EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays.

Megas S, Lorenzi V, Marioni JC.

Genome Biol, 2024

doi:10.1186/s13059-024-03259-x.

The Virtual Child.

Gilbertson RJ, Behjati S, Böttcher AL, Bronner ME, Burridge M, Clausing H, Clifford H, Danaher T, Donovan LK, Drost J, Eggermont AMM, Emerson C, Flores MG, Hamerlik P, Jabado N, Jones A, Kaessmann H, Kleinman CL, Kool M, Kutscher LM, Lindberg G, Linnane E, Marioni JC, Maris JM, Monje M, Macaskill A, Niederer S, Northcott PA, Peeters E, Plieger-van Solkema W, Preußner L, Rios AC, Rippe K, Sandford P, Sgourakis NG, Shlien A, Smith P, Straathof K, Sullivan PJ, Suvà ML, Taylor MD, Thompson E, Vento-Tormo R, Wainwright BJ, Wechsler-Reya RJ, Westermann F, Winslade S, Al-Lazikani B, Pfister SM.

Cancer Discov, 2024

doi:10.1158/2159-8290.cd-23-1500.

A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast.

Reed AD, Pensa S, Steif A, Stenning J, Kunz DJ, Porter LJ, Hua K, He P, Twigger AJ, Siu AJQ, Kania K, Barrow-McGee R, Goulding I, Gomm JJ, Speirs V, Jones JL, Marioni JC, Khaled WT.

Nat Genet, 2024

doi:10.1038/s41588-024-01688-9.

Mitochondrial complex I activity in microglia sustains neuroinflammation.

Peruzzotti-Jametti L, Willis CM, Krzak G, Hamel R, Pirvan L, Ionescu RB, Reisz JA, Prag HA, Garcia-Segura ME, Wu V, Xiang Y, Barlas B, Casey AM, van den Bosch AMR, Nicaise AM, Roth L, Bates GR, Huang H, Prasad P, Vincent AE, Frezza C, Viscomi C, Balmus G, Takats Z, Marioni JC, D'Alessandro A, Murphy MP, Mohorianu I, Pluchino S.

Nature, 2024

doi:10.1038/s41586-024-07167-9.

The dynamic genetic determinants of increased transcriptional divergence in spermatids.

Panten J, Heinen T, Ernst C, Eling N, Wagner RE, Satorius M, Marioni JC, Stegle O, Odom DT.

Nat Commun, 2024

doi:10.1038/s41467-024-45133-1.

Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale.

Imaz-Rosshandler I, Rode C, Guibentif C, Harland LTG, Ton MN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J, Marioni JC, de Bruijn MFTR, Göttgens B.

Development, 2024

doi:10.1242/dev.201867.

Stabilized mosaic single-cell data integration using unshared features.

Ghazanfar S, Guibentif C, Marioni JC.

Nat Biotechnol, 2024

doi:10.1038/s41587-023-01766-z.

Early human lung immune cell development and its role in epithelial cell fate.

Barnes JL, Yoshida M, He P, Worlock KB, Lindeboom RGH, Suo C, Pett JP, Wilbrey-Clark A, Dann E, Mamanova L, Richardson L, Polanski K, Pennycuick A, Allen-Hyttinen J, Herczeg IT, Arzili R, Hynds RE, Teixeira VH, Haniffa M, Lim K, Sun D, Rawlins EL, Oliver AJ, Lyons PA, Marioni JC, Ruhrberg C, Tuong ZK, Clatworthy MR, Reading JL, Janes SM, Teichmann SA, Meyer KB, Nikolić MZ.

Sci Immunol, 2023

doi:10.1126/sciimmunol.adf9988.

A human embryonic limb cell atlas resolved in space and time.

Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Li T, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, Blain R, Chedotal A, FitzPatrick DR, Firth H, Dean A, Bayraktar OA, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA.

Nature, 2023

doi:10.1038/s41586-023-06806-x.

Milo2.0 unlocks population genetic analyses of cell state abundance using a count-based mixed model

Alice K, Marioni JC, Morgan MD.

2023

doi:10.1101/2023.11.08.566176.

Cytotoxic T lymphocytes require transcription for infiltration but not target cell lysis.

Richard AC, Ma CY, Marioni JC, Griffiths GM.

EMBO Rep, 2023

doi:10.15252/embr.202357653.

Precise identification of cell states altered in disease using healthy single-cell references.

