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Johanna Klughammer - Publications

2022   |   2021   |   2020   |   2019   |   2018   |   2017   |   2016   |   2015 and before 

 

2022

SM-Omics is an automated platform for high-throughput spatial multi-omics.
Vickovic S, Lötstedt B, Klughammer J, Mages S, Segerstolpe Å, Rozenblatt-Rosen O, Regev A.
Nat Commun. 2022 Feb 10;13(1):795. PubMed

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2021

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.
Chaligne R, Gaiti F, Silverbush D, Schiffman JS, Weisman HR, Kluegel L, Gritsch S, Deochand SD, Gonzalez Castro LN, Richman AR, Klughammer J, Biancalani T, Muus C, Sheridan C, Alonso A, Izzo F, Park J, Rozenblatt-Rosen O, Regev A, Suvà ML, Landau DA.
Nat Genet. 2021 Oct;53(10):1469-1479. doi: 10.1038/s41588-021-00927-7. PubMed

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation.
Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T; BIOS Consortium, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, van IJzendoorn MH, Uitterlinden AG, Jaddoe VWV, Haley C, McIntosh AM, Evans KL, Murray A, Räikkönen K, Lahti J, Nohr EA, Sørensen TIA, Hansen T, Morgen CS, Binder EB, Lucae S, Gonzalez JR, Bustamante M, Sunyer J, Holloway JW, Karmaus W, Zhang H, Deary IJ, Wray NR, Starr JM, Beekman M, van Heemst D, Slagboom PE, Morange PE, Trégouët DA, Veldink JH, Davies GE, de Geus EJC, Boomsma DI, Vonk JM, Brunekreef B, Koppelman GH, Alarcón-Riquelme ME, Huang RC, Pennell CE, van Meurs J, Ikram MA, Hughes AD, Tillin T, Chaturvedi N, Pausova Z, Paus T, Spector TD, Kumari M, Schalkwyk LC, Visscher PM, Davey Smith G, Bock C, Gaunt TR, Bell JT, Heijmans BT, Mill J, Relton CL.
Nat Genet. 2021 Sep;53(9):1311-1321. doi: 10.1038/s41588-021-00923-x. PubMed

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.
Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A; IMAXT Consortium, Church GM, Marblestone AH, Boyden ES.
Science. 2021 Jan 29;371(6528):eaax2656. doi: 10.1126/science.aax2656. PubMed

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2020

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A.
Nat Med. 2020 May;26(5):792-802. doi: 10.1038/s41591-020-0844-1. Epub 2020 May 11. PubMed

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2019

High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G*, Salmén F*, Klughammer J*, Stenbeck L*, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL.
Nat Methods. 2019 Oct;16(10):987-990. doi: 10.1038/s41592-019-0548-y. Epub 2019 Sep 9. PubMed

The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease.
Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A.
Cancer Cell. 2019 Jan 14;35(1):125-139.e9. doi: 10.1016/j.ccell.2018.11.018. PubMed

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2018

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space.
Klughammer J*, Kiesel B*, Roetzer T, Fortelny N, Nemc A, Nenning KH, Furtner J, Sheffield NC, Datlinger P, Peter N, Nowosielski M, Augustin M, Mischkulnig M, Ströbel T, Alpar D, Ergüner B, Senekowitsch M, Moser P, Freyschlag CF, Kerschbaumer J, Thomé C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, Haybaeck J, Krassnig S, Mahdy Ali K, von Campe G, Payer F, Sherif C, Preiser J, Hauser T, Winkler PA, Kleindienst W, Würtz F, Brandner-Kokalj T, Stultschnig M, Schweiger S, Dieckmann K, Preusser M, Langs G, Baumann B, Knosp E, Widhalm G, Marosi C, Hainfellner JA, Woehrer A, Bock C.
Nat Med. 2018 Oct;24(10):1611-1624. doi: 10.1038/s41591-018-0156-x. Epub 2018 Aug 27. PubMed

Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty-liver-like phenotype in offspring.
Skjærven KH, Jakt LM, Fernandes JMO, Dahl JA, Adam AC, Klughammer J, Bock C, Espe M.
Sci Rep. 2018 Feb 14;8(1):3055. doi: 10.1038/s41598-018-21211-5. PubMed

