Ori Department of Biology | Emory University
Department of Biology
Latest Publications

List of current publications.

Rustom Antia
August 2020
T cell receptor diversity and lineage relationship between virus-specific CD8 T cell subsets during chronic LCMV infection
22. Chang YM, Wieland A, Li ZR, Im SJ, McGuire DJ, Kissick HT, Antia R, Ahmed R. (2020). J Virol. 2020 Aug 5:JVI.00935-20. doi: 10.1128/JVI.00935-20. Online ahead of print.

July 2020
Adjuvanted H5N1 influenza vaccine enhances both cross-reactive memory B cell and strain-specific naive B cell responses in humans
Ellebedy AH, Nachbagauer R, Jackson KJL, Dai YN, Han J, Alsoussi WB, Davis CW, Stadlbauer D, Rouphael N, Chromikova V, McCausland M, Chang CY, Cortese M, Bower M, Chennareddy C, Schmitz AJ, Zarnitsyna VI, Lai L, Rajabhathor A, Kazemian C, Antia R, Mulligan MJ, Ward AB, Fremont DH, Boyd SD, Pulendran B, Krammer F, Ahmed R. (2020). PNAS USA. 117:17957-17964.

March 2020
Successes and failures of the live-attenuated influenza vaccine: can we do better?
Matrajt L, Halloran ME, and Antia R. (2020). Clinical Infectious Diseases 70:1029-37.

March 2020
Varying Inoculum Dose to Assess the Roles of the Immune Response and Target Cell Depletion by the Pathogen in Control of Acute Viral Infections
20. Moore JR, Ahmed H, Manicassamy B, Garcia-Sastre A, Handel A, and Antia R. (2020). Bulletin of Mathematical Biology 82:35.

August 2019
A dynamical motif comprising the interactions between antigens and CD8 T cells may underlie the outcomes of viral infections
Baral S, Antia R, and Dixit NM. (2019). Proceedings of the National Academy of Sciences USA. 116:17393-17398.

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
July 2020
Application of the hierarchical bootstrap to multi-level data in neuroscience
Saravanan, V, Berman, GJ, and Sober, SJ. Neurons, Behavior, Data Analysis, and Theory, 2020.

June 2018
Optogenetic dissection of descending behavioral control in Drosophila
Cande, J, Namiki S, Qiu, J, Korff, W, Card, G, Shaevitz, JW, Stern, DL, and Berman, GJ. eLife, 7, 2018, e34275.

February 2018
Measuring behavior across scales
Berman, GJ. BMC Biology, 16, 2018, 23.

November 2017
Instantaneous Brain Dynamics Mapped to a Continuous State Space
Billings, JC, Medda, A, Shakil, S, Shen, X, Kashyap, A, Chen, S, Abbas, A, Zhang, X, Nezafati, M, Pan, W, Berman, GJ, and Keilholz, SD. NeuroImage, 162, 2017, 344-352.

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

Patrick Cafferty
March 2021
Adaptation and facilitation of small group activities in an online introductory biology class
Cafferty, P. (2021) CourseSource.

January 2021
Taking the office hour out of the office.
 Journal of College Science Teaching. 50(3)

August 2020
Teaching a flipped, fully online class using small group work.
Cafferty, P. (2020) HAPS Educator. Special Edition:55-61.

August 2019
Electrical and chemical communication in the nervous system
Cafferty, P. (2019) HHMI BioInteractive A&P FMN (2019), QUBES Educational Resources.

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
January 2020
Resource fluctuations inhibit the reproduction and virulence of the human parasite Schistosoma mansoni in its snail intermediate host
Civitello, DJ, LH Baker, S Maduraiveeran, RB Hartman. 2020. Proc. Roy. Soc. B. 287: 20192446.

March 2018
Bioenergetic theory predicts infection dynamics of human schistosomes in intermediate host snails across ecological gradients
Civitello, DJ, H Fatima, LR Johnson, RM Nisbet, and JR Rohr. 2018. Ecology Letters 21:692-701.

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.

July 2015
Biodiversity inhibits natural enemies: Broad evidence for the dilution effect
Civitello, DJ, J Cohen, H Fatima, N Halstead, J Liriano, TA McMahon, CN Ortega, E Sauer, T Sehgal, S Young, JR Rohr. 2015. Proceedings of the National Academy of Sciences of the USA.112:8667-8671.

