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Research articles (Bold = Mallarino Lab members; Asterisk = corresponding author(s))


Pre-prints
  • ​Griffing A, Goodwin K, Palmer M, Park CJ, Rothstein M, Brack B, Moreno B, Lemma B, Wang W, Mallarino R*, Nelson C*. A vascular origin for pulmonary smooth muscle in the avian lung. BioRxiv. Download PDF​


​Published​ or in press
  • ​Rogers F, Kim S, Mereby S, Kasper A, Callanan A, Mallarino R*, Peña C*. Agouti integrates environmental cues to regulate paternal behavior. Nature 2026; DOI: https://doi.org/10.1038/s41586-026-10123-4. Download PDF
                            Coverage: The Transmitter
                                             Princeton Press Release
                                             Science News
                                             The Princetonian
                                             Scientific American
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  • Lemma B, Rothstein M, Zhang P, Waas B, Kilwein M, Topiwala S, Zhang S, Sudhakar A, Goodwin K, Gavis E, Mallarino R, Kosmrlj A, Nelson C. Patterns of mitochondrial ATP predict tissue folding. Science Advances 12, eaee6175. Download PDF
 
  • Corrigan E, DeBerardine M, Poddar A, Turrero Garcia M, de la O S, He Siting, Sen H, Duhne M, Lindberg S, Song M, Schmitz M, Sears K, Mallarino R, Berke J, Harwell C, Paredes M, Krienen* F, Pollen A*. (2025). Conservation and alteration of mammalian striatal interneurons. Nature, 647, 187-193. Download PDF
 
  • Lea A, Caldas I, Garske K, Gerlinger E, Arroyo J, Echwa J, Gurven M, Handley C, Kahumbu J, Kamau J, Kinyua P, Lotukoi F, Lopurodoi A, Lowasa S, Njer S, Mallarino R, Martins D, Messer P, Miano C, Muhoya B, Peng J, Phung T, Rabinowitz J, Roichman A, Siford R, Stone A, Taravella Oill, Mathew, Wilson M, Ayroles J. Adaptations to water stress and pastoralisms in the Turkana of northwest Kenya. Science, Vol 389:1246-1251. Download PDF.
 
  • Park J, Ke W, Kaage A, Feigin C, Prytikin Y, Donia M* and Mallarino R*. (2025). Cathelicidin antimicrobial peptides mediate immune protection in marsupial neonates. Science Advances 11, eads6359. Download PDF.​
 
  • Moreno JA, Dudchenko O, Feigin CY, Mereby, SA, Chen Z, Ramos R, Almet AA, Sen H, Brack B, Johnson M, Li S, Wang W, Gaska J, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, St. Leger J, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Lieberman Aiden E*, and Mallarino R*. (2024). Emx2 underlies the development and evolution of marsupial gliding membranes. Nature, 629, 127-135. Download PDF.

                          Coverage: Nature News and Views
                                              Scientific American
                                              Princeton Press Release
                                              Baylor Press Release
                                              Nature Podcast
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  • Staps M, Miller P, Tarnita CE and Mallarino R* (2023). Development shapes the evolutionary diversification of rodent stripe patterns. Proceedings of the National Academy of Sciences USA,120, e2312077120. Download PDF
 
  • Johnson MR, Li S, Guerrero-Juarez C, Miller P, Brack BJ, Mereby SA, Moreno JA, Feigin C, Gaska J, Nie Q, Rivera-Perez J, Ploss A, Shvartsman SY, and Mallarino R*. (2023).  Sfrp2 is a multifunctional regulator of rodent color patterns. Nature Ecology and Evolution, 7, 2143-2159.  Download PDF
                 
                              Coverage: Nature Reviews Genetics Highlights

  • Li S, Mereby S, Rothstein M, Johnson MR, Brack B, and Mallarino R*. (2023). TIGER: Single-step in vivo genome editing in a non-traditional model species. Cell Reports 42: 112980. Download PDF  
 
  • Richardson R, Feigin C, Bano-Otalora B, Johnson MR, Allen AE, Park J, McDowell R, Mereby SA, Lucas RJ*, Mallarino R* (2023). The genomic basis of temporal niche evolution in a diurnal rodent. Current Biology  33, 1-10. Download PDF
                 
                               Coverage: Current Biology Dispatch

  • Feigin C, Moreno JA, Ramos R, Mereby SA, Alivisatos A, Wang W, van Amerongen R, Camacho J, Rasweiler JJ, Behringer R, Ostrow R, Plikus MV, and Mallarino R* (2023). Convergent deployment of ancestral programs during the evolution of mammalian flight membranes. Science Advances 9, eade7511. Download PDF
                 
                                 Coverage: Nature Research Highlight
                                                   Princeton University
                                                   Haaretz

  • Wooldridge TB, Kautt AF, Lassance JM, McFadden S, Domingues VS, Mallarino R, and Hoekstra HE (2022). An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice. Proceedings of the National Academy of Sciences USA 119 e2202862119. Download PDF.
 
