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• Sotola VA, CS Berg, M Samuli, H Chen, SJ Mantel, P A Beardsley, YW Yuan, AL Sweigart, L Fishman. 2023. Genomic mechanisms and consequences of diverse postzygotic barriers between monkeyflower species. Genetics 225.
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• Sandstedt GB, CA Wu, AL Sweigart. 2021. Evolution of multiple postzygotic barriers between species of the Mimulus tilingii complex. Evolution 75: 600-613. 
• Kerwin RE and AL Sweigart. 2020. Rampant misexpression in a Mimulus (monkeyflower) introgression line caused by hybrid sterility, not regulatory divergence. Molecular Biology and Evolution 37: 2084-2098. 
• Mantel SJ and AL Sweigart. 2019. Divergence in drought response traits between sympatric species of Mimulus. Ecology and Evolution 9: 10291-10304. 
• Flagel LE, BK Blackman, L Fishman, PJ Monnahan, AL Sweigart, JK Kelly. 2019. GOOGA: A a platform to synthesize mapping experiments and identify genomic structural diversity. PLoS Computational Biology 15: e1006949.
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• Kenney AM and AL Sweigart. 2016. Reproductive isolation and introgression between sympatric Mimulus species. Molecular Ecology 25: 2499-2517.
• Ahmed-Braimah YH and AL Sweigart. 2015. A single gene causes an interspecific difference in pigmentation in Drosophila. Genetics 200: 331-342.
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• Zuellig MP, AM Kenney, AL Sweigart. 2014. Evolutionary genetics of plant adaptation: insights from new model systems. Curr. Opin. Plant Biol. 18: 44-50.
• Fishman L, AL Sweigart, AM Kenney, S Campbell. 2014. Major QTLs control divergence in critical photoperiod for flowering between selfing and outcrossing species of monkeyflower (Mimulus). New Phytologist 201: 1498-1507.

• Cunningham CB, Shelby EA, McKinney EC, Schmitz RJ, Moore AJ, Moore PJ. The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus. Epigenetics & Chromatin 2023

• Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. The Plant Journal 2023

• Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination. Nucleic Acids Research 2023

• Ivasyk I, Olivos-Cisneros L, Valdés-Rodríguez S, Droual M, Jang H, Schmitz RJ, Kronauer DJC. DNMT1 mutant ants develop normally but have disrupted oogenesis. Nature Communications 2023

• Murray A, Vollmers C, Schmitz RJ. Smar2C2: A simple and efficient protocol for the identification of transcription start sites. Current Protocols 2023

• Yao N, Zhang Z, You L, Hazarika R, Yu C, Jang H, Smith LM, Ton J, Liu L, Stachowicz J, Reusch TBH, Schmitz RJ, Johannes F. An evolutionary epigenetic clock in plants. bioRxiv 2023

• Zee A, Deng DZQ, Adams M, Schimke KD, Corbett-Detig R, Russell SL, Zhang X, Schmitz RJ, Vollmers C: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2. Genome Res 2022.

• Tu X, Marand AP, Schmitz RJ, Zhong S: A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells. Plant Commun 2022, 3:100308.

• Schmitz RJ, Mittelsten Scheid O: Editorial overview: COPB issue 2022 on "epigenetics and gene regulation". Curr Opin Plant Biol 2022, 70:102305.

• Murray A, Mendieta JP, Vollmers C, Schmitz RJ: Simple and Accurate Transcriptional Start Site Identification Using Smar2C2 and Examination of Conserved Promoter Features. Plant J 2022.

• Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rossner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theissen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH: Dynamic genome evolution in a model fern. Nat Plants 2022.

• Hazarika RR, Serra M, Zhang Z, Zhang Y, Schmitz RJ‡, Johannes F‡: Molecular properties of epimutation hotspots. Nat Plants 2022, 8:146-156.

• Bewg WP, Harding SA, Engle NL, Vaidya BN, Zhou R, Reeves J, Horn TW, Joshee N, Jenkins JW, Shu S, Barry KW, Yoshinaga Y, Grimwood J, Schmitz RJ, Schmutz J, Tschaplinski TJ, Tsai CJ: Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant Physiol 2022, 189:516-526.

• Bang S, Galli M, Crisp PA, Gallavotti A, Schmitz RJ: Identifying transcription factor–DNA interactions using machine learning. in silico Plants 2022, 4.

• Zhang Y, Jang H, Xiao R, Kakoulidou I, Piecyk RS, Johannes F‡, Schmitz RJ‡: Heterochromatin is a quantitative trait associated with spontaneous epiallele formation. Nat Commun 2021, 12:6958.

• Yocca AE, Lu Z, Schmitz RJ, Freeling M, Edger PP: Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana. Mol Biol Evol 2021, 38:2692-2703.

• Yao N, Schmitz RJ, Johannes F: Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends Genet 2021, 37:699-710.

• Xu X, Crow M, Rice BR, Li F, Harris B, Liu L, Demesa-Arevalo E, Lu Z, Wang L, Fox N, Wang X, Drenkow J, Luo A, Char SN, Yang B, Sylvester AW, Gingeras TR, Schmitz RJ, Ware D, Lipka AE, Gillis J, Jackson D: Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell 2021, 56:557-568 e556.

• Washington JT, Cavender KR, Amukamara AU, McKinney EC, Schmitz RJ, Moore PJ: The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus. Elife 2021, 10.

• Schmitz RJ, Marand AP, Zhang X, Mosher RA, Turck F, Chen X, Axtell MJ, Zhong X, Brady SM, Megraw M, Meyers BC: Quality control and evaluation of plant epigenomics data. Plant Cell 2021.

• Schmitz RJ, Grotewold E, Stam M: Cis-regulatory sequences in plants: their importance, discovery, and future challenges. Plant Cell 2021.

• Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE: Anno genominis XX: 20 years of Arabidopsis genomics. Plant Cell 2021, 33:832-845.

• Noshay JM, Marand AP, Anderson SN, Zhou P, Mejia Guerra MK, Lu Z, O'Connor CH, Crisp PA, Hirsch CN, Schmitz RJ, Springer NM: Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics 2021, 217:1-13.

• Noshay JM, Liang Z, Zhou P, Crisp PA, Marand AP, Hirsch CN, Schmitz RJ, Springer NM: Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (Bethesda) 2021, 11.

• Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S: Chromatin accessibility profiling methods. Nature Reviews Methods Primers 2021, 1.

• Mendieta JP, Marand AP, Ricci WA, Zhang X, Schmitz RJ: Leveraging histone modifications to improve genome annotations. G3 (Bethesda) 2021, 11.

• Marand AP, Zhang X, Nelson J, Braga Dos Reis PA, Schmitz RJ: Profiling single-cell chromatin accessibility in plants. STAR Protoc 2021, 2:100737.

• Marand AP, Schmitz RJ: Single-cell analysis of cis-regulatory elements. Curr Opin Plant Biol 2021, 65:102094.

• Marand AP‡, Chen Z, Gallavotti A, Schmitz RJ‡: A cis-regulatory atlas in maize at single-cell resolution. Cell 2021, 184:3041-3055 e3021.

• Kamei M, Ameri AJ, Ferraro AR, Bar-Peled Y, Zhao F, Ethridge CL, Lail K, Amirebrahimi M, Lipzen A, Ng V, Grigoriev IV, Schmitz RJ, Liu Y, Lewis ZA: IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains. Proc Natl Acad Sci U S A 2021, 118.

• Jordan WT, Currie S, Schmitz RJ: Multiplex genome editing in Arabidopsis thaliana using Mb3Cas12a. Plant Direct 2021, 5:e344.

• Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, 2nd, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK: De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021, 373:655-662.

• Ferraro AR, Ameri AJ, Lu Z, Kamei M, Schmitz RJ, Lewis ZA: Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin. BMC Genomics 2021, 22:459.

• Zhang Y, Wendte JM, Ji L, Schmitz RJ: Natural variation in DNA methylation homeostasis and the emergence of epialleles. Proc Natl Acad Sci U S A 2020, 117:4874-4884.

• Wang T, Kwon SH, Peng X, Urdy S, Lu Z, Schmitz RJ, Dalton S, Mostov KE, Zhao S: A Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis. iScience 2020, 23:101629.

• Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, van Gurp T, Colome-Tatche M, Verhoeven KJF, Tuskan G, Schmitz RJ, Johannes F: AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol 2020, 21:260.

• Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R: Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PLoS Genet 2020, 16:e1008390.

• Hofmeister BT, Denkena J, Colome-Tatche M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Jacobsen D, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 2020, 21:259.

• Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA: The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. G3 (Bethesda) 2020, 10:1457-1467.

• Crisp PA, Marand AP, Noshay JM, Zhou P, Lu Z, Schmitz RJ, Springer NM: Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proc Natl Acad Sci U S A 2020, 117:23991-24000.

• Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X‡, Schmitz RJ‡. (2019) The prevalence, evolution and chromatin signatures of plant regulatory elements. Nature Plants

• Ricci WA*, Lu Z*, Ji L*, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ‡, Zhang X‡. (2019) Widespread long-range cis-regulatory elements in the maize genome. Nature Plants

• Dekker JD*, Baracho GV*, Zhu Z, Ippolito GC, Schmitz RJ, Rickert RC, Tucker HO. (2019) Loss of the FOXP1 Transcription Factor Leads to Deregulation of B Lymphocyte Development and Function at Multiple Stages. Immuno Horizons

• Drinnenberg IA‡, Berger F‡, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. (2019) EvoChromo: towards a synthesis of chromatin biology and evolution. Development

• Ding Y, Murphy KM, Poretsky E, Mafu S, Yang B, Char SN, Christensen SA, Saldivar E, Wu M, Wang Q, Ji L, Schmitz RJ, Kremling KA, Buckler ES, Shen Z, Briggs SP, Bohlmann J, Sher A, Castro-Falcon G, Hughes CC, Huffaker A, Zerbe P, Schmelz EA. (2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants

• Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, Stitzer MC, Crisp PA, Hirsch CN, Zhang X, Schmitz RJ, Springer NM. (2019) Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS Genetics

• Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Kim KD, Daron J, Slotkin KR, Jackson SA, Parrott WA, Meyers BC‡, Schmitz RJ‡. (2019) Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. Plant Cell

• Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nerd JR, Chen H, Zhang Z, Jupe F, Stepanowa A, Schmitz RJ, Lewsey M, Chory J, Ecker JR. (2019) Epigenetic silencing of a multifunctional plant stress regulator. eLIFE

• Wendte JM*, Zhang Y*, Ji L*, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. (2019) Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLIFE

• Schmitz RJ, Lewis ZA, Goll MG. (2019) DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends in Genetics

• Riley LA, Ji L, Schmitz RJ, Westpheling J, Guss AM. (2019) Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems. Journal of Industrial Microbiology & Biotechnology

• Bewick AJ‡, Zhang Y, Wendte JM, Zhang X, Schmitz RJ‡. (2019) Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression. G3 - Genes Genomes Genetics

• Argueso CT, Assman SM, Birnbaum K, Chen S, Dinneny J, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall-Colon A, Alex Mason G, O’Lexy R, Peck S, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. (2019) Directions for research and training in plant omics: Big questions and big data. Plant Direct

• Bewick AJ‡, Hofmeister BT, Powers R, Mondo S, James TY, Stajich JE, Schmitz RJ‡. (2019) Diversity of cytosine methylation across the fungi tree of life. Nature Ecology & Evolution

• Johannes F and Schmitz RJ (2019) Spontaneous epimutations in plants. New Phytologist

• Bewick AJ, Sanchez Z, McKinney EC, Moore AJ, Moore PJ‡, Schmitz RJ‡ (2019) Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics & Chromatin

• Cunningham CB, Ji L, McKinney EC, Benowitz KM, Schmitz RJ, Moore AJ (2019) Changes Of Gene Expression But Not Cytosine Methylation Are Associated With Behavioural Plasticity Of Parental Care. J Exp Biol

• Galli M, Khakhar A, Chen Z, Lu Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. (2018) The DNA binding landscape of the maize auxin response factor family. Nature Communications

• Lee BH, Weber ZT, Zourelidou M, Hofmeister BT, Schmitz RJ, Schwechheimer C, Dobrista AA (2018) Arabidopsis protein kinase D6PKL3 is involved in formation of distinct plasma-membrane aperture domains on the pollen surface. Plant Cell

