Magaletta ME*, Lobo M*, Kernfeld E*, Aliee H, Huey J, Parsons T, Theis F, Maehr R. Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development. Nature Communications, January 24th, 2022
Guo D, Daman K, Chen JJ, Shi MJ, Yan J, Matijasevic Z, Rickard AM, Bennett MH, Kiselyov A, Zhou H, Bang AG, Wagner K, Maehr R, King O, Hayward L. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling. Elife, January 25th, 2022.
Chang CW, Parsi KM, Somasundaran M, Vanderleeden E, Cruz J, Cousineau A, Liu P, Li Q, Wang Y, Maehr R, Wang JP, Finberg RW. Cell culture model system utilizing engineered A549 cells to express high levels of ACE2 and TMPRSS2 for investigating SARS-CoV-2 infection and antivirals. bioRxiv, December 31st, 2021
Akgol-Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RM, Maehr R, Rando OJ, Mirny L, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nature Methods, September 3, 2021
Koupenova M, Corkrey HA, Vitseva O, Tanriverdi K, Somasundaran M, Liu P, Soofi S, Bhandari R, Godwin M, Parsi KM, Cousineau A, Maehr R, Wang J, Cameron SJ, Rade JJ, Finberg RW, Freedman JE. SARS-CoV-2 Initiates Programmed Cell Death in Platelets. Circulation research, July 23rd, 2021
Humphries F, Shmuel-Galia L, Jiang Z, Wilson R, Landis P, Ng SL, Parsi KM, Maehr R, Cruz J, Morales A, Ramanjulu JM, Bertin J, Pesiridis GS, Fitzgerald KA. A novel diamidobenzimidazole STING agonist protects against SARS-CoV2 infection. Science Immunology, May 18th, 2021
Reis M, Willis GR, Fernandez-Gonzalez A, Yeung V, Taglauer E, Magaletta M, Parsons T, Derr A, Liu X, Maehr R, Kourembanas S, Mitsialis SA. Mesenchymal stromal cell-derived extracellular vesicles restore thymic architecture and T cell function disrupted by neonatal hyperoxia. Front Immunol. March 2021, online
Akgol-Oksuz B, Yang L, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RM, Maehr R, Rando OJ, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. bioRxiv. December 27th, 2020
Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Krishna Mohan Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural details of mammalian chromosome architecture. Mol Cell. March 25th 2020, online
Han L, Choudhury S, Mich-Basso JD, Ammanamanchi N, Ganapathy B, Suresh S, Khaladkar M, Singh J, Maehr R, Zuppo DA, Kim J, Eberwine JH, Wyman SK, Wu Y, Kuhn B. Lamin B2 levels regulate polyploidization of cardiomyocyte nuclei and myocardial regeneragion. Developmental Cell, February 27th, 2020. online
Magaletta M, Siller R, Maehr R. Differentiation of human pluripotent stem cells toward pharyngeal endoderm derivatives: Current status and potential. Current Topics in Developmental Biology. February 25th, 2020. online
Stanney III W, Ladam F, Donaldson IJ, Parsons TJ, Maehr R, Bobola N, Sagerström CG. Combinatorial action of NF–Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish. Developmental Biology, December 17th, 2019. online
Phillips HM, Stothard CA, Mohiuddin S, Qureshi WMS, Kousa AI, Briones-Leon A, Khasawneh R, O’Loughlin C, Sanders R, Mazotta S, Dodds R, Seidel K, Bates T, Nakatomi M, Cockell S, Schneider JE, Mohun TJ, Maehr R, Kist R, Peters H, Bamforth SD. Pax9 is required for cardiovascular development and genetically interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis. Development, August 23rd, 2019
Min SY, Desai A, Zinger Y, Sharma A, DeSouza T, Genga, RMJ, Kucukural A, Lifshitz L, Nielsen S, Scheele C, Maehr R, Garber M, Corvera S. Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells. PNAS, August 16th 2019
Stanney III W, Ladam F, Donaldson IJ, Parsons TJ, Maehr R, Bobola N, Sagerström CG. TALE and NF-Y co-occupancy marks enhancers of developmental control genes during zygotic genome activation in zebrafish. bioRxiv, July 31st, 2019
Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Krishna Mohan Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural details of mammalian chromosome architecture. bioRxiv, May 17th, 2019
Genga RMJ*, Kernfeld E*, Parsi KM, Parsons T, Ziller M, Maehr R. Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development. Cell Reports, April 16th, 2019
Fischer DS, Fiedler AK, Kernfeld E, Genga RMJ, Bastidas-Ponce A, Bakhti M, Lickert H, Hasenauer J, Maehr R, Theis FJ. Inferring population dynamics from single-cell RNA-sequencing time series data. Nature Biotech, April 1st, 2019
Phillips HM, Stothard CA, Qureshi WMS, Kousa AI, Briones-Leon A, Khasawneh R, Sanders R, Mazotta S, Dodds R, Seidel K, Bates T, Nakatomi M, Cockell S, Schneider JE, Mohun TJ, Maehr R, Kist R, Peters H, Bamforth SD. Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis. bioRxiv, March 13 2019
Min SY, Desai A, Yang Z, Sharma A, Genga RMJ, Kucukural A, Lifshitz L, Maehr R, Garber M, Corvera S. Multiple human adipocyte subtypes and mechanisms of their development. bioRxiv, January 31, 2019
Kernfeld EM*, Genga RMJ*, Neherin K, Magaletta ME, Xu P, Maehr R. Single-cell RNA sequencing resolves cellular heterogeneity throughout embryonic development of the thymus. Immunity, Jun 5th 2018 (AOP)
Fischer DS, Fiedler AK, Kernfeld E, Genga RMJ, Hasenauer J, Maehr R, Theis FJ. Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series. bioRxiv, November 14, 2017
Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network**. The 4D nucleome project. Nature. 2017 Sep 13;549(7671):219-226
** Parsi KM, Genga RMJ, and Maehr R are part of the 4D Nucleome Network
Parsi KM, Hennesy E, Kearns NA, Maehr R. Using an Inducible CRISPR-Cas9-KRAB Effector System to Dissect Transcriptional Regulation in Human Embryonic Stem Cells. Methods Mol Biol. 2017;1507:221-233.
Babon JA, DeNicola ME, Blodgett DM, Crèvecoeur I, Buttrick TS, Maehr R, Bottino R, Naji A, Kaddis J, Elyaman W, James EA, Haliyur R, Brissova M, Overbergh L, Mathieu C, Delong T, Haskins K, Pugliese A, Campbell-Thompson M, Mathews C, Atkinson MA, Powers AC, Harlan DM, Kent SC. Analysis of self-antigen specificity of islet-infiltrating T cells from human donors with type 1 diabetes. Nature Medicine, Oct 31st 2016 (AOP).
Genga R, Kearns NA, Maehr R. Controlling transcription in human pluripotent stem cells using CRISPR-effectors. Methods, 2016 May 15th; 101:36-42.doi: 10.1016/j.ymeth.2015.10.014.
Pham H, Kearns NA, Maehr R. Transcriptional Regulation with CRISPR/Cas9 Effectors in Mammalian Cells. Methods Mol Biol. 2016; 1358:43-57. doi: 10.1007/978-1-4939-3067-8_3.
Kearns NA*, Pham H*, Tabak B, Genga RM, Silverstein NJ, Garber M, Maehr R. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nature Methods, 2015 Mar 16. doi: 10.1038/nmeth.3325. [Epub ahead of print]
Blum B, Roose AN, Barrandon O, Maehr R, Arvanites AC, Davidow LS, Davis JC, Peterson QP, Rubin LL, Melton DA. Reversal of β cell de-differentiation by a small molecule inhibitor of the TGFβ pathway. Elife. 2014 Sep 16;3. doi: 10.7554/eLife.02809. [Epub ahead of print]
Chen YJ, Finkbeiner SR, Weinblatt D, Emmett MJ, Tameire F, Yousefi M, Yang C, Maehr R, Zhou Q, Shemer R, Dor Y, Li C, Spence JR, Stanger BZ. De Novo Formation of Insulin-Producing “Neo-β Cell Islets” from Intestinal Crypts. Cell Reports. 2014 Mar 27;6(6):1046-58. doi: 10.1016/j.celrep.2014.02.013. Epub 2014 Mar 6
Kearns NA*, Genga RMJ*, Enuameh MS, Garber, M, Wolfe SA, Maehr R. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan 1. 141(1):219-23
Kearns NA, Genga RM*, Ziller M*, Kapinas K, Peters H, Brehm MA, Meissner A, Maehr R. Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules. Stem Cell Research. 2013 July 31. PMID:23917481.