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
June 2018
Effect of Diet on Bean Beetle Microbial Communities
Megan F. Cole, Tarik Acevedo-Gonzalez, Nicole M. Gerardo, Erica V. Harris, and Christopher W. Beck. Tested Studies for Laboratory Teaching 39: article 3. (2018)

October 2017
As long as you are here, can I interest you in some science? Increasing student engagement by co-opting a social networking site, Facebook for science discussion
Pai A., Cole M, Kovacs J, Lee M, Stovall K, and McGinnis G. J. of Ed. Tech. Systems. 46(2), 153-177. (2017).

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.

September 2005
Core transcriptional regulatory circuitry in human embryonic stem cells
Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA. Cell. 2005 Sep 23;122(6):947-56. doi: 10.1016/j.cell.2005.08.020. PMID: 16153702; PMCID: PMC3006442.

Anita Corbett
July 2020
Dissecting the Roles of Cse1 and Nup2 in Classical NLS Cargo Release in vivo
A. Lange, M.B. Fasken, M. Stewart, and A.H. Corbett (2020) Traffic. Selected for cover image.

July 2020
A Drosophila Model of Pontocerebellar Hypoplasia Reveals a Critical Role for the RNA Exosome in Neurons
D.J. Morton, B. Jalloh, L. Kim, I. Kremsky, R.J. Nair, K.B. Nguyen, J.C. Rounds, M.C. Sterrett, B. Brown, T. Le, M.C. Karkare, K.D. McGaughey, S. Sheng, S.W. Leung, Milo B. Fasken, K.H. Moberg, and A.H. Corbett (2020) PLOS Genetics16, e1008901. PMCID in progress.

March 2019
Proteomic analysis reveals that wildtype and alanine-expanded nuclear poly(A)-binding protein exhibit differential interactions in skeletal muscle
A. Banerjee, K.E. Vest, Q. Deng, N.T. Seyfried, G.K. Pavlath and A.H. Corbett (2019) J. Biol. Chem. 294, 7360-7376.

June 2018
The Polyadenosine RNA Binding Protein ZC3H14 Interacts with the THO Complex and Coordinately Regulates the Processing of Neuronal Transcripts
K.J. Morris and A.H. Corbett (2018) Nucl Acids Res 46, 6561-6575.

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]

Jaap De Roode
June 2020
Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance
Talla, V., Pierce, A.A., Adams, K.L., de Man, T.J.B., Nallu, S., Villablanca, F.X., Kronforst, M.K. & de Roode, J.C. Molecular Ecology 29, 2567-2582.

May 2019
Reduced density and visually complex apiaries reduce parasite load and promote honey production and overwintering survival in honey bees
Dynes, T.L., Berry, J.A., Delaplane, K.S., Brosi, B.J. & de Roode, J.C. (2019). PLoS One 14, e0216286.

September 2018
Demystifying monarch butterfly migration
Reppert, S.M. & de Roode, J.C. (2018). Current Biology 28, R1009-R1022.

August 2018
Within-host competition can delay evolution of drug resistance in malaria
Bushman, M., Antia, R., Udhayakumar, V. & de Roode, J.C. (2018). PLoS Biology 16, e2005712.

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.

Roger Deal
September 2019
Evolutionary flexibility in flooding response circuitry in angiosperms
Reynoso MA, Kajala K, Bajic M1, West DA, Pauluzzi G, Yao AI, Hatch K3, Zumstein K, Woodhouse M, Rodriguez-Medina J, Sinha N*, Brady SM*, Deal RB*, Bailey-Serres J*. (2019). Science. 365: 1291-1295. *Co-corresponding authors.

August 2019
Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome
Sijacic P, Holder DH, Bajic M, Deal RB. (2019). PLoS Genetics. 15: e1008326

July 2019
The Histone Variant H2A.Z and Chromatin Remodeler BRAHMA Act Coordinately and Antagonistically to Regulate Transcription and Nucleosome Dynamics in Arabidopsis
Torres ES, Deal RB. (2019). Plant Journal. 99: 144-162.

April 2018
Chromatin Accessibility Changes Between Arabidopsis Stem Cells and Mesophyll Cells Illuminate Cell Type-specific Transcription Factor Networks
Sijacic P, Bajic M, McKinney EC, Meagher RB, Deal RB. (2018). Plant Journal. 94: 215-231.

