Publications

48. Coneva V, Frank MH, de Luis Balaguer MA, Li M, Sozzani R, Chitwood DH. (2017) Genetic architecture and molecular networks underlying leaf thickness in desert-adapted tomato Solanum pennellii. Plant Physiol. [Epub ahead of print]. DOI: https://doi.org/10.1104/pp.17.00790. Pre-print: http://dx.doi.org/10.1101/111005

 

47. Bender, ALD, Chitwood DH, Bradley, AS (2017) Heritability of the structures and 13C fractionation in tomato leaf wax alkanes: a genetic model system to inform paleoenvironmental reconstructions. Front Earth Sci. [Epub ahead of print]. DOI: https://doi.org/10.3389/feart.2017.00047. Pre-print: http://dx.doi.org/10.1101/110718

 

46. Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese J, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams J, Chitwood DH (2017) Morphological plant modeling: Unleashing geometric and topological potential within the plant sciences. Front Plant Sci. [Epub ahead of print]. DOI: https://doi.org/10.3389/fpls.2017.00900. Pre-print: http://dx.doi.org/10.1101/078832

 

45. Li M, Duncan K, Topp CN, Chitwood DH (2017) Persistent homology and the branching topologies of plants. Am J Bot. [Epub ahead of print]. DOI: http://dx.doi.org/10.3732/ajb.1700046

 

44. Klein LL, Caito M, Chapnick C, Kitchen C, O’Hanlon R, Chitwood DH, Miller A (2017) Digital morphometrics of two North American grapevines (Vitis: Vitaceae) quantifies leaf variation between species, within species, and among individuals. Front Plant Sci. 8:373. DOI: http://dx.doi.org/10.3389/fpls.2017.00373

 

43.  Chitwood DH, Otoni WC (2017) Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade. GigaScience. 6(1):1-13. DOI: http://dx.doi.org/10.1093/gigascience/giw008. Pre-print: http://dx.doi.org/10.1101/067512. The original high-resolution scans of >3,300 leaves for this paper can be found in GigaDatabase: http://gigadb.org/dataset/100251

 

42. Wilson MC, Mutka AM, Hummel AW, Berry J, Chauhan RD Vijayaraghavan A, Taylor NJ, Voytas DF, Chitwood DH, Bart RS (2017) Gene expression analysis provides insight into the physiology of the important staple food crop cassava. New Phytologist. 213(4):1632-1641. DOI: http://dx.doi.org/10.1111/nph.14443. Pre-print: http://dx.doi.org/10.1101/073213

 

41. Andres RJ, Coneva V, Frank M, Tuttle JR, Samayoa LF, Han SW, Kaur B, Zhu L, Fang H, Bowman DT, Rojas-Pierce M, Haigler CH, Jones DC, Holland JB, Chitwood DH, Kuraparthy V (2017) Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.). Proc Natl Acad Sci USA. 114(1):E57-E66. DOI: http://dx.doi.org/10.1073/pnas.1613593114. Pre-print: http://dx.doi.org/10.1101/062612

 

40. Martinez CC, Chitwood DH, Smith RS, Sinha NR (2016) Left-right leaf asymmetry in decussate and distichous phyllotactic systems. Philos Trans R Soc Lond B Biol Sci. 371:20150412. DOI: http://dx.doi.org/10.1098/rstb.2015.0412. Pre-print: http://dx.doi.org/10.1101/043869

 

39. Chitwood DH, Irish VF (2016) A renaissance in plant development. Dev Biol. 419:4-6. DOI: http://dx.doi.org/10.1016/j.ydbio.2016.09.013

 

38. Martinez CC, Koenig D, Chitwood DH, Sinha N (2016) A sister of PIN1 gene in tomato (Solanum lycopersicum) defines organ initiation patterns by maintaining epidermal auxin flux. Dev Biol. 419:85-98. DOI: http://dx.doi.org/10.1016/j.ydbio.2016.08.011. Pre-print: http://dx.doi.org/10.1101/042150

 

37. Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, Sinha NR (2016) A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification. G3. 6:3169-3184. DOI: http://dx.?doi.?org/10.1534/g3.116.030536. Pre-print: http://dx.doi.org/10.1101/040923

 

36. Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L, Ichihashi Y, Zumstein K, Maloof JN, Sinha NR (2016) eQTL regulating transcript levels associated with diverse biological processes in tomato. Plant Physiol. 172:328-40. DOI: ?http://dx.?doi.?org/?10.?1104/?pp.?16.?00289. Pre-print: http://dx.doi.org/10.1101/040592

 

35. Frank MH, Chitwood DH (2016) Plant chimeras: the good, the bad, and the Bizzaria. Dev Biol. 419:41-53. DOI: http://dx.doi.org/10.1016/j.ydbio.2016.07.003. Pre-print: http://dx.doi.org/10.1101/060715

 

34. Chitwood DH, Sinha NR (2016) Evolutionary and environmental forces sculpting leaf development. Curr Biol. 26:R297-R306. DOI: http://dx.doi.org/10.1016/j.cub.2016.02.033

