2025

An ancient evolutionary origin for IL-1 cytokines as mediators of immunity.

Fontenla-Iglesias F, Lin TM, Williams AG, Das S, Lee CY, Rast JP, Cooper MD, Buckley KM, Fugmann SD.

bioRxiv [Preprint]. 2025 Jul 18:2025.07.17.662885. doi: 10.1101/2025.07.17.662885. 

Mesophilic compostability of polylactic acid and the associated microbiome as revealed by metagenomics.  

Hsueh SW,  Kurniadi AC, Amelia TSM, Lee CF, Fugmann SD, Yang SY.

Journal of Hazardous Materials Letters. 2025 

The classical MHC class I and II genes of O. m. formosanus exhibit different polymorphism levels.  

Zhang ZW, Fugmann LA, Yang SY, Gwo JC, Fugmann SD.

Dev Comp Immunol. 2025 Jun;168:105392. doi: 10.1016/j.dci.2025.105392. 

2024

Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development.  

Li YR, Ling LB, Chao A, Fugmann SD, Yang SY..

Life Sci Alliance. 2024 Jul 11;7(10):e202302401. doi: 10.26508/lsa.202302401. 

The cytokine genes of Oncorhynchus masou formosanus include a defective interleukin-4/13A gene.  

Yen YH, Zheng DY, Yang SY, Gwo JC, Fugmann SD.

Dev Comp Immunol. 2024 Jun:155:105156. doi: 10.1016/j.dci.2024.105156. 

2023

Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways.  

Hsueh SW, Jian YH, Fugmann SD, Yang SY.

PLoS One 2023 Oct 3;18(10):e0292137. doi: 10.1371/journal.pone.0292137.

Functional characterization of the MyD88 homologs in Strongylocentrotus purpuratus.  

Chou ST, Lin TM, Yang HY, Fugmann SD.

Dev Comp Immunol 2023 Feb:139:104580. doi: 10.1016/j.dci.2022.104580.

2021

Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation.

Li YR, Lai HW, Huang HH, Chen HC, Fugmann SD, Yang SY.

Genome Res. 2021 Apr 15:gr.271148.120. doi: 10.1101/gr.271148.120. 

2018

AID/APOBEC-like cytidine deaminases are ancient innate immune mediators in invertebrates.

Liu MC, Liao WY, Buckley KM, Yang SY, Rast JP, Fugmann SD.

Nat Commun. 2018 May 16;9(1):1948. doi: 10.1038/s41467-018-04273-x.

2017

Lectins identify distinct populations of coelomocytes in Strongylocentrotus purpuratus.

Liao WY, Fugmann SD.

PLoS One. 2017 Nov 10;12(11):e0187987. doi: 10.1371/journal.pone.0187987. 

Evidence for parallel evolution of a gene involved in the regulation of spermatogenesis.

Wang XR, Ling LB, Huang HH, Lin JJ, Fugmann SD, Yang SY.

Proc Biol Sci. 2017 May 31;284(1855):20170324. doi: 10.1098/rspb.2017.0324.

2016

Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination.

Carmona LM, Fugmann SD, Schatz DG.

Genes Dev. 2016 Apr 15;30(8):909-17. doi: 10.1101/gad.278432.116. Epub 2016 Apr 7.

2014

The identification of a novel SIRT6 modulator from Trigonella foenum-graecum using ligand fishing with protein coated magnetic beads.

Singh N, Ravichandran S, Spelman K, Fugmann SD, Moaddel R.

J Chromatogr B Analyt Technol Biomed Life Sci. 2014 Oct 1;968:105-11. doi: 10.1016/j.jchromb.2014.03.016. 

Form follows function - the three-dimensional structure of antigen receptor gene loci.

Fugmann SD.

Curr Opin Immunol. 2014 Apr;27:33-7. doi: 10.1016/j.coi.2014.01.011. Epub 2014 Feb 16.

Pharmacophore model of the quercetin binding site of the SIRT6 protein.

Ravichandran S, Singh N, Donnelly D, Migliore M, Johnson P, Fishwick C, Luke BT, Martin B, Maudsley S, Fugmann SD, Moaddel R.

J Mol Graph Model. 2014 Apr;49:38-46. doi: 10.1016/j.jmgm.2014.01.004. Epub 2014 Jan 20.

2013

Synthesis and characterization of a SIRT6 open tubular column: predicting deacetylation activity using frontal chromatography.

Singh N, Ravichandran S, Norton DD, Fugmann SD, Moaddel R.

Anal Biochem. 2013 May 15;436(2):78-83. doi: 10.1016/j.ab.2013.01.018. Epub 2013 Jan 29.

2012

Transcription, splicing, and release: are we there yet?

Sen R, Fugmann SD.

Cell. 2012 Jul 20;150(2):241-3. doi: 10.1016/j.cell.2012.07.004.

2011

Synthesis and characterization of SIRT6 protein coated magnetic beads: identification of a novel inhibitor of SIRT6 deacetylase from medicinal plant extracts.