• Rajshekar S, Yao J, Arnold PK, Payne SG, Zhang Y, Bowman TV, Schmitz RJ, Edwards JR, Goll MG (2018) Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLIFE

• Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, Vollmers C (2018) R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA. Proc Natl Acad Sci

• Lu Z, Ricci W, Schmitz RJ, Zhang X. (2018) Identification of Cis-regulatory Elements by Chromatin Structure. Current Opinions in Plant Biology

• Finnegan JE, Ford B, Wallace X, Pettolino F, Griffin PT, Schmitz RJ, Zhang P, Barrero JM, Hayden M, Boden S, Cavanagh C, Swain S, Trevaskis B. (2018) Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. Plant Cell & Environment

• Fallon TR, Lower SE, Chang C, Manabu BU, Martin GJ, Bewick AJ, Behringer M, Debat HJ, Wong I, Dad JC, Suvorov A, Silva CJ, Hall DW, Schmitz RJ, Nelson DR, Lewis S, Shigenobu S, Bybee SM, Larracuente AM, Oba Y, Weng JK. (2018) Firefly genomes illuminate the origin and evolution of bioluminescence. eLIFE

• Hofmeister BT and Schmitz RJ (2018) Enhanced JBrowse plugins for epigenomics data visualization. BMC Bioinformatics 19:159

• Wendte JM and Schmitz RJ (2018) Specification of pathways targeting heterochromatin modifications in plants. Molecular Plant 11 (3), 381-387

• Hofmeister BT, Lee K, Rohr NA, Hall DW, Schmitz RJ (2017) Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. Genome Biology Jun 18:155

• Stathopoulou A, Chhetri J, Esteve P, Ambrose J, Ji L, Edjument-Bromage H, Zhang G, Neubert T, Herrero J, Pradhan S, Schmitz RJ, Ooi STK (2017) A novel requirement for Drosha in maintenance of mammalian CG methylation. Nucleic Acids Research gkx695

• Ji L*, Jordan WT*, Shi X, Hu L, He C, Schmitz RJ (2018) TET-mediated epimutagenesis of the Arabidopsis thaliana methylome. Nature Communications March;9(895)

• Springer NM and Schmitz RJ (2017) Exploiting induced and natural epigenetic variation for crop improvement. Nature Reviews in Genetics July(18):563–575

• Susek K, Braszewska-Zalewska A, Bewick AJ, Hasterok R, Schmitz RJ, Naganowska B. (2017) Epigenomic diversication within the genus Lupinus. PLOS ONE June:e0179821

• Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos WB, Clum A, Lindquist E, Daum C, Northen TR, Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O’Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. (2017) Pervasive Adenine N6-methylation of Active Genes in Fungi. Nature Genetics 49:964-968

• Bewick AJ, Niederhuth CE, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ (2017) The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biology (in press)

• Bewick AJ and Schmitz RJ. (2017) Gene body DNA methylation in plants. Current Opinion in Plant Biology Apr;36:103-110

• Lu Z, Hofmeister BT, DuBois R, Vollmers C, Schmitz RJ. (2017) Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Research gkw1179

• Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Sociality and DNA methylation are not evolutionary dependent. Molecular Biology and Evolution 34(3):654-665

• Hossain MS, Kawakatsu T, Kim KD, Ning Z, Nguyen CT, Khan SM, Hernandez NG, Batek JM, Joshi T, Schmutz J, Schmitz RJ, Xu D, Grimwood J, Jackson SA, Ecker JR, Stacey G. (2017) Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs in response to heat stress. New Phytologist 214:808-819

• Niederhuth CE and Schmitz RJ (2017) Putting methylation in context: from genomes to gene expression in plants. Biochemica et Biophysica Acta Jan;1860(1):149-156

• Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Ecker JR, Briggs SP (2016) Integration of omic networks in a developmental atlas of maize. Science Aug 19:353(6301)

• Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. (2016) Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biology Aug 9;17(170)

• Kawakatsu T*, Huang SC*, Jupe F*, Sasaki E*, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O’Neil R, O’Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR (2016) Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell Jul 14;166(2):481-91

• 1001 Genome Consortium (2016) 1135 sequenced natural inbred lines reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell Jul 14;166(2):481-91

• Hohos NM, Lee KJ, Ji L, Yu M, Kandasamy KM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. (2016) DNA cytosine hydroxymethylation levels are distinct among peripheral blood leukocytes. Journal of Immunological Methods Sep;436;1-15

• Jordan WT and Schmitz RJ. (2016) The shocking consequences of hybrid epigenomes. Genome Biology May 5;17(1):85

• Reynolds DL, Hofmeister BT, Cliffe L, Siegal TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R. (2016). Base J represses genes at the end of polycistronic gene cluster in Leishmania major by promoting RNAP II termination. Molecular Microbiology Aug;101(4):559-74

• Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. (2016) Epigenomic profiling reveals unique cell-type specific patterns of DNA methylation in the root meristem. Nature Plants May(2):e16058

• Yu P, Ji L, Lee KJ, Yu M, He C, Ambati S, McKinney EC, Jackson C, Baile CA, Schmitz RJ, Meagher RB (2016) Subsets of visceral adipose tissue nuclei and distinct levels of 5-hydroxymethylation. PLOS ONE May 12;11(5):e0154949

• Griffin PT, Niederhuth CE, Schmitz RJ (2016) A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation. G3 - Genes Genomes Genetics (in press)

• Niederhuth CE*, Bewick AJ*, Ji L, Alabday M, Kim KD, Page JT, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ (2016) Widespread natural variation of DNA methylation within angiosperms. Genome Biology

• Bewick AJ*, Ji L*, Niederhuth CE*, Willing EM*, Hofmeister BT, Shi X, Wang L, Lu Z, Rohr NA, Hartwig B, Kiefer C, Deal RB, Schmutz J, Grimwood J, Stroud H, Jacobsen SE, Schneeberger K, Zhang X, Schmitz RJ (2016) On the Origin and Evolutionary Consequences of Gene Body DNA Methylation. Proc Natl Acad Sci Aug 9;113(32):9111-6

• Seymour M*, Ji L*, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X, Lewis ZA. (2016) Histone H1 limits DNA methylation in Neurospora crassa. G3 - Genes Genomes Genetics Jul 7;6(7):1879-89

• Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EKS, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araújo ACG, Kozik A, Kim KD, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimarães PM, Isobe S, Guo S, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SCM, Xun X , Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics April;48(4):438-446

• Reynolds D, Hofmeister B, Cliffe L, Alabady M, Siegel NT, Schmitz RJ, Sabatini R. (2016) Histone variant 3 regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei. PLOS Genetics Jan 21;12(1):e1005758

• Basenko EY, Kamei M, Ji L, Schmitz RJ, Lewis ZA (2016) The LSH/DDM1 homolog MUS-30 is required for genome stability, but not for DNA methylation in Neurospora crassa. PLOS Genetics Jan 15;12(1):e1005790

• Bewick AJ, Hofmeister BT, Lee KJ, Zhang X, Hall DW, Schmitz RJ (2016) FASTmC: a suite of predictive models for non-reference-based estimations of DNA methylation. G3 - Genes Genomes Genetics Feb 17;6(2):447-52

•  Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D,Schmitz RJ, Vaughn MW, Springer NM (2015) RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci Nov 24;112(47):14728-33

• Basenko E, Sasaki T, Ji L, Prybol CJ, Burckhardt RM, Schmitz RJ, Lewis ZA. (2015) Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. Proc Natl Acad Sci Nov 17;112(46):E6339-48

• Cunningham CB, Ji L, Wiberg RAW, Shelton J, McKinney EC, Parker DJ, Meagher RB, Benowitz KM, Roy-Zokan EM, Ritchie MG, Brown SJ, Schmitz RJ, Moore AJ. (2015) The genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biology & Evolution Oct 9;7(12):3383-9

• Christensen SA, Huffaker A, Kaplan A, Sims J, Ziemann S, Doehlemann G, Ji L, Schmitz RJ, Kolomeits MV, Alborn HT, Mori N, Ni X, Byers S, Abdo Z, Schmelz EA (2015) Maize death acids, 9-lipoxygenase derived cyclopentenones and derivatives, display activity as cytotoxic phytoalexins and transcriptional mediators. Proc Natl Acad Sci Sep 8;112(36):11407-12

• Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA (2015) Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci Aug 25;112(34):E4802-10

• Yu M*, Ji L*, Neumann DA, Chung D, Groom J, Westpheling J, He C‡, Schmitz RJ‡. (2015) Base-resolution detection ofN4-methylcytosine in genomic DNA using 4mC-Tet-Assisted-Bisulfite-sequencing. Nucleic Acids Research Dec 2;43(21):e148

• Rancour DM, Hatfield RD, Marita JM, Rohr NA, Schmitz RJ. (2015) Cell wall composition and digestibility alterations in Brachypodium distachyon achieved through reduced expression of the UDP-arabinopyranose mutase. Front. Plant Sci.6:446

• van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ‡, Colomé-Tatché M‡, Johannes F‡. (2015) Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc Natl Acad Sci. May 26;112(21):6676-81

• Bewick AJ and Schmitz RJ. (2015) Epigenetics in the wild. eLife 2015;4:e07808

• Jacobs TB, LaFayette PR, Schmitz RJ Parrott WA. (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnology. March(15):16

• Ji L, Neumann DA, Schmitz RJ. (2015) Crop Epigenomics: Identifying, Unlocking and Harnessing Cryptic Variation in Crop Genomes. Molecular Plant. Jun;8(6):860-870

• Vlachogiannis G, Niederhuth CE, Tuna S, Stathopoulou A, Viiri K, de Rooij DG, Jenner RG, Schmitz RJ, Ooi, STK. (2015) The Dnmt3L ADD domain controls cytosine methylation establishment during spermatogenesis. Cell Reports. Feb(10):944–56

• Lane AK, Niederhuth CE, Ji L, Schmitz RJ. (2015) pENCODE: A Plant Encyclopedia of DNA Elements. Annual Review of Genetics. Volume 48, Issue 1

• Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2015) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols. Feb(10):475–483

• Ji L, Sasaki T, Sun X, Ma P, Lewis ZA, Schmitz RJ. (2014) Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Frontiers in Genetics. 5:341. doi: 10.3389/fgene.2014.00341\

• West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer, NM. (2014) Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLOS ONE. Aug;9(8):e105267

• Dinh TT, Gao L, Liu X, O’Leary M, Zhao Y, Li D, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. (2014) DNA Topoisomerase 1α promotes RNA-directed DNA methylation and histone lysine 9 dimethylation at transposable elements in Arabidopsis. PLoS Genetics. Jul;7(10):e1004446

• Eichten S, Schmitz RJ‡, Springer NM‡. (2014) Epigenetics; beyond chromatin modifications and complex gene regulatory systems. Plant Physiology. Jul 165(3):933-947.

• Schmitz RJ. (2014) The Secret Garden - Epigenetic Alleles Underlie Complex Traits. Science. March(343):1082.

• Wang Y, Gu X, Yuan W, Schmitz RJ, He Y. (2014) Photoperiodic Control of the Floral Transition through a Distinct Polycomb Repressive Complex. Developmental Cell. Mar(28):1-10.

• Valdes-Lopez O*, Khan SM*, Schmitz RJ, Cui S, Qiu J, Zhu M, Cheng JJ, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. (2014) Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources. 12(S1):S27-30.

• Niederhuth CE and Schmitz RJ. (2014) Covering your bases: Inheritance of DNA methylation in plant genomes. Molecular Plant. Mar;7(3):472-80.

• Schmitz RJ‡ and Zhang X‡. (2014) Chapter XI: Decoding epigenomes of herbaceous land plants. Advances in Botanical Research: Genomes of Herbaceous Land Plants. Volume 69.

• Hua ZH, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR‡, Vierstra RD‡. (2013) Epigenomic programming contributes to the genomic drift evolution of the F-box protein superfamily in Arabidopsis. Proc Natl Acad Sci. Oct;110(42):16927-32.

• Schmitz RJ*, He Y*, Valdes-Lopez O, Khan S, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G‡, Ecker JR‡. (2013) Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Research. Oct(23):1663-67.

• Chung WY, Schmitz RJ, Biorac T, Ye D, Dudas M, Meredith GD, Adams CC, Ecker JR, Zhang MQ. (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE. Aug:2(4):335-346.