January 2018
Profiling of Accessible Chromatin Regions Across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules
Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West D, Zumstein K, Woodhouse M, Bubb K, Dorrity M, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. (2018). Plant Cell. 30: 15-36.

Arri Eisen
March 2020
A New Model for Increasing Diversity in STEM Faculty
Eisen, A. Issues in Science and Technology 36, no. 3 (Spring 2020): 26-33

March 2018
A model for postdoctoral education that promotes minority and majority success in the biomedical sciences
Eisen, A. and D. Eaton. CBE-Life Sciences, 16(4), 2017.

November 2017
Ethical principles for the use of human cellular biotechnologies
Wolpe, P.R., K. S. Rommelfanger,... A. Eisen, and the Drafting and Reviewing Delegates of the BEINGS Working Groups. Nature Biotechnology 35, 1050¿1058 (2017).

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

Alexander Escobar
September 2020
Could Striate Cortex Microcolumns Serve as the Neural Correlates of Visual Consciousness?
Athens Journal of Sciences, Sep 2020, Vol 7(3), pp127-142. Doi: 10.30958/ajs.7-3-1

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
August 2020
Evolution of animal immunity in the light of beneficial symbioses
Gerardo, N.M., Hoang, K.L. & K.S. Stoy. 2020. Philosophical Transactions of the Royal Society B 375: 20190601

July 2019
Even obligate symbioses show signs of ecological contingency: impacts of symbiosis for an invasive stinkbug are mediated by host plant context
Couret, J., Griffin-Huynh, L., Antolic-Soban, I, Acevedo-Gonzalez, T.S & N.M. Gerardo. 2019. Ecology and Evolution. 9:9087¿9099.

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.

September 2016
Experimental evolution as an underutilized tool for studying beneficial animal¿microbe interactions
Hoang, K., Morran, L. & N.M. Gerardo. 2016. Frontiers in Microbiology. 7:1444.

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.

David Gorkin
July 2020
An atlas of dynamic chromatin landscapes in mouse fetal development
Gorkin*, Barozzi*, Zhang*, Zhao*, Huang*, Lee, Li, Chiou, Wildberg, Ding, Zhang, Wang, Strattan, Davidson, Qiu, Afzal, Akiyama, Plajzer-Frick, Novak, Kato, Garvin, Pham, Harrington, Mannion, Lee, Fukuda-Yuzawa, He, Preissl, Chee, Han, Williams, Trout, Amrhein, Yang, Cherry, Wang, Gaulton, Ecker, Shen, Dickel, Visel, Pennacchio, Ren. . Nature. 2020 Jul;583(7818):744-751.

November 2019
Common DNA sequence variation influences 3-dimensional conformation of the human genome
Gorkin DU*, Qiu Y*, Hu M*, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B. Genome Biol. 2019 Nov 28;20(1):255.

August 2015
A method to predict the impact of regulatory variants from DNA sequence
Lee D*, Gorkin DU*, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer MA. Nat Genet. 2015 Aug;47(8):955-61.

June 2014
The 3D genome in transcriptional regulation and pluripotency
Gorkin DU, Leung D, Ren B. Cell Stem Cell. 2014 Jun 5;14(6):762-75.

November 2012
Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. Genome Res. 2012 Nov;22(11):2290-301.

Dieter Jaeger
December 2019
Unilateral Optogenetic Inhibition and Excitation of Basal Ganglia Output Affect Directional Lick Choices and Movement Initiation in Mice
Morrissette AE, Chen PH, Bhamani C, Borden PY, Waiblinger C, Stanley GB, Jaeger D (2019). Neuroscience 423:55-65.

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.

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.

William Kelly
May 2017
KDM1A/LSD1 regulates the differentiation and maintenance of spermatogonia in mice
Myrick DA, Christopher MA, Scott AM, Simon AK, Donlin-Asp PG, Kelly WG, Katz DJ. 2017. PLoS One. 12(5):e0177473. PMID: 28498828

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.