Yasuda M, Wilson DR, Fugmann SD, Moaddel R.

Anal Chem. 2011 Oct 1;83(19):7400-7. doi: 10.1021/ac201403y. Epub 2011 Sep 2.

Separation of mutational and transcriptional enhancers in Ig genes.

Kothapalli NR, Collura KM, Norton DD, Fugmann SD.

J Immunol. 2011 Sep 15;187(6):3247-55. doi: 10.4049/jimmunol.1101568. Epub 2011 Aug 15.

Characterizing somatic hypermutation and gene conversion in the chicken DT40 cell system.

Kothapalli N, Fugmann SD.

Methods Mol Biol. 2011;748:255-71. doi: 10.1007/978-1-61779-139-0_18.

Classical Mus musculus Igκ enhancers support transcription but not high level somatic hypermutation from a V-lambda promoter in chicken DT40 cells.

Kothapalli NR, Norton DD, Fugmann SD.

PLoS One. 2011 Apr 20;6(4):e18955. doi: 10.1371/journal.pone.0018955.

RAG-2 unleashed: lymphocytes beware.

Fugmann SD.

Immunity. 2011 Feb 25;34(2):137-9. doi: 10.1016/j.immuni.2011.02.007.

Targeting of AID-mediated sequence diversification to immunoglobulin genes.

Kothapalli NR, Fugmann SD.

Curr Opin Immunol. 2011 Apr;23(2):184-9. doi: 10.1016/j.coi.2010.12.009. Epub 2011 Feb 2.

2010

The origins of vertebrate adaptive immunity.

Litman GW, Rast JP, Fugmann SD.

Nat Rev Immunol. 2010 Aug;10(8):543-53. doi: 10.1038/nri2807.

The origins of the Rag genes--from transposition to V(D)J recombination.

Fugmann SD.

Semin Immunol. 2010 Feb;22(1):10-6. doi: 10.1016/j.smim.2009.11.004. Epub 2009 Dec 9.

2009

A coming-of-age story: activation-induced cytidine deaminase turns 10.

Delker RK, Fugmann SD, Papavasiliou FN.

Nat Immunol. 2009 Nov;10(11):1147-53. doi: 10.1038/ni.1799. Epub 2009 Oct 20.

2008

The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails.

Wilson DR, Norton DD, Fugmann SD.

Dev Comp Immunol. 2008;32(10):1221-30. doi: 10.1016/j.dci.2008.03.012. Epub 2008 May 8.

Cutting edge: a cis-acting DNA element targets AID-mediated sequence diversification to the chicken Ig light chain gene locus.

Kothapalli N, Norton DD, Fugmann SD.

J Immunol. 2008 Feb 15;180(4):2019-23. doi: 10.4049/jimmunol.180.4.2019.

AID-mediated diversification within the IgL locus of chicken DT40 cells is restricted to the transcribed IgL gene.

Gopal AR, Fugmann SD.

Mol Immunol. 2008 Apr;45(7):2062-8. doi: 10.1016/j.molimm.2007.10.017. Epub 2007 Nov 26.

2007

The beyond 12/23 restriction is imposed at the nicking and pairing steps of DNA cleavage during V(D)J recombination.

Drejer-Teel AH, Fugmann SD, Schatz DG.

Mol Cell Biol. 2007 Sep;27(18):6288-99. doi: 10.1128/MCB.00835-07. Epub 2007 Jul 16.

Activation-induced cytidine deaminase-mediated sequence diversification is transiently targeted to newly integrated DNA substrates.

Yang SY, Fugmann SD, Gramlich HS, Schatz DG.

J Biol Chem. 2007 Aug 31;282(35):25308-13. doi: 10.1074/jbc.M704231200. Epub 2007 Jul 5.

Control of gene conversion and somatic hypermutation by immunoglobulin promoter and enhancer sequences.

Yang SY, Fugmann SD, Schatz DG.

J Exp Med. 2006 Dec 25;203(13):2919-28. doi: 10.1084/jem.20061835. Epub 2006 Dec 18.

2006

The genome of the sea urchin Strongylocentrotus purpuratus.

Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R.

Science. 2006 Nov 10;314(5801):941-52. doi: 10.1126/science.1133609.

The immune gene repertoire encoded in the purple sea urchin genome.

Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH, Terwilliger DP, Buckley KM, Brockton V, Nair SV, Berney K, Fugmann SD, Anderson MK, Pancer Z, Cameron RA, Smith LC, Rast JP.

Dev Biol. 2006 Dec 1;300(1):349-65. doi: 10.1016/j.ydbio.2006.08.065. Epub 2006 Sep 3.

An ancient evolutionary origin of the Rag1/2 gene locus.

Fugmann SD, Messier C, Novack LA, Cameron RA, Rast JP.

Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3728-33. doi: 10.1073/pnas.0509720103. Epub 2006 Feb 27.

older publications - under construction