• Chang KN, Zhong S, Weirauch MT, Hong G, Pelizzola M, Li H, Huang SC, Schmitz RJ, Urich MA, Kue D, Nery J, Qiao H, Yang A, Jamali A, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR (2013) Temporal transcriptional responses to ethylene gas drives growth hormone cross-regulation in Arabidopsis. eLIFE. Jun;2:e00675.

• Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. (2013) Response to perspective: "Separation anxiety: An analysis of ethylene-induced cleavage of EIN2." Plant Signaling & Behavior. Aug:8(8):127-8.

• Schmitz RJ*, Schultz MD*, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A†, McCosh RB, Chen H, Schork NJ, Ecker JR. (2013) Patterns of Population Epigenomic Diversity. Nature. Mar;495(7440):193-8.

• Woodson JD*, Perez-Ruiz JM*, Schmitz RJ, Ecker JR, Chory J. (2013) Sigma factor mediated plastid retrograde signals control nuclear gene expression. The Plant Journal. Jan;73(1):1-13. PMCID: PMC3605210

• Vollmers C*, Schmitz RJ*, Nathanson J, Yeo G, Ecker JR, Panda S. (2012) Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metabolism. Dec;16(6):833-45. PMCID: PMC3541940

• Schultz MD*, Schmitz RJ*, Ecker JR. (2012) "Leveling" the playing field for analysis of single base resolution DNA methylomes. Trends in Genetics. Dec;28(12):583-5. PMCID: PMC3523709

• Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. (2012) Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas. Science. Oct;338(6105):390-3. PMCID: PMC3523706

• Dowen RJ, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci. Jun;109(32):E2183-91. PMCID: PMC3420206

• Johnson, DBF, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. (2012) Release factor one is not essential for Escherichia coli. ACS Chemical Biology. Jul;7(8):1337-44. PMCID: PMC3423824

• Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Vitron C, Cole BJ, Ivans LJ, Pedmale U, Jung HS, Ecker JR, Kay SA, Chory J. (2012) Linking photoreceptor excitation to changes in plant architecture. Genes & Development. Apr;26(8):785-90. PMCID: PMC3337452

• Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR. (2012) Surveillance and degradation of 3’ non-coding transcripts requires FIERY1 and XRN3 in Arabidopsis thaliana. G3 - Genes Genomes Genetics. PMCID: PMC3337477

• Schmitz RJ, Ecker JR. (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends in Plant Sciences. Mar;17(3):149-54. PMCID: PMC3645451

• Hotto, A, Schmitz RJ, Fei Z, Ecker JR, Stern D. (2011) Unexpected diversity of chloroplast non-coding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome. G3 - Genes Genomes Genetics. Dec;1(7):559-70. PMCID: PMC3276175

• Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA†, Lilbiger O, Schork NJ, Ecker JR. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science. Oct;334(6045):369-373. PMCID: PMC3210014

• Johnson DBF, Xu J, Shen Z, Takimoto J, Schultz MD, Schmitz RJ, Ecker JR, Briggs SP, Wang L. (2011) RF1 Knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nature Chemical Biology. Sep;7(11):779-86. PMCID: PMC3201715

• Arabidopsis Interactome Mapping Consortium. (2011) Evidence for network evolution in an Arabidopsis interacome map. Science. Jul;333(6042):601-7. PMCID: PMC3170756

• Farrona S, Hurtado L, March-Díaz R, Schmitz RJ, Florencio FJ, Turck F, Amasino RM, Reyes JC. (2011) Brahma is required for proper expression of the floral repressor FLC. PLOS ONE. Mar;6(3). PMCID: PMC3061888

• Schmitz RJ‡, Zhang X‡. (2011) High-throughput approaches for studying plant epigenomics. Current Opinions in Plant Biology. Apr;14:130-136. PMCID: PMC3112054

• Belkdhadir Y, Durbak A, Wierzba M, Schmitz RJ, Aquirre A, Michel R, Rowe S, Fujioka S, Tax FE. (2010) Intragenic suppression of a trafficking-defective brassinosteroid receptor mutant in Arabidopsis. Genetics. Aug;185(4):1283-96. PMCID: PMC2927756

• Schmitz RJ*, Tamada Y*, Doyle MR, Zhang X, Amasino RM. (2009) Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiology. Feb;149(2):1196-204. PMCID: PMC2633843

• Schmitz RJ*, Sung S*, Amasino RM. (2008) Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana. Proc Natl Acad Sci. Jan;15:105(2):411-6. PMCID: PMC2206549

• Schmitz RJ, Hong L†, Fitzpatrick KE†, Amasino RM. (2007) DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana. Genetics. Jun;176(2):1359-62. PMCID: PMC1894598

• Reeves PA, He Y, Schmitz RJ, Amasino RM, Panella LW, Richards CM. (2007) Evolutionary conservation of the FLC-mediated vernalization response: evidence from the sugar beet (Beta vulgaris). Genetics. May;176(1):295-307.

• Schmitz RJ and Amasino RM. (2007) Vernalization: a model for investigating epigenetics and eukaryotic gene regulation in plants. Biochemica et Biophysica Acta. Mar/Apr;2(2):127-128.

• Sung S, Schmitz RJ, Amasino RM. (2007) A role for VIN3-Like genes in environmentally induced epigenetic regulation of flowering. Plant Signaling & Behavior. Mar:2(2):127-8.

• Sung S, Schmitz RJ, Amasino RM. (2006) A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis. Genes & Development. Dec;20(23):3244-8.

• Schmitz RJ, Hong L†, Michaels S, Amasino RM. (2005) FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana. Development. Dec;132(24):5471-8.

• Choe S, Schmitz RJ, Fujioka S, Takatsuto S, Lee MO, Yoshida S, Feldmann KA, Tax FE. (2002) Arabidopsis brassinosteroid-insensitive dwarf12 mutants are semidominant and defective in a glycogen synthase kinase 3 beta-like kinase. Plant Physiology. Nov:130(3):1506-15.

• Zhao J, Peng P, Schmitz RJ, Decker AD, Tax FE, Li J. (2002) Two putative BIN2 substrates are nuclear components of brassinosteroid signaling. Plant Physiology. Nov;130(3):1221-9.

