Publications while at Stony Brook University:
#Denotes equal contribution | *Denotes corresponding author
Medwig-Kinney TN, Sirota SS, Gibney TV, Pani AM, Matus DQ. An in vivo toolkit to visualize endogenous LAG-2/Delta and LIN-12/Notch signaling in C. elegans. MicroPubl Biol. 2022 Jul 28;2022:10.17912/micropub.biology.000602. (PDF)
Pani AM, Gibney TV, Medwig-Kinney TN, Matus DQ, Goldstein B. A new toolkit to visualize and perturb endogenous LIN-12/Notch signaling in C. elegans. MicroPubl Biol. 2022 Jul 28;2022:10.17912/micropub.biology.000603. (PDF)
Martinez MAQ and *Matus DQ. CDK activity sensors: genetically encoded ratiometric biosensors for live analysis of the cell cycle. Biochem Soc Trans. 2022 Jun 30;50(3):1081-1090. (PDF)
Smith JJ, Xiao Y, Parsan N, Medwig-Kinney TN, Martinez MAQ, Moore FEQ, Palmisano NJ, Kohrman AQ, Chandhok Delos Reyes M, Adikes RC, Liu S, Bracht SA, Zhang W, Wen K, Kratsios P, *Matus DQ. The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo. PLoS Genet. 2022 Jan 4;18(1):e1009981. (PDF)
Hills-Muckey K, Martinez MAQ, Stec N, Hebbar S, Saldanha J, Medwig-Kinney TN, Moore FEQ, Ivanova M, Morao A, Ward JD, Moss EG, Ercan S, Zinovyeva AY, Matus DQ, Hammell CM. An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans. Genetics. 2021 Oct 12:iyab174. (PDF)
Morabito RD, Adikes RC, Matus DQ, Martin BL. Cyclin-Dependent Kinase Sensor Transgenic Zebrafish Lines for Improved Cell Cycle State Visualization in Live Animals. Zebrafish. 2021 Oct 20. (PDF)
#Medwig-Kinney TN, #Palmisano NJ, *Matus DQ. Deletion of a putative HDA-1 binding site in the hlh-2 promoter eliminates expression in C. elegans dorsal uterine cells. MicroPubl Biol. 2021 Sep 2;2021:10.17912/micropub.biology.000449. (PDF)
#Palmisano NJ, #Azmi MA, Medwig-Kinney TN, Moore FEQ, Rahman R, Zhang W, *Adikes RC, *Matus DQ. A laboratory module that explores RNA interference and codon optimization through fluorescence microscopy using Caenorhabditis elegans. bioRxiv. 2021 July 20. (PDF)
Ashley G, #Duong T, #Levenson MT, #Martinez MAQ, Johnson LC, Hibshman JD, Saeger HN, Palmisano NJ, Doonan R, Martinez-Mendez R, Davidson B, Zhang W, Ragle JM, Medwig-Kinney TN, Sirota SS, Goldstein B, Matus DQ, Dickinson DJ, Reiner DJ, Ward JD. An expanded auxin-inducible degron toolkit for Caenorhabditis elegans. Genetics. 2021 Jan 20:iyab006. (PDF)
#Adikes RC, #Korhman AQ, #Martinez MAQ, Palmisano NJ, Smith JJ, Medwig-Kinney TN, Min M, Sallee MD, Ahmed OB, Kim N, Liu S, Morabito RD, Weeks N, Zhao Q, Zhang W, Feldman JL, Barkoulas M, Pani AM, Spencer SL, Martin BL, *Matus DQ. Visualizing the metazoan proliferation-quiescence decision in vivo. eLife. 2020 Dec 22;9:e63265. (PDF)
Martinez MAQ and *Matus DQ. Auxin-mediated Protein Degradation in Caenorhabditis elegans. Bio Protoc. 2020 Apr 20;10(8):e3589. (PDF)
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Martinez MAQ, Kinney BA, Ashley G, Ragle JM, Johnson L, Aguilera J, Hammell CM, Ward JD, *Matus DQ. Rapid Degradation of Caenorhabditis elegans Proteins at Single-Cell Resolution with a Synthetic Auxin. G3 (Bethesda). 2020 Jan 7;10(1):267-280. (PDF) See protocol in Bio-protocol.
Kelley LC, Chi Q, Cáceres R, Hastie E, Schindler AJ, Jiang Y, Matus DQ, Plastino J, Sherwood DR. Adaptive F-actin Polymerization and Localized ATP Production Drive Basement Membrane Invasion in the Absence of MMPs. Dev Cell. 2019 Feb 11;48(3):313-328.e8. (PDF)
Liu TL, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E. Observing the cell in its native state: Imaging sub cellular dynamics in multicellular organisms. Science. 2018 Apr 20;360(6386). (PDF)
Medwig TN and *Matus DQ. Breaking down barriers: the evolution of cell invasion. Curr Opin Genet Dev. 2017 Dec;47:33-40. (PDF)
Goto H, Kimmey SC, Row RH, Matus DQ, Martin BL. FGF and canonical Wnt signaling cooperate to induce paraxial mesoderm from tailbud neuromesodermal progenitors through regulation of a two-step epithelial to mesenchymal transition. Development. 2017 Apr 15;144(8):1412-1424. See featured movie in Development. (PDF)
Kohrman AQ and *Matus DQ. Divide or Conquer: Cell Cycle Regulation of Invasive Behavior. Trends Cell Biol. 2017 Jan;27(1):12-25. (PDF)
Fu Q, Martin BL, Matus DQ, Gao L. Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy. Nat Commun. 2016 Mar 23;7:11088. (PDF)
Lyons DC, Srivastava M, *Matus DQ (2016). Evolution of Developmental Mechanisms Controlling Cell Fate. Encyclopedia of Evolutionary Biology. 409-419. (PDF)
*Matus DQ, Lohmer LL, Kelley LC, Schindler AJ, Kohrman AQ, Barkoulas M, Zhang W, Chi Q, *Sherwood DR. Invasive Cell Fate Requires G1 Cell-Cycle Arrest and Histone Deacetylase-Mediated Changes in Gene Expression. Dev Cell. 2015 Oct 26;35(2):162-74. (PDF) See highlight in Scientific American.