Tajonar A, Maehr R, Hu G, Sneddon JB, Rivera-Feliciano J, Cohen DE, Melton DA. Vgll4 is a novel regulator of survival in human embryonic stem cells. Stem Cells. 2013 Jun 14. PMID:23765749.
Sherwood RI, Maehr R, Mazzoni EO, Melton DA. Wnt Signaling Specifies and Patterns Intestinal Endoderm. Mech Dev. 2011 Aug 10. [Epub ahead of print]
Maehr R. iPS cells for type 1 diabetes research and treatment. Clin Pharmacol Ther 2011 Mar 23.
Greer PL, Hanayama R, Bloodgood BL, Mardinly AR, Lipton DM, Flavell SW, Kim TK, Griffith EC, Waldon Z, Maehr R, Ploegh HL, Chowdhury S, Worley PF, Steen J, Greenberg ME. The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc. Cell 2010 Mar 5;140(5):704-16.
Niakan KK, Ji H*, Maehr R*, Vokes SA*, Rudolfa KT, Sherwood RI, Dimos JT, Chen AE, Melton DA, McMahon AP, Eggan K. Sox 17 is necessary for extraembryonic endoderm differentiation and represses embryonic stem cell self-renewal. Genes Dev. 2010 Feb 1;24(3):312-26
Maehr R, Chen S, Snitow M, Ludwig T, Yagasaki L, Goland R, Leibel RL, Melton DA. Generation of pluripotent stem cells from patients with type 1 diabetes. Proc Natl Acad Sci U S A. 2009 Aug 31 [Epub ahead of print]
Borowiak M, Maehr R, Chen S, Chen AE, Tang W, Fox JL, Schreiber SL, Melton, DA. Small Molecules Efficiently Direct Endodermal Differentiation of Mouse and Human Embryonic Stem Cells. Cell Stem Cell 4, 1–11, April 3, 2009.
Chen S, Borowiak M, Fox JL, Maehr R, Osafune K, Davidow L, Lam K, Peng LF, Schreiber SL, Rubin LL, Melton D. A small molecule that directs differentiation of human ESCs into the pancreatic lineage. Nat Chem Biol. 2009 Apr;5(4):258-65. Epub 2009 Mar 15.
Huangfu D, Osafune K, Maehr R, Guo W, Eijkelenboom A, Chen S, Muhlestein W, Melton DA. Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat Biotechnol. 2008 Nov;26(11):1269-75. Epub 2008 Oct 12.
Gounaris E, Tung CH, Restaino C, Maehr R, Kohler R, Joyce JA, Plough HL, Barrett TA, Weissleder R, Khazaie K. Live imaging of cysteine-cathepsin activity reveals dynamics of focal inflammation, angiogenesis, and polyp growth. PLoS ONE. 2008 Aug 13;3(8):e2916.
Huangfu D, Maehr R, Guo W, Eijkelenboom A, Snitow M, Chen AE, Melton DA. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol. 2008 Jul;26(7):795-7. Epub 2008 Jun 22.
Westbrook TF, Hu G, Ang XL, Mulligan P, Pavlova NN, Liang A, Leng Y, Maehr R, Shi Y, Harper JW, Elledge SJ. SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation. Nature. 2008 Mar 20;452(7185):370-4.
Ryu KY, Maehr R, Gilchrist CA, Long MA, Bouley DM, Mueller B, Ploegh HL, Kopito RR. The mouse polyubiquitin gene UbC is essential for fetal liver development, cell-cycle progression and stress tolerance. EMBO J. 2007 Jun 6;26(11):2693-706. Epub 2007 May 10.