• Kim, C., D. Zhang, S.A. Auckland, L.K. Rainville, K. Jakob, B. Kronmiller, E.J. Sacks, M. Deuter and A.H. Paterson. 2012. SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. Theoretical and Applied Genetics, in press.
• Wisniewski-Dyé, F., K. Borziak, G. Khalsa-Moyers, G. Alexandre, L.O. Sukharnikov, K. Wuichet, G.B. Hurst, H.W. McDonald, A. Lapidus, V. Barbe, A. Calteau, Z. Rouy, S. Mangenot, C. Prigent-Combaret, P. Normand, M. Boyer, P. Siguier, Yves Dessaux, C. Elmerich, G. Condemine, I. Kennedy, A.H. Paterson, V. González, P. Mavingui and I.B. Zhulin 201#. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. Plos Genetics ##:##-##.
• Wang, X., M. Torres, G. Pierce, C. Lemke, L. Nelson, B. Yuksel, J. Bowers, B. Marler, Y. Xiao, L. Lin, E. Epps, H. Sarazen, C. Rogers, S. Karunakaran, J. Ingles, E.Giattina, J.-H. Mun, Y.-J. Seol, B.-S. Park, R. Amasino, C. Quiros, T. Osborn, C. Pires, C. Town and A. Paterson. 2011. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics 12: 470 (doi:  10.1186/1471-2164-12-470).
• Thor, S.W., D.A. Hilt, J. Kissinger, A.H. Paterson and M.W. Jackwood. 2011.  Recombination in avian gamma-coronaviruses. Viruses 3(9): 1777-1799.
• Zhang, Z., J. Rong, V. Waghmare, P. Chee, O. May, R. Wright, J. Gannaway and A. Paterson. 2011. QTL alleles for improved fiber quality from a wild Hawaiian cotton, Gossypium tomentosum.  Theoretical and Applied Genetics 123(7): 1075-1088.
• Wang, X., et al (The Brassica rapa Genome Sequencing Project Consortium, including X. Wang, H. Tang, H. Guo, T.-H. Lee, J. Li, H. Jin, X. Tan, Y. Wang and A.H. Paterson.  2011. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43: 1035-1039.
• Paterson, A.H. and Z.-K. Li. 2011. Paleo-Green Revolution for rice. Proceedings of the National Academy of Sciences of the USA 108(27): 10931-10932.
• Ratnaparkhe, M.B., X. Wang, J. Li, R.O. Compton, L.K. Rainville, C. Lemke, C. Kim, H. Tang and A.H. Paterson. 2011. Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. New Phytologist 192(1): 164-178.
• Wang, X., H. Tang and A.H. Paterson. 2011. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel in major Poaceae lineages. The Plant Cell 23(1): 27-37.
• Glover, J.D., J.P. Reganold, L.W. Bell, J. Borevitz, E.S. Buckler, C.M. Cox, T.S. Cox, T.E. Crews, S.W. Culman, L.R. DeHaan, D. Eriksson, B.S. Gill, J. Holland, F. Hu, B. Hulke, A.M.H. Ibrahim, S.S. Jones, S.C. Murray, A.H. Paterson, Edmundo Ploschuk, E.J. Sacks, S. Snapp, D. Tao, D.L. Van Tassel, L.J. Wade, D.L. Wyse and Y. Xu. 2010. Increasing Food and Ecosystem Security through Perennial Grain Breeding. Science 328: 1638-1639.
• Lin, L., G. Pierce, J.E. Bowers, J.C. Estill, R.O. Compton, L.K. Nelson, C. Kim, C. Lemke, J. Rong, H. Tang, X. Wang, M. Braidotti, A.H. Chen, K. Collura, E. Epps, W. Golser, C. Grover, K.L. Herrick, J. Ingles, S. Karunakaran, D. Kudrna, J. Olive, N. Tabassum, E. Um, M. Wissotski, Y. Yu, A. Zuccolo, M. ur Rahman, D.G. Peterson, R.A. Wing, J.F. Wendel and A.H. Paterson. 2010. A draft Physical Map of a D-genome Cotton Species (G. raimondii). BMC Genomics 11: 395.
• Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372.
• Tang, H., J.E. Bowers, X. Wang and A.H. Paterson. 2010. Early polyploidy events in the monocotyledon lineage revealed by angiosperm genome comparisons. Proceedings of the National Academy of Sciences of the USA 107: 472-477.
• Wang, X., H. Tang, J.E. Bowers and A.H. Paterson. 2009. Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Research 19: 1026-1032. 
• Paterson, A.H., J.E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, A. Poliakov, J. Schmutz, M. Spannagl, H. Tang, X. Wang, T.Wicker, A.K. Bharti, J. Chapman, F.A. Feltus, U. Gowik, I. Grigoriev, E. Lyons, C.A. Maher, M. Martis, A. Narechania, R. Otillar, B.W. Penning, A.Salamov, Y. Wang, L. Zhang, N.C. Carpita, Michael Freeling, A.R. Gingle, C.T. Hash, B. Keller, P. Klein, S. Kresovich, M.C. McCann, R. Ming, D.G. Peterson, M. ur Rahman, D. Ware, P. Westhoff, K.F.X. Mayer, J. Messing and D.S. Rokhsar. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556. 
• Tang, H., X. Wang, J.E. Bowers, R. Ming, M. Alam and A.H. Paterson. 2008. Unraveling the Consequences of Ancient Hexaploidy through Multiply-aligned Angiosperm Gene Maps. Genome Research 18: 1944-1954.
• Doyle J.J., L.E. Flagel, A.H. Paterson, R.A. Rapp, D.E. Soltis, P.S. Soltis and J.F. Wendel. 2008. Evolutionary genetics of genome merger and doubling in plants. Annual Review of Genetics 42: 443-461.
• Tang, H., J.E. Bowers, X. Wang, R. Ming, M. Alam and A.H. Paterson. 2008. Synteny and colinearity in plant genomes. Science 320: 486-488. 
• Paterson, A.H., P. Felker, S.P. Hubbell and R. Ming. 2008. The fruits of tropical plant genomics. Tropical Plant Biology 1: 3-19. 
• Ray M., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J. Saw, P. Senin, W. Wang, S.Salzberg, H. Tang, E. Lyons, D. Rice, M. Riley, R. Skelton, J. Murray, C. Chen, M. Eustice, E. Tong, H. Albert, R.E. Paull, M.-L. Wang, Y. Zhu, M. Schatz, N. Nagarajan, R. Agbayani, P. Guan, A. Blas, J. Wang, J.-K. Na, T. Michael, E.V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, X. Wang, J.E. Bowers, J. Suzuki, S. Tripathi, K. Neupane, H. Wei, R. Singh, B. Irikura, N. Jiang, W. Zhang, K. Wall, G. Presting, A. Gschwend, Y. Li, A. Windsor, R.N. Pérez, M.J. Torres, F.A. Feltus, B. Porter, M. Paidi, M.-C. Luo, L. Liu, D. Christopher, P.H. Moore, T. Sugimura, C. dePamphilis, J. Jiang, M. Schuler, T. Mitchell-Olds, D. Shippen, J. Palmer, M.R. Freeling, A.H. Paterson, D. Gonsalves, L. Wang and M. Alam. 2008. The draft genome of the tropical fruit tree papaya (Carica papaya, Linnaeus).  Nature 452: 991-996.
• Wang, J., P.H. Moore, A.H. Paterson and R. Ming. 2007. Sex chromosomes in flowering plants. American Journal of Botany 94: 141-150.
• Grover, C.E., H.R. Kim, R.A. Wing, A.H. Paterson and J.F. Wendel. 2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant Journal 50: 995-1006.
• Lohithaswa, H.C., F.A. Feltus, H.P. Singh, C.D. Bacon, C. D. Bailey and A.H. Paterson. 2007. Leveraging rice genome sequence for comparative genomics in monocots. TAG 115: 237-243.
• Yang, T.J., S.-J. Kwon, J. Kim, K.-B. Lim, J.-A. Kim, M. Jin, J.Y. Park, M.-H. Lim, H.-I. Kim, Y.P. Lim, A.H. Paterson and B.-S. Park. 2007. Characterization and genome-wide comparative analysis of terminal-repeat retrotransposon in miniature (TRIM) families in the Brassicaceae. TAG 114: 627-636.
• Mei, H., F. Feng, B. Lu, F.A. Feltus, A.H. Paterson, X. Cai, L. Chen, X. Xu, J. Wu, X. Yu, H. Chen, Y. Li and L. Luo. 2007. Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ‘Nipponbare’ and ‘93-11.’ Chinese Science Bulletin 52: 1327-1337.
• Yu, Q., S. Hou, R. Hobza, F.A. Feltus, X. Wang, W. Jing, R.L. Skelton, A. Blas, C. Lemke, J.H. Saw, P.H. Moore, M. Alam, J. Jiang, A.H. Paterson and R. Ming. 2007. Chromosomal location and gene paucity of the male-specific region on the papaya Y chromosome. Mol. Gen. Genet. 278: 177-185.
• Rong, J., F.A. Feltus, V.N. Waghmare, G.J. Pierce, P.W. Chee, X. Draye, Y. Saranga, R.J. Wright, T.A. Wilkins, O.L. May, C.W. Smith, J.R. Gannaway, J.F. Wendel and A.H. Paterson. Meta-analysis of polyploid cotton QTLs shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176: 2577-2588.
• Wei, F., E. Coe, W. Nelson, A. Bharti, F. Engler, E. Butler, H.-R. Kim, J.L. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J. Bowers, A. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund and R. Wing. 2007. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genetics 3: 1254-1263.
• Desai, A., P.W. Chee, J. Rong, O.L. May and A.H. Paterson. 2006. Chromosome structural changes in diploid and tetraploid A genomes of Gossypium. Genome 49: 336-345.
• Paterson, A.H. 2006. Leafing through the genomes of our major crop plants: strategies for capturing unique infomation. Nature Reviews Genetics 7: 174-184.
• Udall, J.A., J. Swanson, K. Haller, R.A. Rapp, M. Sparks, J. Hatfield, Y. Yu, Y. Wu, D.J. Llewellyn, E. Dennis, A.B. Arpat, B. Sickler, T. A. Wilkins, J. Guo, X. Chen, E. Taliercio, R. Turley, C. Dowd, H. Mcfadden, N. Klueva, P. Payton, R. Allen, D. Zhang, C. Haigler, C. Wilkerson, J. Suo, S. R. Schulze, M. Pierce, M. Essenberg, H. Kim, D. Kudrna, R. Wing, A.H. Paterson, C. Soderlund and J.F. Wendel. 2006. A global assembly of cotton ESTs. Genome Research 16: 441-450.
• Bethel, C.M., E.B. Sciara, J.E. Bowers, J.C. Estill, W. Hanna and A.H. Paterson. 2006. A framework linkage map of Bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments. Theor. Appl. Genet. 112: 727-737.
• Chapman, B.A., J.E. Bowers, F.A. Feltus and A.H. Paterson. 2006. Buffering crucial functions by paleologous duplicated genes may impart cyclicality to angiosperm genome duplication. Proceedings of the National Academy of Sciences of the USA 103: 2730-2735.
• Feltus, F.A., G.E. Hart, K.F. Schertz, A.M. Casa, P. Brown, P. Klein, S. Kresovich and A.H. Paterson. 2006. Genetic map alignment and QTL correspondence between inter- and intra-specific Sorghum populations. Theor. Appl. Genet. 112: 1295-1305.
• Hamblin, M.T., A.M. Casa, H. Sun, S.C. Murray, A.H. Paterson, C.F. Aquadro and S. Kresovich. 2006. Challenges of detecting directional selection after a domestication bottleneck: lessons from Sorghum bicolor. Genetics 173: 953-954.
• Feltus, F.A., H.P. Singh, H.C. Lohithaswa, S.R. Schulze, T. Silva and A.H. Paterson. 2006. A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved noncoding sequences in orphan crops. Plant Physiology 140: 1183-1191.
• Gingle, A.R., H. Yang, P. Chee, O.L. May, J. Rong, D.T. Bowman, E.L. Lubbers and A.H. Paterson. An integrated web resource for cotton. Crop Science 46: 1998-2007.
• Takamiya, T., A.H. Paterson and H. Okuizumi. 2006. Restriction landmark genomic scanning with isoschizomers (MspI/HpaII) for DNA methylation analysis. Electrophoresis 27: 2846-2856.
• Jang, C.S., T.L. Kamps, D.N. Skinner, S.R. Schulze, W.K. Vencill and A.H. Paterson. 2006. Functional classification, genomic organization, putative cis-acting regulatory elements, and relationship to quantitative trait loci, of Sorghum genes with rhizome-enriched expression. Plant Physiology 142: 1148-1159.
• Hamblin, M.T., M.G. Salas-Fernandez, A.M. Casa, S.E. Mitchell, C.F. Aquadro, A.H. Paterson and S. Kresovich. 2005. Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics 171: 1247-1256.
• Van Becelaere, G., E.L. Lubbers, A.H. Paterson and P.W. Chee. 2005. Pedigree versus DNA marker-based genetic similarity estimates in cotton. Crop Science 45: 2281-2287.
• Bowers, J.E., (33 authors, A.H. Paterson as corresponding author). 2005. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc. Natl. Acad. Sci. USA 102: 13206-13211.
• Yuksel, B., J.C. Estill, S.R. Schulze and A.H. Paterson. 2005. Organization and evolution of resistance gene analogs in peanut. Molecular Genetics and Genomics 274: 248-263.
• Rong, J.K., G.J. Pierce, V.N. Waghmare, C.A.J. Rogers, A. Desai, P.W. Chee, O.L. May, J.R. Gannaway, J.F. Wendel, T.A. Wilkins and A.H. Paterson. 2005. TAG 111: 1137-1146.
• Rong J., J.E. Bowers, S.R. Schulze, V.N. Waghmare, C.J. Rogers, G.J. Pierce, H. Zhang, J.C. Estill and A.H. Paterson. 2005. Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy. Genome Research 15: 1198-1210.
• Paterson, A.H., J.E. Bowers and B.A.Chapman. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA 101: 9903-9908.
• Hamblin, M.T., S.E. Mitchell, G.M. White, W. Gallego, R. Kukatla, R.A. Wing, A.H. Paterson and S. Kresovich. 2004. Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics 167: 471-483.
• Rong, J.K., C. Abbey, J.E. Bowers, C.L. Brubaker, C. Chang, P.W. Chee, T.A. Delmonte, X.L. Ding, J.J. Garza, B.S. Marler, C.H. Park, G.J. Pierce, K.M. Rainey, V.K. Rastogi, S.R. Schulze, N.L. Trolinder, J.F. Wendel, T.A. Wilkins, T.D. Williams-Coplin, R.A. Wing, R.J. Wright, X.P. Zhao, L.H. Zhu and A.H. Paterson. 2004. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166: 389-417.
• Ma, H., P.H. Moore, Z.Y. Liu, M.S. Kim, Q.Y. Yu, M.M.M. Fitch, T. Sekioka, A.H. Paterson and R. Ming. 2004. High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166: 419-436.
• Saranga, Y., C.X Jiang., R.J. Wright, D. Yakir and A.H. Paterson. 2004. Genetic dissection of cotton physiological responses to arid conditions and their inter-relationships with productivity. Plant Cell and Environment 27: 263-277.
• Liu, Z.Y., P.H. Moore, H. Ma, C.M. Ackerman, M. Ragiba, Q.Y. Yu, H.M. Pearl, M.S. Kim, J.W. Charlton, J.I. Stiles, F.T. Zee, A.H. Paterson, and R. Ming. 2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427: 348-352.
• Bowers, J.E., C. Abbey, S. Anderson, C. Chang, X. Draye, A.H. Hoppe, R. Jessup, C. Lemke, J. Lennington, Z.K. Li, Y.R. Lin, S.C. Liu, L.J. Luo, B.S. Marler, R.G. Ming, S.E. Mitchell, D. Qiang, K. Reischmann, S.R. Schulze, D.N. Skinner, Y.W. Wang, S. Kresovich, K.F. Schertz and A.H. Paterson. 2003. A high-density genetic recombination map of sequence-tagged sites for Sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165: 367-386.
• Hu, F.Y., D.Y. Tao, E. Sacks, B.Y. Fu, P. Xu, J. Li, Y. Yang, K. McNally, G.S. Khush, A.H. Paterson and Z.K. Li. 2003. Convergent evolution of perenniality in rice and sorghum. Proc. Natl. Acad. Sci. USA 100: 4050-4054.
• Bowers, J.E., B.A. Chapman, J.K. Rong and A.H. Paterson. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
• Paterson, A.H., J.E. Bowers, M.D. Burow, X. Draye, C.G. Elsik, C.X. Jiang, C.S. Katsar , T.H. Lan, Y.R. Lin, R.G. Ming and R.J. Wright. 2000. Comparative genomics of plant chromosomes. Plant Cell 12: 1523-1539.
• Jiang, C.X., P.W. Chee, X. Draye, P.L. Morrell, C.W. Smith and A.H. Paterson. 2000. Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton). Evolution 54: 798-814.
• Wright, R.J., P.M. Thaxton, K.M. El-Zik and A.H. Paterson. 1998. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (Cotton) suggests that polyploid formation has created novel avenues for evolution. Genetics 149: 1987-1996.
• Jiang, C.X., R.J. Wright, K.M. El-Zik and A.H. Paterson. 1998. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. USA 95: 4419-4424.
• Multani, D.S., R.B. Meeley, A.H. Paterson, J. Gray, S.P. Briggs and G.S. Johal. 1998. Plant-pathogen microevolution: Molecular basis for the origin of a fungal disease in maize. Proc. Natl. Acad. Sci. USA 95: 1686-1691.
• Paterson, A.H., T.H. Lan, K.P. Reischmann, C. Chang, Y.R. Lin, S.C. Liu, M.D. Burow, S.P. Kowalski, C.S. Katsar, T.A. DelMonte, K.A. Feldmann, K.F. Schertz and J.F. Wendel. 1997. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nature Genetics 14: 380-382.
• Paterson, A.H., Y.R. Lin, Z.K. Li, K.F. Schertz, J.F. Doebley, S.R.M. Pinson, S.C. Liu, J.W. Stansel, and J.E. Irvine. 1995. Science 269: 1714-1718.
• Paterson, A.H., E.S. Lander, J.D. Hewitt, S. Peterson, S.E. Lincoln and S.D. Tanksley. 1988. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721-726.

Books

• Losos, J., Baum, D. A., Futuyma, D. J., Hoekstra, H. E., Lenski, R. E., Moore, A. J., Peichel, C, L., Schluter, D., & Whitlock, M. J. (editors). 2013. Princeton Guide to Evolution. Princeton University Press.