Wang L, Shen W, Lei S, Matus D, Sherwood D, Wang Z. MIG-10 (Lameillipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans. Biochem Biophys Res Commun. 2014 Sep 26;452(3):328-33. (PDF)
*Matus DQ, Chang E, Makohon-Moore SC, Hagedorn MA, Chi Q, Sherwood DR. Cell division and targeted cell cycle arrest opens and stabilizes basement membrane gaps. Nat Commun. 2014 Jun 13;5:4184. (PDF)
Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AW, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev. 2015 May-Jun;17(3):198-219. (PDF)
Publications prior to Stony Brook University:
I. Cell and developmental biology:
Matus DQ, Li X, Durbin S, Agarwal D, Chi Q, Weiss S, Sherwood DR. In vivo identification of regulators of cell invasion across basement membranes. Sci Signal. 2010 May 4;3(120):ra35. See comment in Nat Rev Cancer. 2010 Jul;10(7):452 and Science. 2010 May 28; 328:1077. See podcast in Matus DQ, Sherwood DR, VanHook AM. 2010. Sci. Signal. 3 (121), pc10.
Ziel JW, Matus DQ, Sherwood DR. An expression screen for RhoGEF genes involved in C. elegans gonadogenesis. Gene Expr Patterns. 2009 Sep;9(6):397-403.
II. Evolutionary developmental biology (evo-devo):
Marlow H, Matus DQ, Martindale MQ. Ectopic activation of the canonical wnt signaling pathway affects ectodermal patterning along the primary axis during larval development in the anthozoan Nematostella vectensis. Dev Biol. 2013 Aug 15;380(2):324-34.
Marlow HQ, Srivastava M, Matus DQ, Rokhsar D, Martindale MQ. Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian. Dev Neurobiol. 2009 Mar;69(4):235-54.
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sorensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008 Apr 10;452(7188):745-9.
Matus DQ, Magie CR, Pang K, Martindale MQ, Thomsen GH. The Hedgehog gene family of the cnidarian, Nematostella vectensis, and implications for understanding metazoan Hedgehog pathway evolution. Dev Biol. 2008 Jan 15;313(2):501-18.
Fröbius AC, Matus DQ, Seaver EC. Genomic organization and expression demonstrate spatial and temporal Hox gene colinearity in the lophotrochozoan Capitella sp. I. PLoS One. 2008;3(12):e4004.
Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella vectensis. PLoS One. 2007 Jan 24;2(1):e153.
Matus DQ, Thomsen GH, Martindale MQ. FGF signaling in gastrulation and neural development in Nematostella vectensis, an anthozoan cnidarian. Dev Genes Evol. 2007 Feb;217(2):137-48.
Matus DQ, Pang K, Daly M, Martindale MQ. Expression of Pax gene family members in the anthozoan cnidarian, Nematostella vectensis. Evol Dev. 2007 Jan-Feb;9(1):25-38.
Matus DQ, Halanych KM, Martindale MQ. The Hox gene complement of a pelagic chaetognath, Flaccisagitta enflata. Integr Comp Biol. 2007 Dec;47(6):854-64.
Adamska M, Matus DQ, Adamski M, Green K, Rokhsar DS, Martindale MQ, Degnan BM. The evolutionary origin of hedgehog proteins. Curr Biol. 2007 Oct 9;17(19):R836-7.
Lee PN, Pang K, Matus DQ, and Martindale, MQ (2006). A WNT of things to come: Evolution of Wnt signaling and polarity in cnidarians. Seminars in Cell & Developmental Biology 17, 157-167.
Matus DQ, Thomsen GH, Martindale MQ. Dorso/ventral genes are asymmetrically expressed and involved in germ-layer demarcation during cnidarian gastrulation. Curr Biol. 2006 Mar 7;16(5):499-505.
Matus DQ, Pang K, Marlow H, Dunn CW, Thomsen GH, Martindale MQ. Molecular evidence for deep evolutionary roots of bilaterality in animal development. Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11195-200.
Matus DQ, Copley RR, Dunn CW, Hejnol A, Eccleston H, Halanych KM, Martindale MQ, Telford MJ. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Curr Biol. 2006 Aug 8;16(15):R575-6.
Extavour CG, Pang K, Matus DQ, Martindale MQ. vasa and nanos expression patterns in a sea anemone and the evolution of bilaterian germ cell specification mechanisms. Evol Dev. 2005 May-Jun;7(3):201-15.
Pang K, Matus DQ, Martindale MQ. The ancestral role of COE genes may have been in chemoreception: evidence from the development of the sea anemone, Nematostella vectensis (Phylum Cnidaria; Class Anthozoa). Dev Genes Evol. 2004 Mar;214(3):134-8.
III. Marine mammal cognition:
Herman LM, Matus DS, Herman EYK, Ivancic M, Pack AA. The bottlenosed dolphin’s (Tursiops truncatus) understanding of gestures as symbolic representations of its body parts. Animal Learning and Behavior. 2001;29(3):250-264.