Dann E, Cujba AM, Oliver AJ, Meyer KB, Teichmann SA, Marioni JC.

Nat Genet, 2023

doi:10.1038/s41588-023-01523-7.

Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation.

Wang R, Yang X, Chen J, Zhang L, Griffiths JA, Cui G, Chen Y, Qian Y, Peng G, Li J, Wang L, Marioni JC, Tam PPL, Jing N.

Nat Commun, 2023

doi:10.1038/s41467-023-41482-5.

Yolk sac cell atlas reveals multiorgan functions during human early development.

Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Quiroga Londoño M, Mather M, Mende N, Imaz-Rosshandler I, Yang L, Horsfall D, Basurto-Lozada D, Chipampe NJ, Rook V, Lee JTH, Ton ML, Keitley D, Mazin P, Vijayabaskar MS, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck E, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu DM, Acres M, Dixon D, Ness T, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park JE, Polanski K, Marioni J, van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M.

Science, 2023

doi:10.1126/science.add7564.

An atlas of rabbit development as a model for single-cell comparative genomics.

Ton MN, Keitley D, Theeuwes B, Guibentif C, Ahnfelt-Rønne J, Andreassen TK, Calero-Nieto FJ, Imaz-Rosshandler I, Pijuan-Sala B, Nichols J, Benito-Gutiérrez È, Marioni JC, Göttgens B.

Nat Cell Biol, 2023

doi:10.1038/s41556-023-01174-0.

Mapping interindividual dynamics of innate immune response at single-cell resolution.

Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI, Schwartzentruber J, Ghoussaini M, Lyons PA, Calero-Nieto FJ, Göttgens B, Barnes JL, Worlock KB, Yoshida M, Nikolić MZ, Stephenson E, Reynolds G, Haniffa M, Marioni JC, Stegle O, Hagai T, Teichmann SA.

Nat Genet, 2023

doi:10.1038/s41588-023-01421-y.

Tracking Early Mammalian Organogenesis – Prediction and Validation of Differentiation Trajectories at Whole Organism Scale

Imaz-Rosshandler I, Rode C, Guibentif C, Ton MN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J, Marioni JC, de Bruijn MF, Göttgens B.

2023

doi:10.1101/2023.03.17.532833.

A transcriptional and regulatory map of mouse somitogenesis

Ibarra-Soria X, Thierion E, Mok GF, Münsterberg AE, Odom DT, Marioni JC.

2023

doi:10.1101/2023.01.24.525253.

Precise identification of cell states altered in disease with healthy single-cell references

Dann E, Teichmann SA, Marioni JC.

2022

doi:10.1101/2022.11.10.515939.

Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies

Rosen LU, Stapel LC, Argelaguet R, Barker CG, Yang A, Reik W, Marioni JC.

2022

doi:10.1101/2022.09.27.509783.

Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors.

Lin X, Swedlund B, Ton MN, Ghazanfar S, Guibentif C, Paulissen C, Baudelet E, Plaindoux E, Achouri Y, Calonne E, Dubois C, Mansfield W, Zaffran S, Marioni JC, Fuks F, Göttgens B, Lescroart F, Blanpain C.

Nat Cell Biol, 2022

doi:10.1038/s41556-022-00947-3.

Mapping the developing human immune system across organs.

Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA.

Science, 2022

doi:10.1126/science.abo0510.

Supervised spatial inference of dissociated single-cell data with SageNet

Heidari E, Lohoff T, Tyser RCV, Marioni JC, Robinson MD, Ghazanfar S.

2022

doi:10.1101/2022.04.14.488419.

StabMap: Mosaic single cell data integration using non-overlapping features

Ghazanfar S, Guibentif C, Marioni JC.

2022

doi:10.1101/2022.02.24.481823.

Expression Atlas update: gene and protein expression in multiple species.

Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1030.

Differential abundance testing on single-cell data using k-nearest neighbor graphs.

Dann E, Henderson NC, Teichmann SA, Morgan MD, Marioni JC.

Nat Biotechnol, 2022

doi:10.1038/s41587-021-01033-z.

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.

Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC.

Nat Biotechnol, 2022

doi:10.1038/s41587-021-01006-2.

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni JC.

Genome Biol, 2021

doi:10.1186/s13059-021-02548-z.

Cells of the human intestinal tract mapped across space and time.

