.

February 2016
Dopaminergic Contributions to Vocal Learning.
Hoffmann LA, Saravanan V, Wood AN, He L, Sober SJ. J Neurosci. 2016 Feb 17;36(7):2176-89. doi: 10.1523/JNEUROSCI.3883-15.2016.

November 2015
Universal mechanisms of sound production and control in birds and mammals.
Elemans CP, Rasmussen JH, Herbst CT, Düring DN, Zollinger SA, Brumm H, Srivastava K, Svane N, Ding M, Larsen ON, Sober SJ, Švec JG. Nat Commun. 2015 Nov 27;6:8978. doi: 10.1038/ncomms9978.

December 2014
Millisecond-scale motor encoding in a cortical vocal area.
Tang C, Chehayeb D, Srivastava K, Nemenman I, Sober SJ. PLoS Biol. 2014 Dec 9;12(12):e1002018. doi: 10.1371/journal.pbio.1002018. eCollection 2014 Dec.

April 2014
Vocal generalization depends on gesture identity and sequence.
Hoffmann LA, Sober SJ. J Neurosci. 2014 Apr 16;34(16):5564-74. doi: 10.1523/JNEUROSCI.5169-13.2014.

Rachelle Spell
March 2014
Redefining Authentic Research Experiences in Introductory Biology Laboratories and Barriers to Their Implementation
Spell RM, Guinan JA, Miller KR, Beck CW. CBE Life Sci Educ. 2014 Spring;13(1):102-10. doi: 10.1187/cbe.13-08-0169.

Barry Yedvobnick, Emeritus
November 2015
Drosophila domino Exhibits Genetic Interactions with a Wide Spectrum of Chromatin Protein-Encoding Loci
Ellis K, Friedman C, Yedvobnick B (2015) PLoS ONE 10(11): e0142635. doi:10.1371/journal.pone.0142635

May 2013
A targeted genetic modifier screen links the SWI2/SNF2 protein Domino to growth and autophagy genes in Drosophila melanogaster.
Kwon MH, Callaway H, Zhong J, Yedvobnick B. G3 (Bethesda). 2013 May 20;3(5):815-25. doi: 10.1534/g3.112.005496.

September 2010
Linking model systems to cancer therapeutics: the case of Mastermind.
Yedvobnick, B. and K. Moberg. 2010. Disease Models and Mechanisms: 3: 540-544.

August 2009
Targeted gain-of-function screening in Drosophila using GAL4-UAS and random transposon insertions.
Zhong J, Yedvobnick B. Genet Res. 2009 Aug;91(4):243-58.

November 2008
A male-specific effect of dominant negative Fos.
Pierre W, Morra R, Lucchesi J, Yedvobnick B. Dev Dyn. 2008 Nov;237(11):3361-72. doi: 10.1002/dvdy.21751.

Shozo Yokoyama, Emeritus
March 2017
Possible Roles of New Mutations Shared by Asian and American Zika Viruses.
Yokoyama S, Starmer WT. Mol Biol Evol. 2017 Mar 1;34(3):525-534. doi: 10.1093/molbev/msw270.

March 2016
A simple method for studying the molecular mechanisms of ultraviolet and violet reception in vertebrates.
Yokoyama S, Tada T, Liu Y, Faggionato D, Altun A. BMC Evol Biol. 2016 Mar 22;16(1):64. doi: 10.1186/s12862-016-0637-9.

September 2015
Adaptive evolutionary paths from UV reception to sensing violet light by epistatic interactions.
Yokoyama S, Altun A, Jia H, Yang H, Koyama T, Faggionato D, Liu Y, Starmer WT. Sci Adv. 2015 Sep 18;1(8):e1500162. doi: 10.1126/sciadv.1500162. eCollection 2015 Sep.

August 2015
Spectral Tuning of Phototaxis by a Go-Opsin in the Rhabdomeric Eyes of Platynereis.
Gühmann M, Jia H, Randel N, Verasztó C, Bezares-Calderón LA, Michiels NK, Yokoyama S, Jékely G. Curr Biol. 2015 Aug 31;25(17):2265-71. doi: 10.1016/j.cub.2015.07.017. Epub 2015 Aug 6.

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