• Székely, T., A. J. Moore & J. Komdeur (eds) 2010. Social Behaviour: Genes, Ecology and Evolution. Cambridge University Press.

Journal Articles:

• Benowitz, K. M., A. U. Amukamara, E. C. McKinney & A. J. Moore. 2019. Development and the effects of extended parenting in the cold-breeding burying beetle Nicrophorus sayi. Ecological Entomology 44: 11-16.

• Benowitz, K. M., E. C. McKinney, C. B. Cunningham & A. J. Moore. 2019. Predictable gene expression related to behavioural variation in the burying beetle Nicrophorus vespilloides. Behavioral Ecology 30: 402-407.

• Bewick, A.J., Z. Sanchez, E. C. McKinney, A. J. Moore, R. J. Schmitz & P. J. Moore. 2019. Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics & Chromatin 12:6 doi:10.1186/s13072-018-0246-5.

• Carter, M. J., A. J. Wilson, A. J. Moore & N. J. Royle. 2019. The role of indirect genetic effects in the evolution of interacting reproductive behaviors in the burying beetle, Nicrophorus vespilloides. Ecology and Evolution 9: 998-1009 (DOI:10.1002/ece3.4731).

• Cunningham, C. B., L. Ji, E. C. McKinney, K. M. Benowitz, R. J. Schmitz & A. J. Moore. 2019. Changes of gene expression but not cytosine methylation are associated with male parental care reflecting behavioural state, social context, and individual flexibility. Journal of Experimental Biology 222, jeb188649. doi:10.1242/jeb.188649.

• Moore, A. J. & K. M. Benowitz. 2019. From phenotype to genotype: the precursor hypothesis predicts genetic influences that facilitates transitions to social behaviour. Current Opinion in Insect Science, in press.

• Ziadie, M. A., F. Ebot-Ojong, E. C. McKinney & A. J. Moore. 2019. Evolution of personal and social immunity in the context of parental care. American Naturalist 193: 296-308.

• Bailey, N. W. & A. J. Moore. 2018. Evolutionary consequences of social isolation. Trends in Ecology and Evolution 33: 595-607.

• Bailey, N. W., L. Marie-Orleach & A. J. Moore. 2018. Indirect genetic effects in behavioural ecology: Does behaviour play a special role in evolution? Behavioral Ecology 29: 1-11. doi:10.1093/beheco/arx127.

• Bailey, N. W., L. Marie-Orleach & A. J. Moore. 2018. If everything is special, is anything special? A response to comments on Bailey et al. Behavioral Ecology 29: 17-18. doi:10.1093/beheco/arx191

• Benowitz, K. M., M. E. Sparks, E. C. McKinney, P. J. Moore & A. J. Moore. 2018. Variation in mandible development and its relationship to dependence on parents across burying beetles. Ecology and Evolution 8: 12832-12840.

• Benowitz, K. M., E. C. McKinney, E. M. Roy-Zokan, C. B. Cunningham & A. J. Moore. 2017. The role of lipid metabolism during parental care in two species of burying beetle (Nicrophorus spp.). Animal Behaviour 129: 143-149.

• Bacigalupe, L. D., A. J. Moore, R. F. Nespolo, E. L. Rezende & F. Bozinovic. 2017. Quantitative genetic modelling of the parental care hypothesis for the evolution of endothermy. Frontiers in Physiology 8: 1006. doi: 10.3389/fphys.2017.

• Benowitz, K. M., E. C. McKinney, C. B. Cunningham & A. J. Moore. 2017. Relating quantitative variation within a behavior to variation in transcription. Evolution 71: 1999-2009.

• Bewick, A. J., K. J. Vogel, A. J. Moore & R. J. Schmitz. 2017. Evolution of DNA methylation across insects. Molecular Biology & Evolution 34: 656-664. doi: 10.1093/molbev/msw264

• Cunningham, C. B., M. Badgett, R. B. Meagher, R. Orlando & A. J. Moore. 2017. Ethological principles predict the neuropeptides co-opted to influence parenting. Nature Communications 8:14225 | DOI: 10.1038/ncomms14225.

• Mehlferber, E. C., K. M. Benowitz, E. M. Roy-Zokan, E. C. McKinney, C. B. Cunningham & A. J. Moore. 2017. Duplication and sub/neofunctionalization of Malvolio, an insect equivalent of Nramp, in the subsocial beetle Nicrophorus vespilloides. G3 7:3393-3403. https://doi.org/10.1534/g3.117.300183

• Moore, A. J., J. Firn & A. Beckerman. 2017. Academic practice in ecology and evolution: soliciting a new category of manuscript. Ecology and Evolution 7: 5030-5031.

• Benowitz, K. M., E. C. McKinney & A. J. Moore. 2016. Differences in parenting in two species of burying beetle, Nicrophorus orbicollis and Nicrophorus vespilloides. Journal of Ethology 34: 315-319.

• Benowitz, K. M., & A. J. Moore. 2016. Biparental care is predominant and beneficial to parents in the burying beetle Nicrophorus orbicollis (Coleoptera: Silphidae). Biological Journal of the Linnean Society 119: 1082-1088.

• Cunningham, C. B., K. VanDenHeuvel, D. B. Khana, E. C. McKinney & A. J. Moore. 2016. The role of neuropeptide F in a transition to parental care. Biology Letters 12: 20160158.

• Hopwood, P. E., M. L. Head, E. J. Jordan, M. J. Carter, E. Davey, A. J. Moore & N. J. Royle. 2016. Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides.  Evolution 70: 1180-1188.

• Hopwood, P. E., G. P. F. Mazué, M. J. Carter, M. L. Head, A. J. Moore, & N. J. Royle. 2016. Do female Nicrophorus vespilloides reduce direct costs by choosing males that mate less frequently? Biology Letters 12: 20151064.

• Hopwood, P. E., A. J. Moore, T. Tregenza & N. J. Royle. 2016. The effect of size and sex-ratio experiences on reproductive competition in Nicrophorus vespilloides burying beetles in the wild. Journal of Evolutionary Biology 29: 541-550.

• Hopwood, P. E., A. J. Moore, T. Tregenza & N. J. Royle. 2016. Niche variation and the maintenance of variation in body size in burying beetles. Ecological Entomology 41: 96-104.

• Miller, C. W., G. C. McDonald & A. J. Moore. 2016. The tale of the shrinking weapon: seasonal changes in nutrition affect weapon size and sexual dimorphism, but not evolvability. Journal of Evolutionary Biology 29: 2266-2275.

• Moore, A. J. & A. P. Beckerman. 2016. Ecology and Evolution in an open world (or: why supplementary data are evil). Ecology and Evolution 6: 2655-2656.

• Royle, N. J., S. H. Alonzo & A. J. Moore. 2016. Co-evolution, conflict and complexity: what have we learned about the evolution of parental care behaviours? Current Opinion in Behavioral Sciences 12: 30-36.

• Shaw, R. G., A. J. Moore, M. Noor, M. G. Ritchie. 2016. Transparency and reproducibility in evolutionary research. Ecology and Evolution 6: 4605-4606.

• Whitlock, M. C., J. L. Bronstein, E. M. Bruna, A. M. Ellison, C. W. Fox. M. A. McPeek. A. J. Moore, M. A F. Noor, M. D. Rausher, L. H. Rieseberg, M. G. Ritchie, R. G. Shaw. 2016. A balanced data archiving policy for long-term studies. Trends in Ecology and Evolution 31: 84-85.

• Benowitz, K. M., K. J. Moody & A. J. Moore. 2015. The evolution of species differences in maternal effects. Journal of Evolutionary Biology 28: 503-509.

• Carter, M. J., M. L. Head, A. J. Moore & N. J. Royle. 2015, Behavioural plasticity and GxE of reproductive tactics in Nicrophorus vespilloides burying beetles. Evolution 69: 969-978.

• Cunningham, C. B., M. K. Douthit & A. J. Moore. 2015. Expression of octopaminergic receptor genes in four non-neural tissues in the beetle Nicrophorus vespilloides. Insect Science 22: 495-502.

• Cunningham, C. B., L. Ji, R. A. W. Wiberg, J. M. Shelton, E. C. McKinney, D. J. Parker, R. B. Meagher, K. M. Benowitz, E. M. Roy-Zokan, M. G. Ritchie, S. J. Brown, R. J. Schmitz, A. J. Moore. The genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biology and Evolution doi:10.1093/gbe/evv194

• Flores, E. E., M. Stevens, A. J. Moore, H. M. Rowland & J. D. Blount. 2015. Body size but not warning signal luminance influences predation risk in recently metamorphosed poison frogs. Ecology and Evolution 5:4603-4616.

• Hopwood, P. E., A. J. Moore, T. Tregenza & N. J. Royle. 2015. Male burying beetles extend, not reduce, parental care duration when reproductive competition is high. Journal of Evolutionary Biology 28: 1394-1402.

• Newcombe, D., P. J. Moore & A. J. Moore. 2015. The role of maternal effects in adaptation to different diets. Biological Journal of the Linnaean Society 114: 202-211.

• Newcombe, D., J. Hunt, C. Mitchell & A. J. Moore. 2015. Maternal effects and maternal selection arising from variation in allocation of free amino acids to eggs. Ecology and Evolution 5: 2397-2410.

• Parker, D. J., C. B. Cunningham, C. A. Walling, C. E. Stamper, M. L. Head, E. M. Roy-Zokan, E. C., McKinney, M. G. Ritchie, A. J. Moore. 2015. Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle. Nature Communications 6:8449 doi: 10.1038/ncomms9449.

• Roy-Zokan, E. M., C. B. Cunningham, L. E. Hebb, E. C. McKinney & A. J. Moore. 2015. Vitellogenin and vigellogenin receptor gene expression is associated with male and female parenting in a subsocial insect. Proceedings of the Royal Society B, 20150787. http://dx.doi.org/10.1098/rspb.2015.0787.

• Addesso, K. M., K. A. Short, A. J. Moore & C. W. Miller. 2014. Context-dependent female mate preferences in leaf-footed cactus bug. Behaviour 151: 479-492.

• Cunningham, C. B., M. K. Douthit & A. J. Moore. 2014. Octopaminergic gene expression and flexible social behaviour in the subsocial beetle, Nicrophorus vespilloides. Insect Molecular Biology 23: 391-404.

• Gillespie, S., M. Tudor, A. J. Moore & C. W. Miller. 2014. Sexual selection is influenced by both developmental and adult environments. Evolution 68:3421-3432.

• Head, M., C. Hinde, A. J. Moore & N. J. Royle. 2014. Correlated evolution in parental care in females but not males in response to selection on paternity assurance behaviour. Ecology Letters 17: 803-810.

• Hopwood, P. E., A. J. Moore & N. J. Royle. 2014. Effects of resource variation during early life and adult social environment on contest outcomes in burying beetles. Proceedings of the Royal Society B 281: 20133102. (doi.org/10.1098/rspb.2013.3102).

• McGlothlin, J. W, J. B. Wolf, E. D. Brodie III & A. J. Moore. 2014.  Quantitative genetic versions of Hamilton's rule with empirical applications. Philosophical Transactions of the Royal Society B 369 20130358 (doi:10.1098/rstb.2013.0358).

• Attisano, A. A., T. Tregenza, A. J. Moore & P. J. Moore. 2013. Oosorption and migratory strategy of the milkweed bug, Oncopeltus fasciatus. Animal Behaviour 86: 651-657.

• Bacigalupe, L. D., K. Barrientos, A. P. Beckerman, M. Carter, C. C. Figueroa, S. P. Foster, A. J. Moore, A. X. Silva & R. F. Nespolo. 2013. Can invasions occur without change? A comparison of G matrices and selection in the peach-potato aphid, Myzus persicae. Ecology and Evolution 3: 5109-5118.

• Benowitz, K., M. L. Head, C. Williams, A. J. Moore & N. J. Royle. 2013. Male age mediates reproductive investment and response to paternity assurance. Proceedings of the Royal Society B 280: 20131124 (doi: 10.1098/rspb.2013.1124).

• Bleakley, B. H., S. M. Welter, K. McCauley-Cole, S. M. Shuster & A. J. Moore. 2013. Cannibalism as an interacting phenotype: pre-cannibalistic aggression is influenced by social partners in the endangered Socorro isopod (Thermosphaeroma theromophilum). Journal of Evolutionary Biology 26: 832-842.