Kumazaki K, Tirosh B, Maehr R, Boes M, Honjo T, Ploegh HL. AID-/-mus-/- mice are agammaglobulinemic and fail to maintain B220-CD138+ plasma cells. J Immunol. 2007 Feb 15;178(4):2192-203.
Hang HC, Loureiro J, Spooner E, van der Velden AW, Kim YM, Pollington AM, Maehr R, Starnbach MN, Ploegh HL. Mechanism-based probe for the analysis of cathepsin cysteine proteases in living cells. ACS Chem Biol. 2006 Dec 20;1(11):713-23.
Koch KS, Son KH, Maehr R, Pellicciotta I, Ploegh HL, Zanetti M, Sell S, Leffert HL. Immune-privileged embryonic Swiss mouse STO and STO cell-derived progenitor cells: major histocompatibility complex and cell differentiation antigen expression patterns resemble those of human embryonic stem cell lines. Immunology. 2006 Sep;119(1):98-115. Epub 2006 Jul 10.
Maehr R, Mintern JD, Herman AE, Lennon-Dumenil A, Mathis D, Benoist C, Ploegh HL. Cathepsin L is essential for onset of autoimmune diabetes in NOD mice. J Clin Invest. 2005 Oct;115(10):2934-43. Epub 2005 Sep 22.
Maehr R, Hang HC, Mintern JD, Kim YM, Cuvillier A, Nishimura M, Yamada K, Shirahama-Noda K, Hara-Nishimura I, Ploegh HL. Asparagine Endopeptidase Is Not Essential for Class II MHC Antigen Presentation but Is Required for Processing of Cathepsin L in Mice. J Immunol. 2005 Jun 1;174(11):7066-74.
Maehr R*, Kraus M*, Ploegh HL. Mice deficient in invariant chain and MHCII exhibit a normal mature B2 cell compartment. Eur J Immunol. 2004 Aug;34(8):2230-6
Van Swieten PF, Maehr R, van den Nieuwendijk AMCH, Kesseler BM, Reich M, Wong CS, Kalbacher H, Leeuwenburgh MA, Driessen C, van der Marel GA, Ploegh HL, and Overkleeft HS. Development of an isotype-coded activity based probe for the quantitative profiling of cysteine proteases. Bioorg Med Chem Lett. 2004 Jun 21;14(12):3131-4
Schmidt-Supprian M, Tian J, Grant EP, Pasparakis M, Maehr R, Ovaa H, Ploegh HL, Coyle AJ, Rajewsky K. Differential dependence of CD4+CD25+ regulatory and natural killer-like T cells on signals leading to NF-{kappa}B activation. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4566-71.
Kocks C*, Maehr R*, Overkleeft HS, Wang EW, Iyer LK, Lennon-Dumenil AM, Ploegh HL, Kessler BM. Functional Proteomics of the Active Cysteine Protease Content in Drosophila S2 Cells. Mol Cell Proteomics. 2003 Nov;2(11):1188-1197.
Fiebiger E, Maehr R, Villadangos J, Weber E, Erickson A, Bikoff E, Ploegh HL, Lennon-Dumenil AM. Invariant chain controls the activity of extracellular cathepsin L. J Exp Med. 2002 Nov 4;196(9):1263-9.
Vugmeyster Y, Borodovsky A, Maurice MM, Maehr R, Furman MH, Ploegh HL. The ubiquitin-proteasome pathway in thymocyte apoptosis: caspase-dependent processing of the deubiquitinating enzyme USP7 (HAUSP). Mol Immunol. 2002 Nov;39(7-8):431-41.
Lennon-Dumenil AM*, Bakker AH*, Maehr R, Fiebiger E, Overkleeft HS, Rosemblatt M, Ploegh HL, Lagaudriere-Gesbert C. Analysis of protease activity in live antigen-presenting cells shows regulation of the phagosomal proteolytic contents during dendritic cell activation. J Exp Med. 2002 Aug 19;196(4):529-40.
* these authors contributed equally to the work