Katia Koelle
May 2020
Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Miller, D.*, Martin, M.A.*, Harel, N.*, Kustin, T*, Tirosh, O.*, Meir, M., Sorek, N., Gefen-Halevi, S, Amit, S., Vorontsov, O., Wolf, D., Peretz, A., Shemer-Avni, Y., Roif-Kaminsky, D., Kopelman, N., Huppert, A., Koelle, K., and A.Stern (in press). Nature Communications. (medRxiv)

July 2019
Within-host infectious disease models accommodating cellular coinfection, with an application to influenza
Koelle, K., Farrell, A., Brooke, C., and R. Ke (2019). Virus Evolution.

November 2018
Causes and consequences of spatial within-host viral spread
Gallagher, M. E., Brooke, C.B., Ke, R., and K. Koelle (2018). Viruses.

June 2018
Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context
Ben-Shachar, R. and K. Koelle (2018). Nature Communications.

May 2017
Transmission bottleneck size estimation from pathogen deep-sequencing data, with an application to human influenza A virus
Sobel Leonard, A., Weissman, D., Greenbaum, B., Ghedin, E., and K. Koelle (2017). Journal of Virology.

Steven L'Hernault, Chairman
May 2018
MIB-1 Is required for spermatogenesis and facilitates LIN-12 and GLP-1 activity in Caenorhabditis elegans
Ratliff, M., K. L. Hill-Harfe, E. J. Gleason, H. Ling, T. L. Kroft and S. W. L'Hernault Genetics 209: 173-193.

September 2017
Spermatogenesis
Nishimura, H. and S. W. L'Hernault 2017. Curr. Biol. 27: R988-994.

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., T. Tajima, H. S. Comstra, E. J. Gleason and S. W. L'Hernault 2015. Curr Biol. 25: 3225-3231

December 2013
Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes
Tornieri, K., S. Zlatic, A. Mullin, E. Werner, R. Harrison, S. W. L'Hernault and V. Faundez 2013. Hum. Mol. Genet. 22: 5215-5228.

Bruce Levin
August 2018
Leaky resistance and the conditions for the existence of lytic bacteriophage
Chaudhry WN, Pleska M, Shah NN, Weiss H, McCall IC, Meyer JR, Gupta A, Guet CC, Levin BR. (2018). PLoS Biol 16:e2005971.

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.

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.

March 2013
The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity
Levin, B.R., S. Moineau, M. Bushman, R. Barrangou 2013. PLoS Genetics 9: 3 e1003312

March 2011
The Population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility
Wei,Y. X. Wang, J Liu, I Nemenman, A. H. Singh, H Weiss, and B.R. Levin 2011. PNAS 108:4047-4052

Robert Liu
May 2020
Becoming a better parent: mice learn sounds that improve a stereotyped maternal behavior
A. G. Dunlap, C. Besosa, L. M. Pascual, K. K. Chong, H. Walum, D. B. Kacsoh, B. B. Tankeu, K. Lu and R. C. Liu. Hormones and Behavior 124: 104779 (May 2020). doi: 10.1016/j.yhbeh.2020.104779.

April 2020
Experience-Dependent Coding of Time-Dependent Frequency Trajectories by Off Responses in Secondary Auditory Cortex
K. K. Chong, D. B. Anandakumar, A. G. Dunlap, D. B. Kacsoh and R. C. Liu. Journal of Neuroscience 40(23): 4469-4482 (April 2020). doi: 10.1523/JNEUROSCI.2665-19.2020

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.
E. A. Amadei*, Z. V. Johnson*, Y. J. Kwon, A. C. Shpiner, V. Saravanan, W. Mays, S. Ryan, H. Walum, D. Rainnie, L. J. Young and R. C. Liu. Nature 546(7657): 297-301 (May 2017) PMC5499998 doi: 10.1038/nature22381.

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.

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

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.

Levi Morran
June 2020
The evolution of parasite host range in heterogeneous host populations
Gibson AK, Baffoe-Bonnie H, Penley MJ, Lin J, Owens R, Khalid A, Morran LT.J Evol Biol. 2020 Jun;33(6):773-782. doi: 10.1111/jeb.13608.

January 2020
Host heterogeneity mitigates virulence evolution
White PS, Choi A, Pandey R, Menezes A, Penley M, Gibson AK, de Roode J, Morran L.Biol Lett. 2020 Jan;16(1):20190744. doi: 10.1098/rsbl.2019.0744.

September 2019
Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes
Cutter AD, Morran LT, Phillips PC.Genetics. 2019 Sep;213(1):27-57. doi: 10.1534/genetics.119.300244.