• Flores, E. E., M. Stevens, A. J. Moore, & J. D. Blount. 2013. Diet, development and the optimisation of warning signals in post-metamorphic green and black poison frogs. Functional Ecology 27: 816-829.

• Hopwood, P. E., A. J. Moore & N. J. Royle. 2013. Nutrition during sexual maturation affects competitive ability but not reproductive productivity in burying beetles. Functional Ecology 27: 1350-1357.

• Komdeur, J., M. J. J. Schrama, K. Meijer, A. J. Moore & L. W. Beukeboom. 2013. Co-breeding in the burying beetle, Nicrophorus vespilloides: Tolerance rather than cooperation. Ethology 119: 1138-1148.

• Moore, A. J. 2013. Genetic influences on social dominance: cow wars. Heredity 110: 1-2.

• Moore, A. J., L. D. Bacigalupe & R. R. Snook. 2013. Integrated and independent evolution of heteromorphic sperm types. Proceedings of the Royal Society B 280: 20131647. (doi: 10.1098/rspb.2013.1647)

• Newcombe, D., J. D. Blount, C. Mitchell & A. J. Moore. 2013. Chemical defence in the large milkweed bug Oncopeltus fasciatus (Dallas) derives from maternal but not paternal diet. Entomologia Experimentalis et Applicata 149: 197-205.

• Attisano, A., A. J. Moore & P. J. Moore. 2012. Reproduction-longevity trade-offs reflect diet, not adaptation. Journal of Evolutionary Biology 25: 873-880.

• Bailey, N. W. & A. J. Moore. 2012. Runaway sexual selection without genetic correlations: social environments and flexible mate choice initiate and enhance the Fisher process. Evolution 66: 2674-2684.

• Flores, E. E., A. J. Moore & J. D. Blount. 2012. Unusual whitish eggs in the poison frog Dendrobates auratus Gerard, 1855. Tropical Zoology 25: 67-73.

• Head, M. L., L. K. Berry, N. J. Royle & A. J. Moore. 2012. Paternal care: direct and indirect genetic effects of fathers on offspring performance. Evolution 66: 3570-3581.

• Hunt, J., R. R. Snook, C. Mitchell, H. S. Crudgington & A. J. Moore. 2012. Sexual selection and experimental evolution of chemical signals in Drosophila pseudoobscura. Journal of Evolutionary Biology 25: 2232-2241.

• Procter, D. S., A. J. Moore & C.W. Miller. 2012. The form of sexual selection arising from male-male competition depends on the presence of females in the social environment. Journal of Evolutionary Biology 25: 803-812.

• Abbot, P. et al. 2011. Inclusive fitness theory and eusociality. Nature 471:E1-E4.

• House, C. M., B. H. Bleakley, C. A. Walling, T. A. R. Price, C. E. Stamper & A. J. Moore. 2011. The influence of maternal effects on indirect benefits associated with polyandry. Proceedings of the Royal Society B 278 : 1177-1182.

• Moore, A. J. 2011. Open debate and progress in ecology and evolution. Ecology and Evolution 1:doi:10.1002/ece3.5

• South, S. H., C. M. House, A. J. Moore, S. J. Simpson & J. Hunt. 2011. Male cockroaches prefer a high carbohydrate diet that makes them more attractive to females: implications for the study of condition dependence. Evolution 65: 1594-1606.

• McGlothlin, J. W., A. J. Moore, J. B. Wolf & E. D. Brodie III 2010. Interacting phenotypes and the evolutionary process. III. Social evolution. Evolution 64: 2558-2574.

• Moore, A. J. 2010. What would Darwin do? Journal of Evolutionary Biology 23: 1-5.

• Moore, A. J., M. A. McPeek, L. Reiseberg & M. C. Whitlock 2010. The need for archiving data in evolutionary biology. Journal of Evolutionary Biology 23: 659-660.

• Rausher, M. D., M. A. McPeek, A. J. Moore, L. Rieseberg & M. C. Whitlock 2010. Data archiving. Evolution 64: 603-604.

• Snook, R. R., L. D. Bacigalupe & A. J. Moore 2010. The quantitative genetics and coevolution of male and female reproductive traits. Evolution 64: 1926-1934.

• Whitlock, M. C., M. A. McPeek, M. D. Rausher, L. Rieseberg & A. J. Moore. 2010. Data archiving. American Naturalist 175: 145-146.

• Barrett, E. L. B., A. J. Moore & P. J. Moore 2009. Diet and social conditions during sexual maturation have unpredictable influences on female life history trade-offs. Journal of Evolutionary Biology 22: 571-581.

• Barrett, E. L. B., A. J. Moore & P. J. Moore 2009. Does the scent of a potential mate prevent the resoprtion of oocytes by apoptosis in Nauphoeta cinerea (Oliver)? Insect Science 16: 393-398.

• Barrett, E. L. B., A. J. Moore & P. J. Moore 2009. A potential function for oocyte apoptosis in unmated Nauphoeta cinerea.  Physiological Entomology 34: 272-277.

• Barrett, E. L. B., J. Hunt, A. J. Moore & P. J. Moore 2009. Effects of nutrition during juvenile and sexual development on female life-history trajectories: the thrifty phenotype in a cockroach. Proceedings of the Royal Society B 276: 3257-3264.

• Edvardsson, M., J. Hunt, A. J. Moore & P. J. Moore 2009. Quantitative genetic variation in the control of ovarian apoptosis under different environments. Heredity 103: 217-222.

• House, C. M., C. A. Walling, C. E. Stamper & A. J. Moore 2009. Females benefit from multiple mating but not multiple mates in the burying beetle Nicrophorus vespilloides. Journal of Evolutionary Biology 22: 1961-1966.

• Hunt, J., C. J. Breuker, J. A. Sadowski & A. J. Moore 2009. Male-male competition, female mate choice and their interaction: determining total sexual selection. Journal of Evolutionary Biology 22: 13-26.

• McPeek, M. A., D. L. DeAngelis, R. G. Shaw, A. J. Moore, M. D. Rausher, D. R. Strong, A. M. Ellison, L. Barrett, L. Rieseberg, M. D. Breed, J. Sullivan, C. W. Osenberg, M. Holyoak & M. A. Elgar 2009. The golden rule of reviewing. American Naturalist 173: E155-E158.

• Walling, C. A., C. E. Stamper, C. Salisbury & A. J. Moore 2009. Experience does not alter alternative mating tactics in the burying beetle, Nicrophorus vespilloides. Behavioral Ecology 20: 153-159.

• Bacigalupe, L. D., H. S. Crudginton, J. Slate, A. J. Moore & R. R. Snook. 2008. Sexual selection and interacting phenotypes in experimental evolution: a study of Drosophila pseudoobscura mating behavior. Evolution 62: 1804-1812.

• Barrett, E. L. B., R. F. Preziosi, A. J. Moore & P. J. Moore 2008. Effects of mating delay and nutritional signals on resource recycling in a cyclically breeding cockroach. Journal of Insect Physiology 54: 25-31.

• Edvardsson, M., J. Hunt, P. J. Moore & A. J. Moore 2008. Female agreement over male attractiveness is not affected by cost of mating with experienced males. Behavioral Ecology 19: 854-859.

• Gibbs, M., C. J. Breuker, P. T. Smiseth & A. J. Moore 2008. Does sibling competition have a sex-specific effect on offspring growth and development in the burying beetle Nicrophorus vespilloides? Entomologia Experimentalis et Applica 126: 158-164.

• House, C. M., G. M. V. Evans, P. T. Smiseth, C. E. Stamper, C. A. Walling & A. J. Moore 2008. The evolution of repeated mating in the burying beetle, Nicrophorus vespilloides. Evolution 62: 2004-2014.

• Montrose, V. T., W. E. Harris, A. J. Moore & P. J. Moore 2008. Sperm competition within a dominance hierarchy: investment in social status versus investment in ejaculates. Journal of Evolutionary Biology 21: 1290-1296.

• Smiseth, P. T. & A. J. Moore 2008. Parental distribution of resources in relation to hunger and size rank in the burying beetle Nicrophorus vespilloides. Ethology 114: 789-796.

• Walling, C. A., C. E. Stamper, P. T. Smiseth & A. J. Moore. 2008. Genetic architecture of sex differences in parental care. Proceedings of the National Academy of Sciences USA 105: 18430-18435.

• Bacigalupe, L. D, H. S. Crudington, F. Hunter, A. J. Moore, & R. R. Snook 2007. Sexual conflict does not drive reproductive isolation in experimental populations of Drosophila pseudoobscura. Journal of Evolutionary Biology 20: 1763-1771.

• Gowaty, P. A., W. W. Anderson, C. K. Blum, L. C. Drickamer, Y.-K. Kim, & A. J. Moore 2007. The hypothesis of reproductive compensation and its assumptions about mate preferences and offspring viability. Proceedings of the National Academy of Sciences USA 104: 15023-15027.

• Harris, W. E., A. J. Moore & P. J. Moore 2007. Variation in sperm size within and between ejaculates in a cockroach. Functional Ecology  21: 598-602.

• House, C. M., J. Hunt & A. J. Moore 2007. Sperm competition, alternative mating tactics, and context-dependent fertilisation success in the burying beetle, Nicrophorus vespilloides. Proceedings of the Royal Society of London B 274: 1309-1315.

• Hunt, J., J. B. Wolf & A. J. Moore 2007. The biology of multivariate evolution. Journal of Evolutionary Biology 20: 24-27.

• Lock, J. E., P. T. Smiseth, P. J. Moore & A. J. Moore 2007. Coadaptation of prenatal and postnatal maternal effects. American Naturalist 170: 709-718.

• Miller, C. W. & A. J. Moore 2007. A potential resolution to the lek paradox through indirect genetic effects. Proceedings of the Royal Society of London B 274: 1279-1286.

• Moore, P. J., W. E. Harris & A. J. Moore 2007. The cost of keeping eggs fresh: quantitative genetic variation in females that mate late relative to sexual maturation. American Naturalist 169: 311-322.

• Oldekop, J. A., P. T. Smiseth, H. D. Piggins & A. J. Moore 2007. Adaptive switch from infancticide to parental care: How do beetles time their behaviour? Journal of Evolutionary Biology 20: 1998-2004.

• Smiseth, P. T., L. Lennox & A. J. Moore 2007. Interaction between parental care and sibling competition: parents enhance offspring growth and exacerbate sibling competition. Evolution 61: 2331-2339.

• Smiseth, P. T. & A. J. Moore 2007. Signalling of hunger by senior and junior larvae in asynchronous broods of the burying beetle Nicrophorus vespilloides. Animal Behaviour 74: 699-705.

• Smiseth, P. T., R. J. S. Ward & A. J. Moore 2007. Parents influence asymmetric sibling competition: Experimental evidence with partially dependent young. Ecology 88: 3174-3182.

• Astles, P. A., A. J. Moore & R. F Preziosi 2006. A comparison of methods to estimate cross environment genetic correlations.  Journal of Evolutionary Biology 19: 114-122.

• Gibbs M., L. A. Lace, M. J. Jones & A. J. Moore 2006. Multiple host plant use may arise from gender-specific fitness effects. Journal of Insect Science 6:04, insectscience.org/6.04.

• Lessells, C.M. et al. 2006. Debating sexual selection and mating strategies. Science 312: 689-690.

• Smiseth, P. T., S. Musa & A. J. Moore 2006. Negotiation between parents: does the timing of mate loss affect female compensation in Nicrophorus vespilloides? Behavior 143: 293-301.

• Smiseth, P. T., R. J. S. Ward & A. J. Moore 2006. Asynchronous hatching in Nicrophorus vespilloides, an insect in which parents provide food for their offspring.  Functional Ecology 20: 151-156.

• Astles, P. A., A. J. Moore & R. F Preziosi 2005.  Genetic variation in traits responding to an indirect ecological effect.  Proceedings of the Royal Society of London B 272: 2577-2581.

• Gibbs M., L. A. Lace, M. J. Jones & A. J. Moore 2005. Egg size-number trade-off and a decline in oviposition site choice quality: Female Pararge aegeria butterflies pay a cost of having males present at oviposition.  Journal of Insect Science 5:39, insectscience.org/5.39.

• Kölliker, M., E. D. Brodie III, & A. J. Moore 2005. The coadaptation of parental supply and offspring demand.  American Naturalist 166: 506-516.