 

33. Fahlgren N, Bart R, Herrera-Estrella L, Rellán-Álvarez R, Chitwood DH, Dinneny JR (2016) Plant scientists: GM technology is safe. Science. 351:824. DOI: http://dx.doi.org/10.1126/science.351.6275.824-a

 

32. Chitwood DH, Rundell SM, Li DY, Woodford QL, Yu TT, Lopez JR, Greenblatt D, Kang J, Londo JP (2016) Climate and developmental plasticity: interannual variability in grapevine leaf morphology. Plant Physiol. 170:1480-91. DOI: http://dx.doi.org/10.1104/pp.15.01825. Pre-print: http://dx.doi.org/10.1101/030957

 

31. Warschefsky E, Klein L, Frank M, Chitwood DH, Londo JP, Bishop-von Wettberg EJ, Miller AJ (2016) Rootstocks: diversity, domestication and impacts on shoot phenotypes. Trends in Plant Sci. 21:418-37 [Featured cover article, May 2016 issue]. DOI: http://dx.doi.org/10.1016/j.tplants.2015.11.008

 

30. Ostria-Gallardo E, Ranjan A, Zumstein K, Chitwood DH, Kumar R, Townsley B, Ichihashi Y, Corcuera LJ, Sinha NR (2016) Transcriptomic analysis suggests a key role for SQUAMOSA PROMOTER BINDING PROTEIN LIKE, NAC and YUCCA genes in the heteroblastic development of the temperate rainforest tree Gevuina avellana Mol. (Proteaceae). New Phytol. 210:694-708. DOI: http://dx.doi.org/10.1111/nph.13776

 

29. Chitwood DH, Klein LL, O’Hanlon R, Chacko S, Greg M, Kitchen C, Miller AJ, Londo JP (2016) Latent developmental and evolutionary shapes embedded within the grapevine leaf. New Phytol. 210:343-55. DOI: http://dx.doi.org/10.1111/nph.13754. Pre-print: http://dx.doi.org/10.1101/018291

 

28. Chitwood DH, Kumar R, Ranjan A, Pelletier J, Townsley B, Ichihashi Y, Martinez CC, Zumstein K, Harada J, Maloof JN, Sinha NR (2015) Light-induced indeterminacy alters shade avoiding tomato leaf morphology. Plant Physiol. 169:2030-47. DOI: http://dx.doi.org/10.1104/pp.15.01229. Pre-print: http://dx.doi.org/10.1101/024018

 

27. Coneva V, Chitwood DH (2015) Plant architecture without multicellularity: quandaries over patterning and the soma-germline divide in siphonous algae. Front Plant Sci. 6:287. DOI: http://dx.doi.org/10.3389/fpls.2015.00287

 

26. Chitwood DH, Topp CN (2015) Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits. Curr Opin Plant Biol. 24C:54-60. DOI: http://dx.doi.org/10.1016/j.pbi.2015.01.009

 

25. Ranjan A, Townsley BT, Ichihashi Y, Sinha NR, Chitwood DH (2015) An intracellular transcriptomic atlas of the giant coenocyte Caulerpa taxifolia. PLoS Genet. 11:e1004900. [Featured journal image, January issue]. DOI: http://dx.doi.org/10.1371/journal.pgen.1004900

 

24. Chitwood DH & Sinha NR (2014) Plant Development: Small RNAs and the metamorphosis of leaves. Curr Biol. 24:R1087-9. DOI: http://dx.doi.org/10.1016/j.cub.2014.10.013

 

23. Chitwood DH (2014) Imitation, genetic lineages, and time influenced the morphological evolution of the violin. PLOS ONE. 9:e109229. [Featured in NPR’s Science Friday, Scientific American, Los Angeles Times, International New York Times, El País, and others. One of the 2014 Top 20 PLOS ONE papers]. DOI: http://dx.doi.org/10.1371/journal.pone.0109229

 

22. Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland LR, Ostria-Gallardo E, Aguilar-Martínez JA, Bush S, Carriedo L, Fulop D, Martinez CC, Peng J, Maloof JN, Sinha NR (2014) Resolving distinct genetic regulators of tomato leaf shape within a heteroblastic and ontogenetic context. Plant Cell. 26:3616-29. DOI: http://dx.doi.org/10.1105/tpc.114.130112

 

21. Ichihashi Y, Aguilar-Martinez JA, Farhi M, Chitwood DH, Kumar R, Millon LV, Peng J, Maloof JN, Sinha NR (2014) Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proc Natl Acad Sci USA. 111:E2616-21. DOI: http://dx.doi.org/10.1073/pnas.1402835111

 

20. Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya M, Prins B, Li L, Myles S, Sinha N (2014) A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol. 164:259-72. [Featured cover article, January issue]. DOI: http://dx.doi.org/10.1104/pp.113.229708

 