Reviews

  • Johnson MR, Mallarino R. Genome-wide profiling of cis-regulatory elements in mammalian skin. Methods in Molecular Biology: Tissue Morphogenesis, in press. 
 
  • Kratochwil C and Mallarino R (2023). Mechanisms underlying the formation and evolution of vertebrate color patterns. Annual Review of Genetics 57:4.1-4.22. Download PDF

                                Coverage: Knowable magazine
                                                    The New Yorker

  • Rogers FD, Peña CJ, and Mallarino R (2023). African striped mice (Rhabdomys pumilio) as a neurobehavioral model for male parental care. Hormones and Behavior 152, 105364. Download PDF 
 
  • Feigin C, Li S, Moreno J, Mallarino R (2022). The GRN concept as a guide for evolutionary developmental biology. Journal of Experimental Zoology B Molecular and Developmental Evolution. DOI: 10.1002/jez.b.23132. Download PDF.
 
  • Mallarino R, Manceau M, Kronforst M. (2021). Editorial: EvoDevo of color pattern formation. Frontiers in Ecology and Evolution 9: 727516. Download PDF.
 
  • Caro T and Mallarino R (2019). Coloration in mammals. Trends in Ecology and Evolution; https://doi.org/10.1016/j.tree.2019.12.008. Download PDF.
 
  • Johnson MR, Barsh GS, Mallarino R (2019). Periodic patterns in Rodentia: Development and Evolution. Journal of Experimental Dermatology, DOI: 10.1111/exd.13852. Download PDF
 
  • Feigin CY, Mallarino R (2018). Phenotypic diversity: Setting the bar. eLife, 7:e39068. Download PDF


Ricardo's papers prior to Princeton 

  • Barret RDH*, Laurent S*, Mallarino R*, Xu C, Pfeiffer S, Jensen J, Hoekstra HE (2019). Linking a mutation to survival in wild mice. Science, 636:499-504. Download PDF.
           *co-first authors

  • Kocher S, Mallarino R, Rubin B, Yu D, Hoekstra HE, Pierce N (2018). The genetic basis of a social polymorphism in halictid bees. Nature Communications, 9: 4338. Download PDF
 
  • Mallarino R, Pillay N, Hoekstra HE, Schradin (2018). African striped mice. Current Biology, 28:R299-R301. Download PDF
 
  • Mallarino R, Henegar C, Mirasierra M, Manceau M, Shradin C, Vallejo M, Beronja S, Barsh GS, Hoekstra HE (2016). Developmental mechanisms of stripe patterns in rodents. Nature, 539: 518-523. Download PDF
 
  • Mallarino R, Hoekstra HE, Manceau M (2016). Non-model rodents for evolutionary developmental genetics. Current Opinion in Genetics and Development, 39:182-186. Download PDF
 
  • Mallarino R, Linden TA, Linnen CR, Hoesktra HE (2016). The role of Agouti isoforms in the evolution of cryptic light coloration in Peromyscus mice. Molecular Ecology, 26:10.1111/mec.13663. Download PDF
 
  • Mallarino R and Abzhanov A (2012). Paths less traveled: Evo-Devo approaches to investigating animal morphological evolution. Annual Review of Cell and Developmental Biology. 28:743-63. Download PDF
 
  • Mallarino R, Campas O, Fritz J, Burns K, Weeks O, Brenner M, Abzhanov A (2012). Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. Proceedings of the National Academy of Sciences USA 109:16222-7. Download PDF 
 
  • Mallarino R, Herrel A, Kuo W, Grant BR, Grant PR, Abzhanov A (2011). Two developmental modules establish 3D beak-shape variation in Darwin’s finches. Proceedings of the National Academy of Sciences USA 108:4057-62. Download PDF
 
  • Manceau M, Domingues V, Mallarino R, Hoekstra HE (2011). The developmental role of Agouti in color pattern evolution. Science 331:1062-5. Download PDF
 
  • Campas O, Mallarino R, Herrel A, Abzhanov A, Brenner MP (2010). Scaling and shear transformations capture beak shape variation in Darwin’s Finches. Proceedings of the National Academy of Sciences USA 107:3356-60. Download PDF
 
  • Jiggins CD, Mallarino R, Willmott KW, Bermingham E (2006). The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera; Nymphalidae). Evolution 60:1454-66. Download PDF
 
  • Whinnett A, Zimmermann A, Willmott KR, Herrera N, Mallarino R, Simpson F, Joron, M, Lamas G, Mallet J (2005). Strikingly variable divergence times inferred across an Amazonian butterfly “suture zone”. Proceedings of the Royal Society of London B. 272:2525-33. Download PDF​
 
  • Mallarino R, ​Bermingham E, Willmott KR, Whinnett A, Jiggins CD (2005). Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes. Molecular Phylogenetics and Evolution 34:625-44. Download PDF
 


Picture
Illustration by: Caroline Hu (www.hudrewthis.com)
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