• Moore, A. J. & T. Pizzari 2005.  Quantitative genetic models of sexual conflict based on interacting phenotypes.  American Naturalist 165: S88-S97.

• Smiseth, P. T., C. Dawson, E. Varley & A. J. Moore 2005.  How do caring parents respond to mate loss? Differential response by males and females.  Animal Behaviour 69: 551-559.

• Lock, J. E., P. T. Smiseth & A. J. Moore 2004.  Selection, inheritance and the evolution of parent-offspring interactions.  American Naturalist 164: 13-24.

• Gibbs, M., L. A. Lace, M. J. Jones & A. J. Moore 2004.  Intraspecific competition in the speckled wood butterfly Parage aegeria: effect of rearing density and gender on larval life history.  Journal of Insect Science 4(16): 1-6.

• Gibbs, M., L. A. Lace, M. J. Jones & A. J. Moore 2004. Differences in search behaviour of the two Madeiran speckled butterflies, Pararge aegeria and Pararge xiphia (Lepidoptera: Satyridae), implications for interspecific competition? Boletim do Museu Municipal do Funchal 55: 5-15.

• Moore, A. J. 2004.  All in the family.  Nature 427: 517-518.

• Moore, P. J., W. E. Harris, V. T. Montrose, D. Levin & A. J. Moore 2004.  Constraints on evolution and post-copulatory sexual selection: trade-offs among ejaculate characteristics.  Evolution 58: 1773-1780.

• Rauter, C. M. & A. J. Moore 2004. Time constraints and trade-offs among parental care behaviours: effects of brood size, sex, and loss of mate.  Animal Behaviour 68: 695-702.

• Smiseth, P. T. & A. J. Moore 2004. Behavioral dynamics between caring males and females in a beetle with facultative biparental care.  Behavioral Ecology 15: 621-628.

• Smiseth, P. T. & A. J. Moore 2004. Signalling of hunger when offspring forage by both begging and self-feeding. Animal Behaviour 67: 1083-1088.

• Moore, A. J., P. A. Gowaty & P. J. Moore 2003. Females avoid manipulative males and live longer.  Journal of Evolutionary Biology 16: 523-530.

• Moore, P. J. & A. J. Moore 2003.  Developmental flexibility and the effect of social environment on fertility and fecundity in parthenogenetic reproduction.  Evolution & Development 5: 163-168.

• Smiseth, P. T., C. T. Darwell & A. J. Moore 2003.  Partial begging: An empirical model for the early evolution of offspring begging.  Proceedings of the Royal Society B. 270: 1773-1777.

• Beeler, A. E., C. M. Rauter & A. J. Moore 2002.  Mate discrimination by females in the burying beetle Nicrophorus orbicollis: the influence of male size on attractiveness to females.  Ecological Entomology 27: 1-6.

• Boake, C. R. B., F. Breden & A. J. Moore 2002.  Behavior genetics for behavioral ecologists.  American Naturalist 160: i.

• Boake, C. R. B., S. J. Arnold, F. Breden, L. M. Meffert, M. J. Ritchie, B. Taylor, J. B. Wolf & A. J. Moore 2002.  Genetic tools for studying adaptation and the evolution of behavior.  American Naturalist 160: S143-S159.

• Evenden, M. L., B. G. Spohn, A. J. Moore, R. F. Preziosi & K. F. Haynes 2002.  Inheritance and evolution of male response to sex pheromone in Trichoplusia ni (Lepidoptera: Noctuidae).  Chemoecology 12: 53-59.

• Moore, A. J., K. F. Haynes, R. F. Preziosi & P. J. Moore 2002.  The evolution of interacting phenotypes: genetics and evolution of social dominance.  American Naturalist 160: S186-S197.

• Moore, A. J. & P. Kukuk 2002.  Quantitative genetic analysis in natural populations. Nature Reviews Genetics 3: 971-978.

• Rauter, C. M. & A. J. Moore 2002.  Quantitative genetics of growth and development time in the burying beetle Nicrophorus pustulatus in the presence and absence of post-hatching parental care.  Evolution 56: 96-110.

• Rauter, C. M. & A. J. Moore 2002.  Evolutionary importance of parental care performance, food resources, and direct and indirect genetic effects in a burying beetle.  Journal of Evolutionary Biology 15: 407-417.

• Sadowski, J. A., J. L. Grace & A. J. Moore 2002. Complex courtship behavior in the striped ground cricket, Allonemobius socius (Orthoptera: Gryllidae): Does social environment affect male and female behavior? Journal of Insect Behavior 15: 69-84.

• Smiseth, P. T. & A. J. Moore 2002. Does resource availability affect offspring begging and parental provisioning in a partially begging species?  Animal Behaviour 63: 577-585.

• Corley, L. S., J. R. Blankenship & A. J. Moore  2001 Genetic variation and asexual reproduction in the facultatively parthenogenetic cockroach Nauphoeta cinerea: Implications for the evolution of sex.  Journal of Evolutionary Biology 14:68-74.

• Gemeno, C., A. J. Moore, R. F. Preziosi & K. F. Haynes 2001.  Quantitative genetics of signal evolution: a comparison of the pheromonal signal in two populations of the cabbage looper, Trichoplusia ni. Behavior Genetics 31:157-165.

• Moore, A. J., P. A. Gowaty, W. Wallin, & P. J. Moore 2001. Sexual conflict and the evolution of female mate choice and male dominance.  Proceedings of the Royal Society of London B 268:517-523.

• Moore, P. J. & A. J. Moore 2001. Reproductive aging and mating: the ticking of the biological clock in female cockroaches.  Proceedings of the National Academy of Sciences USA 98:9171-9176.

• Wolf, J. B., W. A. Frankino, A. F. Agrawal, E. D. Brodie III & A. J. Moore 2001.  Developmental interactions and the constituents of quantitative variation.  Evolution 55:232-245.

• Snyder, W.E., S. B. Joseph, R. F. Preziosi & A. J. Moore  2000.  Nutritional benefits of cannibalism for the lady beetle Harmonia axyridis (Coleoptera: Coccinellidae) when prey quality is poor.  Environmental Entomology 29:1173-1179.

• Beeler, A. E., C. M. Rauter & A. J. Moore 1999. Pheromonally-mediated mate attraction by males of the burying beetle Nicrophorus orbicollis: Alternative calling tactics conditional on both intrinsic and extrinsic factors.  Behavioral Ecology 10: 578-584.

• Corley, L. S., J. R. Blankenship, A. J. Moore & P. J. Moore 1999.  Developmental constraints on the mode of reproduction in the facultatively parthenogenetic cockroach Nauphoeta cinerea.  Evolution & Development 1: 90-99.

• Corley, L. S. & A. J. Moore 1999.  Fitness of alternative modes of reproduction: Developmental constraints and the evolutionary maintenance of sex.  Proceedings of the Royal Society of London B 266: 471-476.

• Joseph, S. B., W. E. Snyder & A. J. Moore 1999.  Cannibalizing Harmonia axyridis (Coleoptera: Coccinellidae) larvae use endogenous cues to avoid eating relatives.  Journal of Evolutionary Biology 12: 792-797.

• Moore, A. J. & P. J. Moore 1999.  Balancing sexual selection through opposing mate choice and male competition.  Proceedings of the Royal Society of London B 266: 711-716.

• Preziosi, R. F., W. E. Snyder, C. P. Grill & A. J. Moore 1999.  The fitness of manipulating phenotypes: Implications for studies of fluctuating asymmetry and multivariate selection.  Evolution 53: 1312-1318.

• Rauter, C. M. & A. J. Moore 1999.  Do honest signalling models of offspring solicitation apply to insects?  Proceedings of the Royal Society of London B 266: 1691-1696.

• Sadowski, J. A., A. J. Moore & E. D. Brodie III 1999.  The evolution of empty nuptial gifts in a dance fly, Empis snoddyi (Diptera: Empididae): Bigger isn’t always better.  Behavioural Ecology and Sociobiology 45:161-166.

• Wagner, J. D., M. D. Glover, J. B. Moseley, & A. J. Moore 1999.  Heritability and fitness consequences of cannibalism in Harmonia axyridis.  Evolutionary Ecology Research 1:375-388.

• Wolf, J. B., E. D. Brodie III & A. J. Moore 1999.  Interacting phenotypes and the evolutionary process. II.  Selection resulting from social interactions.  American Naturalist 153:254-266.

• Wolf, J. B., E. D. Brodie III & A. J. Moore 1999.  The role of maternal and paternal effects in the evolution of parental quality by sexual selection.  Journal of Evolutionary Biology 12: 1157-1167.

• Grill, C. P. & A. J. Moore 1998.  Effects of a larval antipredator response and larval diet on adult phenotype in an aposematic ladybird beetle.  Oecologica 114:274-282.

• Wolf, J. B., E. D. Brodie III, J. M. Cheverud, A. J. Moore & M. J. Wade 1998.  Evolutionary consequences of indirect genetic effects.  Trends in Ecology & Evolution 13:64-69.

• Clark, D. C., S. J. DeBano, & A. J. Moore 1997.  The influence of environmental quality on sexual selection in Nauphoeta cinerea (Dictyoptera: Blaberidae).  Behavioral Ecology 8:46-53.

• Grill, C. P., A. J. Moore & E. D. Brodie III 1997. Genetic aspects of phenotypic plasticity in a colonising population of the ladybird Harmonia axyridis.  Heredity 78:261-269.

• Moore, A. J. 1997.  The evolution of social signals: morphological, functional and genetic integration of the sex pheromone in Nauphoeta cinerea.  Evolution 51:1920-1928.

• Moore, A. J., E. D. Brodie III & J. B. Wolf 1997. Interacting phenotypes and the evolutionary process: I. direct and indirect genetic effects of social interactions. Evolution 51:1352-1362.

• Moore, P. J., N. L. Reagan-Wallin, K. F. Haynes & A. J. Moore 1997.  Odour conveys status on cockroaches.  Nature 389:25.

• Spohn, B. G. & A. J. Moore 1997.  Environmental effects on agonistic interactions between males of the cockroach Nauphoeta cinerea.  Ethology 103:855-864.

• Wolf, J. B., A. J. Moore & E. D. Brodie III 1997.  The evolution of indicator traits for parental quality: the role of maternal and paternal effects. American Naturalist 150:639-649.

• Brodie, E. D. III & A. J. Moore 1995.  Experimental studies of coral snake mimicry: Do snakes mimic millipedes?  Animal Behaviour 49:534-536.

• Brodie, E. D. III, A. J. Moore, & F. J. Janzen 1995. Visualizing and quantifying natural selection.  Trends in Ecology & Evolution 10:313-318. 

• Clark, D. C., D. D. Beshear, & A. J. Moore 1995.  The role of familiarity in structuring male-male social interactions in Gromphadorhina portentosa (Dictyoptera: Blaberidae).  Annals of the Entomological Society of America 88:554-561.

• Clark, D. C. & A. J. Moore 1995.  Genetic aspects of communication during male-male competition in the Madagascar hissing cockroach: honest signalling of size. Heredity 75:198-205.

• Clark, D. C. & A. J. Moore 1995.  Variation and repeatability of male agonistic hiss characteristics and their relationship to social rank in Gromphadorhina portentosa.  Animal Behaviour 50:719-729.

• Clark, D. C. & A. J. Moore 1995.  Social communication in the Madagascar hissing cockroach: Features of male courtship hisses and a comparison of courtship and agonistic hisses.  Behaviour 132:401-417.

• Moore, A. J., N. L. Reagan, & K. F. Haynes 1995.  Conditional signalling strategies: Effects of ontogeny, social experience and social status on the pheromonal signal of male Nauphoeta cinerea.  Animal Behaviour 50:191-202.

• Clark, D. C. & A. J. Moore 1994. Social interactions and aggression among male Madagascar hissing cockroaches (Gromphadorhina portentosa).  Journal of Insect Behaviour 7:199-215.

• Dugatkin, L. A., M. Alfieri, & A. J. Moore 1994.  The replicability of dominance hierarchies: Form - reform experiments using the cockroach Nauphoeta cinerea.  Ethology 97:94-102.

• Moore, A. J. 1994.  Genetic evidence for the 'good genes' process of sexual selection. Behavioral Ecology and Sociobiology 35:235-241.

• Moore, A. J. & C. R. B. Boake 1994.  Optimality and evolutionary genetics: Complementary procedures for evolutionary analysis in behavioural ecology.  Trends in Ecology & Evolution 9:69-72.