Elmentaite R, Kumasaka N, Roberts K, Fleming A, Dann E, King HW, Kleshchevnikov V, Dabrowska M, Pritchard S, Bolt L, Vieira SF, Mamanova L, Huang N, Perrone F, Goh Kai'En I, Lisgo SN, Katan M, Leonard S, Oliver TRW, Hook CE, Nayak K, Campos LS, Domínguez Conde C, Stephenson E, Engelbert J, Botting RA, Polanski K, van Dongen S, Patel M, Morgan MD, Marioni JC, Bayraktar OA, Meyer KB, He X, Barker RA, Uhlig HH, Mahbubani KT, Saeb-Parsy K, Zilbauer M, Clatworthy MR, Haniffa M, James KR, Teichmann SA.

Nature, 2021

doi:10.1038/s41586-021-03852-1.

A roadmap for the Human Developmental Cell Atlas.

Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S, Human Cell Atlas Developmental Biological Network.

Nature, 2021

doi:10.1038/s41586-021-03620-1.

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

Cuomo AS, Heinen T, Vagiaki D, Horta D, Marioni JC, Stegle O.

2021

doi:10.1101/2021.09.01.458524.

Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition.

Nowicki-Osuch K, Zhuang L, Jammula S, Bleaney CW, Mahbubani KT, Devonshire G, Katz-Summercorn A, Eling N, Wilbrey-Clark A, Madissoon E, Gamble J, Di Pietro M, O'Donovan M, Meyer KB, Saeb-Parsy K, Sharrocks AD, Teichmann SA, Marioni JC, Fitzgerald RC.

Science, 2021

doi:10.1126/science.abd1449.

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni J.

2021

doi:10.1101/2021.08.10.455720.

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation.

Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B.

Genome Biol, 2021

doi:10.1186/s13059-021-02414-y.

Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells

Lim K, Tang W, Sun D, He P, Teichmann SA, Marioni JC, Meyer KB, Rawlins EL.

2021

doi:10.1101/2021.06.30.450501.

Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs.

Aztekin C, Hiscock TW, Gurdon J, Jullien J, Marioni J, Simons BD.

Development, 2021

doi:10.1242/dev.199158.

Mapping Rora expression in resting and activated CD4+ T cells.

Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Griffin JL, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie ANJ, Teichmann SA.

PLoS One, 2021

doi:10.1371/journal.pone.0251233.

Computational principles and challenges in single-cell data integration.

Argelaguet R, Cuomo ASE, Stegle O, Marioni JC.

Nat Biotechnol, 2021

doi:10.1038/s41587-021-00895-7.

Single-cell multi-omics analysis of the immune response in COVID-19.

Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M.

Nat Med, 2021

doi:10.1038/s41591-021-01329-2.

Cells of the human intestinal tract mapped across space and time

Elmentaite R, Kumasaka N, King H, Roberts K, Dabrowska M, Pritchard S, Bolt L, Vieira S, Mamanova L, Huang N, Goh Kai’En I, Stephenson E, Engelbert J, Botting R, Fleming A, Dann E, Lisgo S, Katan M, Leonard S, Oliver T, Hook C, Nayak K, Perrone F, Campos L, Dominguez-Conde C, Polanski K, Van Dongen S, Patel M, Morgan M, Marioni J, Bayraktar O, Meyer K, Zilbauer M, Uhlig H, Clatworthy M, Mahbubani K, Saeb Parsy K, Haniffa M, James K, Teichmann S.

2021

doi:10.1101/2021.04.07.438755.

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups.

Nature, 2021

doi:10.1038/s41586-021-03287-8.

Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors.

Bach K, Pensa S, Zarocsinceva M, Kania K, Stockis J, Pinaud S, Lazarus KA, Shehata M, Simões BM, Greenhalgh AR, Howell SJ, Clarke RB, Caldas C, Halim TYF, Marioni JC, Khaled WT.

Nat Commun, 2021

doi:10.1038/s41467-021-21783-3.

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.

Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, Mountjoy E, Ghoussaini M, Lancaster MA, HipSci Consortium, Marioni JC, Merkle FT, Gaffney DJ, Stegle O.

Nat Genet, 2021

doi:10.1038/s41588-021-00801-6.

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network.

Nat Med, 2021

doi:10.1038/s41591-020-01227-z.

Publisher Correction: The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.

Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ.

Nat Cell Biol, 2021

doi:10.1038/s41556-021-00645-6.

The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.

Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ.

Nat Cell Biol, 2021

doi:10.1038/s41556-020-00611-8.

Characterization of a common progenitor pool of the epicardium and myocardium.