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.

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.

Malavika Murugan
August 2019
Choice-selective sequences in cortical inputs to the NAc provide a potential substrate for credit assignment
N.F. Parker, A. Baidya, M. Murugan, B. Engelhard, A. Zhukovskaya, M.S. Goldman, I.B. Witten. (2019). bioRxiv.

July 2019
Increased Cocaine Motivation Is Associated with Degraded Spatial and Temporal Representations in IL-NAc Neurons
C Cameron, M. Murugan, CY Choi JY,I.B. Witten. (2019). Neuron.

December 2017
Combined social and spatial coding in a descending projection from the prefrontal cortex
M. Murugan, H.J. Jang, M. Park, E.M. Miller, J. Cox, J.P. Taliaferro, N.F. Parker, V. Bhave, H. Hur, Y. Liang, A.R. Nectow, J.W. Pillow1, I.B. Witten. (2017). Cell.

December 2013
Diminished FoxP2 levels affect dopaminergic modulation of corticostriatal signaling important to song variability
M. Murugan, S. Harward, C. Scharff, R. Mooney. (2013). Neuron (Cover article).

September 2012
Motor circuits are required to encode a sensory model for imitative learning
T.F. Roberts, S.M.H. Gobes, M. Murugan, B.P. Olveczky, R. Mooney. (2012). Nature Neuroscience.

Edward Nam
August 2016
ERF11 Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling Pathways in Arabidopsis
X, Zhang Z-L, Tyler L, Yusuke J, Qiu K, Park J, Nam EA, Lumba S, Desveaux D, McCourt P, Kamiya Y, and Sun T-p. (2016). Plant Physiology 171(4): 2760-70.

October 2015
Gene Prioritization by Compressive Data Fusion and Chaining
Žitnick M, Nam EA, Dinh C, Kuspa A, Shaulsky G, and Zupan B. (2015). PLoS Computational Biology. 11: e1004552.

January 2015
The ABC transporter, AbcB3, mediates cAMP export in D. discoideum development
Nam, EA, Miranda, ER, Kuspa A, and Shaulsky G. (2015). Developmental Biology. 397: 203-211.

Ilya Nemenman
May 2020
Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons
A Sederberg, I Nemenman. PLOS Computational Biology 16 (5), e1007875, 2020.

November 2019
Physical limit to concentration sensing in a changing environment
T Mora, I Nemenman. Physical review letters 123 (19), 198101, 2019.

April 2019
Automated, predictive, and interpretable inference of Caenorhabditis elegans escape dynamics
BC Daniels, WS Ryu, I Nemenman. Proceedings of the National Academy of Sciences 116 (15), 7226-7231, 2019.

August 2018
Chance, long tails, and inference in a non-Gaussian, Bayesian theory of vocal learning in songbirds
B Zhou, D Hofmann, I Pinkoviezky, SJ Sober, I Nemenman. Proceedings of the National Academy of Sciences 115 (36), E8538-E8546, 2018.

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.

Astrid Prinz
July 2019
Building and replicating models of visual search behavior with Tensorflow, Nengo, and the scientific Python stack
Nicholson D, Prinz A (2019). SciPy 2019, Austin, TX.

April 2019
Dramatically Amplified Thoracic Sympathetic Postganglionic Excitability and Integrative Capacity Revealed with Whole-Cell Patch-Clamp Recordings
McKinnon ML, Tian K, Li Y, Sokoloff AJ, Galvin ML, Choi MH, Prinz A, Hochman S (2019). eNeuro 6(2) e0433-18.2019: 1¿18.

September 2018
Rhythmic Pattern Generation in Invertebrates
Prinz AA (2018). In: Byrne JH, ed. The Oxford Handbook of Invertebrate Neurobiology. Oxford University Press: DOI: 10.1093/oxfordhb/9780190456757.013.17.

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.

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.

Leslie Real, Emeritus
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.

Leila Rieder
December 2019
Targeting of the dosage-compensated male X-chromosome during early Drosophila development
Rieder, LE*, WT Jordan III*, EN Larschan (2019). Cell Reports 29(13): 4268-4275. *Equal contributors

July 2017
Histone locus body regulation by the D. melanogaster dosage compensation adaptor protein CLAMP
Rieder, LE*, KP Koreski*, KA Boltz, G Kuzu, JA Urban, S Bowman, A Zeidman, WT Jordan, III, MY Tolstrukov, WF Marzluff, RJ Duronio, EN Larschan (2017). Genes and Development 31(14): 1494-1508. *Equal contributors

June 2016
Wisdom from the fly
Rieder, LE, EN Larschan (2014). Trends in Genetics 30(11): 479-81.