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2017

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.
Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Álava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, Holter W, Windhager R, Dirksen U, Ambros PF, Delattre O, Kovar H, Bock C, Tomazou EM.
Nat Med. 2017 Mar;23(3):386-395. doi: 10.1038/nm.4273. Epub 2017 Jan 30. PubMed

Pooled CRISPR screening with single-cell transcriptome readout.
Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C.
Nat Methods. 2017 Mar;14(3):297-301. doi: 10.1038/nmeth.4177. Epub 2017 Jan 18. PubMed

Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease.
Klughammer J, Dittrich M, Blom J, Mitesser V, Vogel U, Frosch M, Goesmann A, Müller T, Schoen C.
PLoS One. 2017 Jan 12;12(1):e0169892. doi: 10.1371/journal.pone.0169892. eCollection 2017. PubMed

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2016

Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity.
Li J, Casteels T, Frogne T, Ingvorsen C, Honoré C, Courtney M, Huber KVM, Schmitner N, Kimmel RA, Romanov RA, Sturtzel C, Lardeau CH, Klughammer J, Farlik M, Sdelci S, Vieira A, Avolio F, Briand F, Baburin I, Májek P, Pauler FM, Penz T, Stukalov A, Gridling M, Parapatics K, Barbieux C, Berishvili E, Spittler A, Colinge J, Bennett KL, Hering S, Sulpice T, Bock C, Distel M, Harkany T, Meyer D, Superti-Furga G, Collombat P, Hecksher-Sørensen J, Kubicek S.
Cell. 2017 Jan 12;168(1-2):86-100.e15. doi: 10.1016/j.cell.2016.11.010. Epub 2016 Dec 1. PubMed

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.
Farlik M, Halbritter F, Müller F, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A, Uppal R, Stunnenberg HG, Ouwehand WH, Laurenti E, Lengauer T, Frontini M, Bock C.
Cell Stem Cell. 2016 Dec 1;19(6):808-822. doi: 10.1016/j.stem.2016.10.019. Epub 2016 Nov 17. PubMed

Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis.
Tschurtschenthaler M, Kachroo P, Heinsen FA, Adolph TE, Rühlemann MC, Klughammer J, Offner FA, Ammerpohl O, Krueger F, Smallwood S, Szymczak S, Kaser A, Franke A.
Sci Rep. 2016 Aug 19;6:31640. doi: 10.1038/srep31640. PubMed

Specification of tissue-resident macrophages during organogenesis.
Mass E, Ballesteros I, Farlik M, Halbritter F, Günther P, Crozet L, Jacome-Galarza CE, Händler K, Klughammer J, Kobayashi Y, Gomez-Perdiguero E, Schultze JL, Beyer M, Bock C, Geissmann F.
Science. 2016 Sep 9;353(6304):aaf4238. doi: 10.1126/science.aaf4238. Epub 2016 Aug 4. PubMed

Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.
Li J*, Klughammer J*, Farlik M*, Penz T*, Spittler A, Barbieux C, Berishvili E, Bock C, Kubicek S.
EMBO Rep. 2016 Feb;17(2):178-87. doi: 10.15252/embr.201540946. Epub 2015 Dec 21. PubMed

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2015 and before

Differential DNA Methylation Analysis without a Reference Genome.
Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C.
Cell Rep. 2015 Dec 22;13(11):2621-2633. doi: 10.1016/j.celrep.2015.11.024. Epub 2015 Dec 8. PubMed

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.
Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C.
Cell Rep. 2015 Mar 3;10(8):1386-97. doi: 10.1016/j.celrep.2015.02.001. Epub 2015 Feb 26. PubMed

Divergent expression regulation of gonad development genes in medaka shows incomplete conservation of the downstream regulatory network of vertebrate sex determination.
Herpin A, Adolfi MC, Nicol B, Hinzmann M, Schmidt C, Klughammer J, Engel M, Tanaka M, Guiguen Y, Schartl M.
Mol Biol Evol. 2013 Oct;30(10):2328-46. doi: 10.1093/molbev/mst130. Epub 2013 Jul 24. PubMed

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