Tyser RCV, Ibarra-Soria X, McDole K, Arcot Jayaram S, Godwin J, van den Brand TAH, Miranda AMA, Scialdone A, Keller PJ, Marioni JC, Srinivas S.

Science, 2021

doi:10.1126/science.abb2986.

Diverse Routes toward Early Somites in the Mouse Embryo.

Guibentif C, Griffiths JA, Imaz-Rosshandler I, Ghazanfar S, Nichols J, Wilson V, Göttgens B, Marioni JC.

Dev Cell, 2021

doi:10.1016/j.devcel.2020.11.013.

Coordinated Changes in Gene Expression Kinetics Underlie both Mouse and Human Erythroid Maturation

Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B.

2020

doi:10.1101/2020.12.21.423773.

<i>Milo:</i> differential abundance testing on single-cell data using k-NN graphs

Dann E, Henderson NC, Teichmann SA, Morgan MD, Marioni JC.

2020

doi:10.1101/2020.11.23.393769.

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths J, Bardot E, Eng C, Tyser R, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons B, Hadjantonakis A, Göttgens B, Reik W, Nichols J, Cai L, Marioni J.

2020

doi:10.1101/2020.11.20.391896.

Guidelines for reporting single-cell RNA-seq experiments.

Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I.

Nat Biotechnol, 2020

doi:10.1038/s41587-020-00744-z.

Transposable element expression at unique loci in single cells with CELLO-seq

Berrens RV, Yang A, Laumer CE, Lun AT, Bieberich F, Law C, Lan G, Imaz M, Gaffney D, Marioni JC.

2020

doi:10.1101/2020.10.02.322073.

LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups.

Nature, 2020

doi:10.1038/s41586-020-2715-9.

Ageing compromises mouse thymus function and remodels epithelial cell differentiation.

Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F, Sit RV, Neff NF, Darmanis S, Tan W, May AP, Marioni JC, Ponting CP, Holländer GA.

Elife, 2020

doi:10.7554/elife.56221.

ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung.

Schuijs MJ, Png S, Richard AC, Tsyben A, Hamm G, Stockis J, Garcia C, Pinaud S, Nicholls A, Ros XR, Su J, Eldridge MD, Riedel A, Serrao EM, Rodewald HR, Mack M, Shields JD, Cohen ES, McKenzie ANJ, Goodwin RJA, Brindle KM, Marioni JC, Halim TYF.

Nat Immunol, 2020

doi:10.1038/s41590-020-0745-y.

Investigating higher-order interactions in single-cell data with scHOT.

Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC, Yang JYH.

Nat Methods, 2020

doi:10.1038/s41592-020-0885-x.

Secreted inhibitors drive the loss of regeneration competence in<i>Xenopus</i>limbs

Aztekin C, Hiscock TW, Gurdon JB, Jullien J, Marioni JC, Simons BD.

2020

doi:10.1101/2020.06.01.127654.

Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling.

Ma CY, Marioni JC, Griffiths GM, Richard AC.

Elife, 2020

doi:10.7554/elife.53948.

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.

Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, Stegle O.

Genome Biol, 2020

doi:10.1186/s13059-020-02015-1.

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division.

Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC, Odom DT, Gergely F.

Nat Commun, 2020

doi:10.1038/s41467-020-14978-7.

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O.

Nat Commun, 2020

doi:10.1038/s41467-020-15098-y.

Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.

Morgan MD, Patin E, Jagla B, Hasan M, Quintana-Murci L, Marioni JC.

PLoS Genet, 2020

doi:10.1371/journal.pgen.1008686.

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O.

Nat Commun, 2020

doi:10.1038/s41467-020-14457-z.

Eleven grand challenges in single-cell data science.

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowska A, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A.

Genome Biol, 2020

doi:10.1186/s13059-020-1926-6.

Expression Atlas update: from tissues to single cells.

Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz947.

Toward a Common Coordinate Framework for the Human Body.

Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R.

Cell, 2019

doi:10.1016/j.cell.2019.11.019.

Multi-omics profiling of mouse gastrulation at single-cell resolution.

Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Krueger F, Göttgens B, Rugg-Gunn PJ, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W.

Nature, 2019

doi:10.1038/s41586-019-1825-8.

Investigating higher order interactions in single cell data with scHOT

Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC, Yang JYH.

2019

doi:10.1101/841593.

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis.