• Moore, P. J., A. J. Moore, & G. B. Collins 1994.  Genotypic and developmental regulation of transient expression of a reporter gene in soybean cotyledons.  Plant Cell Reports 13:556-560.

• Cheverud, J. M., S. C. Jacobs, & A. J. Moore 1993.  Genetic differences among subspecies of the Saddle-back tamarin (Saguinus fuscicollis): Evidence from hybrids.  American Journal of Primatology 31:23-39.

• Moore, A. J. 1993.  Towards an evolutionary view of dominance.  Animal Behaviour 46:594-596.

• Moore, A. J. & P. Wilson 1993. The evolution of sexually dimorphic earwig forceps: Social interactions among adults of the toothed earwig.  Behavioral Ecology 4:40-48.

• Moore, A. J. & J. M Cheverud 1992.  The systematics of the Bare-face tamarins: Evidence from facial morphology.  American Journal of Physical Anthropology 89:73-84.

• Moore, A. J. 1991. Genetics, inheritance, and social behaviour. Animal Behaviour 42:497-498.

• Cheverud, J. M., D. Falk, C. Hildebolt, A. J. Moore, R. C. Helmcamp, & M. Vannier 1990.  Cortical asymmetry in rhesus macaque (Macaca mulatta) frontal lobes is heritable.  Brain, Behaviour and Evolution 35:368-372.

• Cheverud, J. M. & A. J. Moore 1990. Subspecific morphological variation in the saddle-back tamarin (Saguinus fuscicollis).  American Journal of Primatology 21:1-15.

• Moore, A. J. 1990. The inheritance of social dominance, mating behaviour, and attractiveness to mates in Nauphoeta cinerea. Animal Behaviour 39:388-397.

• Moore, A. J. 1990. Sexual selection and the genetics of pheromonally mediated behavior in Nauphoeta cinerea (Dictyoptera: Blaberidae). Entomologia Generalis 15:133-147.

• Moore, A. J. 1990. The evolution of sexual dimorphism by sexual selection: The separate effects of intrasexual selection and intersexual selection. Evolution 44:315-331.

• Breed, M. D., K. B. Rogers, J. A. Hunley, & A. J. Moore 1989. A correlation between guard behaviour and defensive response in the honey bee.  Animal Behaviour 37:515-516.

• Coelho, J. R. & A. J. Moore 1989. Allometry of resting metabolic rate in cockroaches (Insecta: Dictyoptera).  Comparative Biochemistry and Physiology 94A:587-590.

• Moore, A. J. 1989. Sexual selection in Nauphoeta cinerea: Inherited mating preference?  Behavior Genetics 19:717-724.

• Moore, A. J. 1989. The behavioral ecology of Libellula luctuosa (Burmeister) (Odonata:Libellulidae): III. Male density, OSR, and male and female mating behavior.  Ethology 80:120-136.

• Moore, A. J. 1988. Female preferences, male social status, and sexual selection in Nauphoeta cinerea.  Animal Behaviour 36:303-305.

• Moore, A. J., W. J. Ciccone, & M. D. Breed 1988. The influence of social experience on the behavior of male cockroaches, Nauphoeta cinerea.  Journal of Insect Behavior 1:157-168.

• Moore, A. J. & P. J. Moore 1988. Female strategy during mate choice: Threshold assessment.  Evolution 42:387-391.

• Breed, M. D., J. H. Fewell, A. J. Moore, K. R. Williams 1987. Graded recruitment in a ponerine ant.  Behavioral Ecology and Sociobiology 20:407-411.

• Moore, A. J. 1987. The behavioral ecology of Libellula luctuosa (Burmeister) (Anisoptera: Libellulidae): I. Temporal changes in the population density and the effects on male territorial behavior.  Ethology 75:246-254.

• Moore, A. J. 1987. Behavioral ecology of Libellula luctuosa (Burmeister) (Anisoptera: Libellulidae): II. Proposed functions for territorial behaviors.  Odonatologica 16:385-391.

• Moore, A. J., M. D. Breed, & M. J. Moor 1987. The guard honey bee: ontogeny and behavioural variability of workers performing a specialized task.  Animal Behaviour 35:1159-1167.

• Moore, A. J. & M. D. Breed 1986. Mate assessment in a cockroach, Nauphoeta cinerea.  Animal Behaviour 34:1160-1165.

Book Chapters

• Royle, N. J. & A. J. Moore 2018. Nature and nurture in parental care. Pp. 131-156 in: Hosken, D. J., J. Hunt, N. Weddell, (eds) Genes and Behaviour: Beyond Nature and Nurture. Wiley Press.

• Moore, A. J. 2013. Evolution of Behavior, Society and Humans. In: Losos, J., Baum, D. A., Futuyma, D. J., Hoekstra, H. E., Lenski, R. E., Moore, A. J., Peichel, C, L., Schluter, D., & Whitlock, M. J. (eds.) Princeton Guide to Evolution. Princeton University Press

• Bleakley, B. H., J. B. Wolf & A. J. Moore 2010. Evolutionary quantitative genetics of social behaviour. Pp. 29-54 in: Social Behaviour: Genes, Ecology and Evolution. T. Székely, A. J. Moore & J. Komdeur (eds.). Cambridge University Press.

• Moore, A. J., T. Székely, & J. Komdeur 2010. Prospects for research on social behaviour: systems biology meets behaviour. Pp. 538-550 in: Social Behaviour: Genes, Ecology and Evolution. T. Székely, A. J. Moore & J. Komdeur (eds.). Cambridge University Press.

• Székely, T., A. J. Moore & J. Komdeur 2010. The uphill climb of sociobiology: towards a new synthesis. Pp. 1-4 in: Social Behaviour: Genes, Ecology and Evolution. T. Székely, A. J. Moore & J. Komdeur (eds.). Cambridge University Press.

• Wolf, J. B. & A. J. Moore 2010. Interacting phenotypes and indirect genetic effects: a genetic perspective on the evolution of social behavior. Pp. 225-245 in: Evolutionary Behavioral Ecology. D. F. Westneat & C. W. Fox (eds). Oxford University Press.

• Wolf, J. B. & A. J. Moore 2010. A very brief introduction to quantitative genetics. Pp. 75-79 in: Evolutionary Behavioral Ecology. D. F. Westneat & C. W. Fox (eds). Oxford Univ. Press.

• Simmons, L. W. & A. J. Moore 2009. Evolutionary quantitative genetics of sperm. Pp. 405-434 in: Sperm Biology: An Evolutionary Perspective. T. R. Birkhead, D. J. Hosken & S. Pitnick (eds.). Academic Press.

• d’Ettorre, P. & A. J. Moore 2008. Chemical communication and the coordination of social interactions in insects. Pp. 81-96 in: Sociobiology of Communication: An Interdisciplinary Perspective. P. d’Ettore & D. P. Hughes (eds.). Oxford University Press.

• Moore, A. J. & P. J. Moore 2006. Genetics of sexual selection.  Pp. 339-349 in: Ecological Genetics.  C. W. Fox and J. B. Wolf (eds.).  Oxford Univ. Press, Oxford.

• Moore, A. J., J. B. Wolf & E. D. Brodie III 1998.  The influence of direct and indirect genetic effects on the evolution of behavior: Social and sexual selection meet maternal effects.  Pp. 22-41 in: Maternal Effects as Adaptations.  T. A. Mousseau & C. W. Fox (eds.).  Oxford Univ. Press, Oxford.

• Cheverud, J. M. & A. J. Moore 1994.  Quantitative genetics and the role of the environment provided by relatives in behavioral evolution.  pp. 67-100, In: Quantitative Genetic Studies of Behavioral Evolution.  C. R. B. Boake, (ed.).  Univ. Chicago Press, Chicago.

• Breed, M. D. & A. J. Moore 1988. The guard bee as a component of the defensive response. In: Proceedings of the International Conference on African Honey Bees and Bee Mites. M. Delfinado-Baker, G. Needham, and R. E. Page (eds.), pp. 105-109. Ellis Harwood, Ltd.

• Moore, A. J. 1988. Experimental demonstrations of the nature of sexual selection involving pheromones in a cockroach, Nauphoeta cinerea (Olivier). Proceedings of the International Congress of Entomology 18:236.

1. Rasys, A.M., Park, S., Ball, R.E., Alcala, A.J., Lauderdale, J.D., Menke, D.B. 2019. CRISPR-Cas9 Gene Editing in Lizards through Microinjection of Unfertilized Oocytes. Cell Rep. Aug 27;28(9):2288-2292.e3.
2. Thompson, A.C., Capellini, T.D., Guenther, C.A., Chan, Y.F., Infante, C.R., Menke, D.B., Kingsley, D.M. 2018. A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. eLife. 7. pii: e38555.
3. VanLeuven, A.J., Park, S., Menke, D.B., Lauderdale JD. 2018. A PAGE screening approach for identifying CRISPR-Cas9-induced mutations in zebrafish. Biotechniques. 64(6):275-278.
4. Tollis, M., Hutchins, E.D., Stapley, J., Rupp, S.M., Eckalbar, W.L., Maayan, I., Lasku, E., Infante, C.R., Dennis, S.R., Robertson, J.A., May, C.M., Crusoe, M.R., Bermingham, E., DeNardo, D.F., Hsieh, S.T., Kulathinal, R.J., McMillan, W.O., Menke, D.B., Pratt, S.C., Rawls, J.A., Sanjur, O., Wilson-Rawls, J., Wilson Sayres, M.A., Fisher, R.E., Kusumi, K. 2018. Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. Genome Biol Evol. 10(2):489-506.
5. Wang, J.S., Infante, C.R., Park, S., Menke, D.B. 2018. PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. Dev Biol. 434(1):186-195.
6. Ching, S.T., Infante, C.R., Du, W., Sharir, A., Park, S., Menke, D.B., Klein, O.D. 2018. Isl1 mediates mesenchymal expansion in the developing external genitalia via regulation of Bmp4, Fgf10 and Wnt5a. Hum Mol Genet. 27(1):107-119.
7. Infante, C.R., Rasys, A.M., Menke, D.B. 2018. Appendages and gene regulatory networks: Lessons from the limbless. Genesis. 56(1). doi: 10.1002/dvg.23078.
8. Domyan, E.T, Z. Kronenberg, C. R. Infante, A.I. Vickrey, S.A. Stringham, R. Bruders, M.W. Guernsey, S. Park, J. Payne, R.B. Beckstead, G. Kardon, D.B. Menke, M. Yandell, M.D. Shapiro. 2016. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife. 5: e12115.
9. Infante, C.R., A.G. Mihala, S. Park, J.S. Wang, K.K. Johnson, J.D. Lauderdale, and D.B. Menke. 2015. Shared enhancer activity in the limbs and phallus and functional divergence of a limb-genital cis-regulatory element in snakes. Dev Cell. 35(1):107-19.
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11. Park, S., C.R. Infante, L.C. Rivera-Davila and D.B. Menke. 2014. Conserved regulation of hoxc11 by pitx1 in Anolis lizards. Journal of Experimental Zoology B. 322: 156-165.
12. D.B. Menke. 2013. Engineering subtle targeted mutations into the mouse genome. Genesis. 51: 605-618.
13. Infante, C.R., S. Park, A. Mihala, D.M. Kingsley and D.B. Menke. 2013. Pitx1 Broadly Associates with Limb Enhancers and is Enriched on Hindlimb cis-Regulatory Elements. Developmental Biology. 374: 234-244.
14. Kusumi, K., R.J. Kulanthinal, A. Abzhanov, S. Boissinot, N.G. Crawford, B.C. Faircloth, T.C. Glenn, D.E. Janes, J.B. Losos, D.B. Menke, S. Poe, T.J. Sanger, C.J. Schneider, J. Stapley, J. Wade and J. Wilson-Rawls. 2011. Developing a community-based genetic nomenclature for anole lizards. BMC Genomics. 12: 554.
15. McLean, C.Y., P.L. Reno, A.A. Pollen, A.I. Bassan, T.D. Capellini, C. Guenther, V.B. Indjeian, X. Lim, D.B. Menke, B.T. Schaar, A.M. Wenger, G. Bejerano and D.M. Kingsley. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 471: 216-219.
16. Menke, D.B., C. Guenther and D.M. Kingsley. 2008. Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs. Development. 135: 2543-2553.