January 2015
Dynamic response of RNA editing to temperature in Drosophila
Rieder, LE, YA Savva, MA Reyna, YJ Chang, JS Dorsky*, A Rezaei*, RA Reenan (2015). BMC Biology 13(1): 1. *Highly Accessed

August 2013
Tertiary structural elements determine the extent and specificity of messenger RNA editing
Rieder, LE, CJ Staber, B Hoopengardener, RA Reenan (2013). Nature Communications 4: 2232.

Iain Shepherd
July 2018
Identification of Variants in RET and IHH Pathway Members in a Large Family With History of Hirschsprung Disease
Y. Sribudiani, R.K. Chauhan, M.M. Alves, L. Petrova, E. Brosens, C.Harrison, T. Wabbersen, B.M. de Graaf, T. Ru¿genbrinck, G. Burzynski, R.W.W. Brouwer, W.F.J. van IJcken, S.M. Maas, A. de Klein, J. Osinga6, B.J.L. Eggen, A.J. Burns, A.S. Brooks, I.T. Shepherd, R.M.W. Hofstra. (2018). Gastroenterology 155(1) 118-129.

October 2016
Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes.
Gui H, et al. (2017) Genome Biology 18(1):48. doi: 10.1186/s13059-017-1174-6.

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.

Sam Sober
April 2020
Application of the hierarchical bootstrap to multi-level data in neuroscience
Saravanan V, Berman GJ, Sober SJ (2020). Neurons, Behavior, Data analysis, and Theory 3;5.

October 2018
Millisecond Spike Timing Codes for Motor Control
Sober SJ, Sponberg S, Nemenman I, Ting LH (2018). Trends in Neurosciences 41(10):644-648.

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.

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.

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.

Jitendra Thakur
September 2019
Architectural RNA is required for heterochromatin organization
Thakur J, Fang H, Llagas T, Disteche CM, Henikoff S. (2019) . biorxiv doi: https://doi.org/10.1101/784835

January 2018
Unexpected conformational variations of the human centromeric chromatin complex
Thakur J, Henikoff S. (2018). Genes & Dev. 32:20-25

July 2016
CENP-T bridges adjacent CENP-A nucleosomes on young human ¿-satellite dimers
Thakur J, Henikoff S. (2016). Genome Res. Sep;26(9):1178-87

February 2013
Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans
Thakur J, Sanyal K. (2013). Genome Res. Apr;23(4):638-52.

December 2008
Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts, Candida albicans and Candida dubliniensis
Padmanabhan S*, Thakur J*, Siddharthan R, Sanyal K. (2008). Proc Natl Acad Sci U S A. Dec 16;105(50):19797-802. * S.P and * J.T. equal contribution.

Nic Vega
October 2019
Simple Organizing Principles in Microbial Communities
Vega, NM., and Jeff Gore. 2018. Current Opinion in Microbiology, Antimicrobials * Microbial systems biology, 45 (October): 195¿202.

October 2019
The Population and Evolutionary Dynamics of Bacteriophage: Why Be Temperate Revisited
Chaudhry, Waqas, Nicole Vega, Adithi R. Govindan, Rodrigo Garcia, Esther Lee, Ingrid C. McCall, and Bruce R. Levin. 2019. BioRxiv, October, 824235.

February 2019
Experimental Evolution Reveals Microbial Traits for Association with the Host Gut
Vega, NM. 2019. PLOS Biology 17 (2): e3000129.

March 2017
Stochastic Assembly Produces Heterogeneous Communities in the Caenorhabditis Elegans Intestine
Vega, NM., and Jeff Gore. 2017. PLOS Biology 15 (3): e2000633. https://doi.org/10.1371/journal.pbio.2000633.

March 2012
Signaling-Mediated Bacterial Persister Formation
Vega, Nicole M., Kyle R. Allison, Ahmad S. Khalil, and James J. Collins. 2012. Nature Chemical Biology 8 (5): 431¿33.

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

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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