Dobie R, Wilson-Kanamori JR, Henderson BEP, Smith JR, Matchett KP, Portman JR, Wallenborg K, Picelli S, Zagorska A, Pendem SV, Hudson TE, Wu MM, Budas GR, Breckenridge DG, Harrison EM, Mole DJ, Wigmore SJ, Ramachandran P, Ponting CP, Teichmann SA, Marioni JC, Henderson NC.

Cell Rep, 2019

doi:10.1016/j.celrep.2019.10.024.

MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data

Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, Stegle O.

2019

doi:10.1101/837104.

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.

Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA.

Cell Syst, 2019

doi:10.1016/j.cels.2019.08.003.

12 Grand Challenges in Single-Cell Data Science

Laehnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Stephan-Otto Attolini C, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Jessurun Lobo T, Keizer EM, Khatri I, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, de Ridder J, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A.

2019

doi:10.7287/peerj.preprints.27885v3.

Resolving the fibrotic niche of human liver cirrhosis at single-cell level.

Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP, Luu NT, Portman JR, Matchett KP, Brice M, Marwick JA, Taylor RS, Efremova M, Vento-Tormo R, Carragher NO, Kendall TJ, Fallowfield JA, Harrison EM, Mole DJ, Wigmore SJ, Newsome PN, Weston CJ, Iredale JP, Tacke F, Pollard JW, Ponting CP, Marioni JC, Teichmann SA, Henderson NC.

Nature, 2019

doi:10.1038/s41586-019-1631-3.

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using <tt>CellBender</tt>

Fleming SJ, Chaffin MD, Chaffin MD, Arduini A, Akkad A, Banks E, Marioni JC, Philippakis AA, Ellinor PT, Babadi M.

2019

doi:10.1101/791699.

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.

Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L, Jorissen M, Gibbs M, O'Flynn C, McGrane S, Mombaerts P, Marioni JC, Mainland JD, Logan DW.

Sci Adv, 2019

doi:10.1126/sciadv.aax0396.

<i>Rora</i>regulates activated T helper cells during inflammation

Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Griffin JL, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie AN, Teichmann SA.

2019

doi:10.1101/709998.

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC, Odom DT, Gergely F.

2019

doi:10.1101/709030.

IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.

Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M.

EMBO Rep, 2019

doi:10.15252/embr.201847379.

Author Correction: Challenges in measuring and understanding biological noise.

Eling N, Morgan MD, Marioni JC.

Nat Rev Genet, 2019

doi:10.1038/s41576-019-0142-2.

Challenges in measuring and understanding biological noise.

Eling N, Morgan MD, Marioni JC.

Nat Rev Genet, 2019

doi:10.1038/s41576-019-0130-6.

Identification of a regeneration-organizing cell in the <i>Xenopus</i> tail.

Aztekin C, Hiscock TW, Marioni JC, Gurdon JB, Simons BD, Jullien J.

Science, 2019

doi:10.1126/science.aav9996.

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Cuomo AS, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, Vallier L, Marioni JC, Chhatriwala M, Stegle O, HipSci Consortium.

2019

doi:10.1101/630996.

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas Jamboree, Marioni JC.

Genome Biol, 2019

doi:10.1186/s13059-019-1662-y.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT.

Nat Commun, 2019

doi:10.1038/s41467-019-09182-1.

A single-cell molecular map of mouse gastrulation and early organogenesis.

Pijuan-Sala B, Griffiths JA, Guibentif C, Hiscock TW, Jawaid W, Calero-Nieto FJ, Mulas C, Ibarra-Soria X, Tyser RCV, Ho DLL, Reik W, Srinivas S, Simons BD, Nichols J, Marioni JC, Göttgens B.

Nature, 2019

doi:10.1038/s41586-019-0933-9.

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H, Lun ATL, Marioni JC, Reik W.

Cell Rep, 2019

doi:10.1016/j.celrep.2018.12.099.

SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.

Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M, Robson SC, Hermida-Prado F, Yang YH, Babaei-Jadidi R, Garyfallos DA, Ponstingl H, Dias JML, Gallipoli P, Seiler M, Buonamici S, Vick B, Bannister AJ, Rad R, Prinjha RK, Marioni JC, Huntly B, Batson J, Morris JC, Pina C, Bradley A, Jeremias I, Bates DO, Yusa K, Kouzarides T, Vassiliou GS.

Nat Commun, 2018

doi:10.1038/s41467-018-07620-0.