19. Chitwood DH*, Kumar K*, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR (2013) A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. Plant Cell. 25:2465-81. DOI: http://dx.doi.org/10.1105/tpc.113.112391

 

18. Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci USA. 110:E2655-62. DOI: http://dx.doi.org/10.1073/pnas.1309606110

 

17. Chitwood DH, Maloof JN, Sinha NR (2013) Dynamic transcript profiles between tomato and a wild relative reflect distinct developmental architectures. Plant Physiol.162:537-52. DOI: http://dx.doi.org/10.1104/pp.112.213546

 

16. Chitwood DH & Sinha NR (2013) A census of cells in time: quantitative genetics meets developmental biology. Curr. Opin. Plant Biol. 16:92-9. DOI: http://dx.doi.org/10.1016/j.pbi.2012.11.003

 

15. Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN, Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. DOI: http://dx.doi.org/10.3389/fpls.2012.00202

 

14. Chitwood DH, Naylor DT, Thammapichai P, Weeger AC, Headland LR, Sinha NR (2012) Conflict between intrinsic leaf asymmetry and phyllotaxis in the resupinate leaves of Alstroemeria psittacina. Front. Plant Sci. 3:182. DOI: http://dx.doi.org/10.3389/fpls.2012.00182

 

13. Chitwood DH, Headland LR, Ranjan A, Martinez CC, Braybrook SA, Koenig DP, Kuhlemeier C, Smith RS, Sinha N (2012) Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. Plant Cell. 24:2318-27. DOI: http://dx.doi.org/10.1105/tpc.112.098798

 

12. Chitwood DH, Headland LR, Kumar R, Peng J, Maloof JN, Sinha NR (2012) The developmental trajectory of leaflet morphology in wild tomato species. Plant Physiol. 158:1230-1240 [Featured cover article, March issue]. DOI: http://dx.doi.org/10.1104/pp.111.192518

 

11. Chitwood DH*, Headland LR*, Filiault DL, Kumar R, Jiménez-Gómez JM, Schrager AV, Park DS, Peng J, Sinha NR, Maloof JN (2012) Native environment modulates leaf size and response to simulated foliar shade across wild tomato species. PLOS ONE. 7:e29570. DOI: http://dx.doi.org/10.1371/journal.pone.0029570

 

10. Chitwood DH & Timmermans MC (2010) Small RNAs are on the move. Nature. 467:415-419. DOI: http://dx.doi.org/10.1038/nature09351

 

9. Husbands AY, Chitwood DH, Plavskin Y, Timmermans MC (2009) Signals and prepatterns: new insights into organ polarity in plants. Genes & Dev. 23:1986-1997. DOI: http://dx.doi.org/10.1101/gad.1819909

 

8. Chitwood DH, Nogueira FT, Howell MD, Montgomery TA, Carrington JC, Timmermans MC (2009) Pattern formation via small RNA mobility. Genes & Dev. 23:549-554. DOI: http://dx.doi.org/10.1101/gad.1770009

 

7. Nogueira FT*, Chitwood DH*, Madi S, Ohtsu K, Scanlon MJ, Schnable PS, Timmermans MC (2009) Regulation of small RNA accumulation in the maize shoot apex. PLoS Genet. 5:e1000320. DOI: http://dx.doi.org/10.1371/journal.pgen.1000320

 

6. Chitwood DH & Timmermans MC (2007) Target mimics modulate miRNAs. Nat. Genet. 39:935-936. DOI: http://dx.doi.org/10.1038/ng0807-935

 

5. Nogueira FT, Madi S, Chitwood DH, Juarez MT, Timmermans MC (2007) Two small regulatory RNAs establish opposing fates of a developmental axis. Genes & Dev. 21:750-755. DOI: http://dx.doi.org/10.1101/gad.1528607

 

4. Chitwood DH, Guo M,  Nogueira FT, Timmermans MC (2007) Establishing leaf polarity: The role of small RNAs and positional signals in the shoot apex. Development. 134:813-823. DOI: http://dx.doi.org/10.1242/dev.000497

 

3. Irvine DV, Zaratiegui M, Tolia NH, Goto DB, Chitwood DH, Vaughn MW, Joshua-Tor L, Martienssen RA (2006) Argonaute slicing is required for heterochromatic silencing and spreading. Science. 313:1134-1137. DOI: http://dx.doi.org/10.1126/science.1128813

 

2. Nogueira FT, Sarkar AK, Chitwood DH, Timmermans MC (2006) Organ polarity in plants is specified through the opposing activity of two distinct small regulatory RNAs. CSHL Symp. on Quant. Biol. 71:157-164. DOI: http://dx.doi.org/10.1101/sqb.2006.71.045

 

1. Lee JY, Baum SF, Alvarez J, Patel A, Chitwood DH, Bowman JL (2005) Activation of CRABS CLAW in the nectaries and carpels of Arabidopsis. Plant Cell. 17:25-36. DOI: http://dx.doi.org/10.1105/tpc.104.026666