Altered composition of the <i>γδ</i> T cell pool in lymph nodes during ageing enhances tumour growth

Chen H, Eling N, Martinez-Jimenez CP, O’Brien LM, Marioni JC, Odom DT, la Roche Md.

2018

doi:10.1101/480327.

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.

Laumer CE, Gruber-Vodicka H, Hadfield MG, Pearse VB, Riesgo A, Marioni JC, Giribet G.

Elife, 2018

doi:10.7554/elife.36278.

COMRADES determines in vivo RNA structures and interactions.

Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA.

Nat Methods, 2018

doi:10.1038/s41592-018-0121-0.

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.

Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA.

Cell Syst, 2018

doi:10.1016/j.cels.2018.06.011.

CTCF maintains regulatory homeostasis of cancer pathways.

Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT.

Genome Biol, 2018

doi:10.1186/s13059-018-1484-3.

T cell cytolytic capacity is independent of initial stimulation strength.

Richard AC, Lun ATL, Lau WWY, Göttgens B, Marioni JC, Griffiths GM.

Nat Immunol, 2018

doi:10.1038/s41590-018-0160-9.

Detection and removal of barcode swapping in single-cell RNA-seq data.

Griffiths JA, Richard AC, Bach K, Lun ATL, Marioni JC.

Nat Commun, 2018

doi:10.1038/s41467-018-05083-x.

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Lun ATL, Riesenfeld S, Andrews T, Gomes T, Marioni JC, The Phuong Dao, participants in the 1st Human Cell Atlas Jamboree.

2018

doi:10.1101/234872.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT.

2018

doi:10.1101/350868.

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

Morgan MD, Marioni JC.

Genome Biol, 2018

doi:10.1186/s13059-018-1461-x.

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

Do DV, Strauss B, Cukuroglu E, Macaulay I, Wee KB, Hu TX, Igor RLM, Lee C, Harrison A, Butler R, Dietmann S, Jernej U, Marioni J, Smith CWJ, Göke J, Surani MA.

Cell Discov, 2018

doi:10.1038/s41421-018-0032-3.

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O.

Mol Syst Biol, 2018

doi:10.15252/msb.20178124.

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT.

Nucleic Acids Res, 2018

doi:10.1093/nar/gky437.

Using single-cell genomics to understand developmental processes and cell fate decisions.

Griffiths JA, Scialdone A, Marioni JC.

Mol Syst Biol, 2018

doi:10.15252/msb.20178046.

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

Haghverdi L, Lun ATL, Morgan MD, Marioni JC.

Nat Biotechnol, 2018

doi:10.1038/nbt.4091.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W.

Nat Commun, 2018

doi:10.1038/s41467-018-03149-4.

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.

Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D.

Mol Biol Evol, 2018

doi:10.1093/molbev/msx336.

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC.

Nat Cell Biol, 2018

doi:10.1038/s41556-017-0013-z.

Detection and removal of barcode swapping in single-cell RNA-seq data

Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC.

2017

doi:10.1101/177048.

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT.

2017

doi:10.1101/234930.

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.

Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT.

Nat Commun, 2017

doi:10.1038/s41467-017-02001-5.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants.

Elife, 2017

doi:10.7554/elife.27041.

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M.

Nature, 2017

doi:10.1038/nature24675.

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

Griffiths JA, Scialdone A, Marioni JC.

BMC Genomics, 2017

doi:10.1186/s12864-017-4253-x.

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.

Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC.

Stem Cell Reports, 2017

doi:10.1016/j.stemcr.2017.10.018.

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O.

Genome Biol, 2017

doi:10.1186/s13059-017-1334-8.

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P.

Nat Commun, 2017

doi:10.1038/s41467-017-01037-x.

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.

Lun ATL, Calero-Nieto FJ, Haim-Vilmovsky L, Göttgens B, Marioni JC.

Genome Res, 2017

doi:10.1101/gr.222877.117.

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

Marioni JC, Arendt D.

Annu Rev Cell Dev Biol, 2017

doi:10.1146/annurev-cellbio-100616-060818.

Whole-body single-cell sequencing of the <i>Platynereis</i> larva reveals a subdivision into apical versus non-apical tissues

Achim K, Eling N, Martinez Vergara H, Bertucci PY, Brunet T, Collier P, Benes V, Marioni JC, Arendt D.

2017

doi:10.1101/167742.

Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours

Haghverdi L, Lun ATL, Morgan MD, Marioni JC.

2017

doi:10.1101/165118.

Impact of Alternative Splicing on the Human Proteome.

Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO.

Cell Rep, 2017

doi:10.1016/j.celrep.2017.07.025.

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W.

Cell Rep, 2017

doi:10.1016/j.celrep.2017.07.009.

Normalizing single-cell RNA sequencing data: challenges and opportunities.

Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC.

Nat Methods, 2017

doi:10.1038/nmeth.4292.

Testing for differential abundance in mass cytometry data.

Lun ATL, Richard AC, Marioni JC.

Nat Methods, 2017

doi:10.1038/nmeth.4295.

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Triglia ET, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA.

2017

doi:10.1101/117267.

Aging increases cell-to-cell transcriptional variability upon immune stimulation.

Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT.

Science, 2017

doi:10.1126/science.aah4115.

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.

Lun ATL, Marioni JC.

Biostatistics, 2017

doi:10.1093/biostatistics/kxw055.

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA.

Elife, 2017

doi:10.7554/elife.22345.

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

Lun ATL, Marioni JC.

2016

doi:10.1101/073973.

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

Vallejos CA, Richardson S, Marioni JC.

2016

doi:10.1101/035949.

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

Lun AT, McCarthy DJ, Marioni JC.

F1000Res, 2016

doi:10.12688/f1000research.9501.2.

Resolving early mesoderm diversification through single-cell expression profiling.

Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B.

Nature, 2016

doi:10.1038/nature18633.

HDTD: analyzing multi-tissue gene expression data.

Touloumis A, Marioni JC, Tavaré S.

Bioinformatics, 2016

doi:10.1093/bioinformatics/btw224.

Structure and evolutionary history of a large family of NLR proteins in the zebrafish.

Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M.

Open Biol, 2016

doi:10.1098/rsob.160009.

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT.

PLoS Genet, 2016

doi:10.1371/journal.pgen.1006024.

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

Lun AT, Bach K, Marioni JC.

Genome Biol, 2016

doi:10.1186/s13059-016-0947-7.

Beyond comparisons of means: understanding changes in gene expression at the single-cell level.

Vallejos CA, Richardson S, Marioni JC.

Genome Biol, 2016

doi:10.1186/s13059-016-0930-3.

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M.

Cell, 2016

doi:10.1016/j.cell.2016.01.047.

Classification of low quality cells from single-cell RNA-seq data.

Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA.

Genome Biol, 2016

doi:10.1186/s13059-016-0888-1.

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.

Nat Commun, 2016

doi:10.1038/ncomms10415.

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni J, Soylemez O, Kondrashov F, Leptin M.

2015

doi:10.1101/022061.

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.

Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW.

Sci Rep, 2015

doi:10.1038/srep18178.

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.

Nat Commun, 2015

doi:10.1038/ncomms9687.

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA.

Cell Stem Cell, 2015

doi:10.1016/j.stem.2015.09.011.

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.

Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR.

Genome Biol, 2015

doi:10.1186/s13059-015-0749-3.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.

PLoS One, 2015

doi:10.1371/journal.pone.0137367.

Computational assignment of cell-cycle stage from single-cell transcriptome data.

Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F.

Methods, 2015

doi:10.1016/j.ymeth.2015.06.021.

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.

Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW.

Sci Rep, 2015

doi:10.1038/srep11487.

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

Vallejos CA, Marioni JC, Richardson S.

PLoS Comput Biol, 2015

doi:10.1371/journal.pcbi.1004333.

The technology and biology of single-cell RNA sequencing.

Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA.

Mol Cell, 2015

doi:10.1016/j.molcel.2015.04.005.

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.

Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC.

Nat Biotechnol, 2015

doi:10.1038/nbt.3209.

Computational and analytical challenges in single-cell transcriptomics.

Stegle O, Teichmann SA, Marioni JC.

Nat Rev Genet, 2015

doi:10.1038/nrg3833.

Testing the mean matrix in high-dimensional transposable data.

Touloumis A, Tavaré S, Marioni JC.

Biometrics, 2015

doi:10.1111/biom.12257.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O.

Nat Biotechnol, 2015

doi:10.1038/nbt.3102.

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.

Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C.

Cancer Res, 2015

doi:10.1158/0008-5472.can-13-3131.

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W.

Cell Rep, 2014

doi:10.1016/j.celrep.2014.11.034.

Single Cell Genomics meeting in Stockholm: from single cells to cell types.

Scialdone A, Achim K, Marioni JC.

Genome Biol, 2014

doi:10.1186/s13059-014-0496-x.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.

Elife, 2014

doi:10.7554/elife.02626.

RNA-Seq gene profiling--a systematic empirical comparison.

Fonseca NA, Marioni J, Brazma A.

PLoS One, 2014

doi:10.1371/journal.pone.0107026.

Identifying cell types from spatially referenced single-cell expression datasets.

Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J.

PLoS Comput Biol, 2014

doi:10.1371/journal.pcbi.1003824.

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.

Genome Res, 2014

doi:10.1101/gr.176784.114.

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.

Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F.

Nat Genet, 2014

doi:10.1038/ng.2971.

Random monoallelic gene expression increases upon embryonic stem cell differentiation.

Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL.

Dev Cell, 2014

doi:10.1016/j.devcel.2014.01.017.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1270.

Accounting for technical noise in single-cell RNA-seq experiments.

Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG.

Nat Methods, 2013

doi:10.1038/nmeth.2645.

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.

Cell, 2013

doi:10.1016/j.cell.2013.07.007.

Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.

Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE.

Br J Cancer, 2013

doi:10.1038/bjc.2013.396.

bioWeb3D: an online webGL 3D data visualisation tool.

Pettit JB, Marioni JC.

BMC Bioinformatics, 2013

doi:10.1186/1471-2105-14-185.

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S.

Proc Natl Acad Sci U S A, 2013

doi:10.1073/pnas.1219747110.

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.

Kim JK, Marioni JC.

Genome Biol, 2013

doi:10.1186/gb-2013-14-1-r7.

Tools for mapping high-throughput sequencing data.

Fonseca NA, Rung J, Brazma A, Marioni JC.

Bioinformatics, 2012

doi:10.1093/bioinformatics/bts605.

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.

Genome Res, 2012

doi:10.1101/gr.142281.112.

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.

Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y.

Proc Natl Acad Sci U S A, 2012

doi:10.1073/pnas.1115761109.

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y.

Genome Res, 2012

doi:10.1101/gr.130468.111.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.

Bioinformatics, 2011

doi:10.1093/bioinformatics/btr330.

Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.

Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC.

Gut, 2011

doi:10.1136/gut.2010.234179.

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y.

PLoS Genet, 2011

doi:10.1371/journal.pgen.1001316.

Gene expression differences among primates are associated with changes in a histone epigenetic modification.

Cain CE, Blekhman R, Marioni JC, Gilad Y.

Genetics, 2011

doi:10.1534/genetics.110.126177.

Functional comparison of innate immune signaling pathways in primates.

Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y.

PLoS Genet, 2010

doi:10.1371/journal.pgen.1001249.

Genomic-scale capture and sequencing of endogenous DNA from feces.

Perry GH, Marioni JC, Melsted P, Gilad Y.

Mol Ecol, 2010

doi:10.1111/j.1365-294x.2010.04888.x.

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK.

Nature, 2010

doi:10.1038/nature08872.

Sex-specific and lineage-specific alternative splicing in primates.

Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.

Genome Res, 2010

doi:10.1101/gr.099226.109.

The pitfalls of platform comparison: DNA copy number array technologies assessed.

Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavaré S, Caldas C.

BMC Genomics, 2009

doi:10.1186/1471-2164-10-588.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp579.

Hidden copy number variation in the HapMap population.

Marioni JC, White M, Tavaré S, Lynch AG.

Proc Natl Acad Sci U S A, 2008

doi:10.1073/pnas.0711252105.

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.

Nat Biotechnol, 2008

doi:10.1038/nbt1414.

ESR1 gene amplification in breast cancer: a common phenomenon?

Brown LA, Hoog J, Chin SF, Tao Y, Zayed AA, Chin K, Teschendorff AE, Quackenbush JF, Marioni JC, Leung S, Perou CM, Neilsen TO, Ellis M, Gray JW, Bernard PS, Huntsman DG, Caldas C.

Nat Genet, 2008

doi:10.1038/ng0708-806.

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).

Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.

Genome Res, 2008

doi:10.1101/gr.077479.108.

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y.

Genome Res, 2008

doi:10.1101/gr.079558.108.

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S, Hurles ME.

Genome Biol, 2007

doi:10.1186/gb-2007-8-10-r228.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C.

Genome Biol, 2007

doi:10.1186/gb-2007-8-10-r215.

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments.

Lynch AG, Marioni JC, Tavaré S.

Am J Hum Genet, 2007

doi:10.1086/519393.

BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data.

Marioni JC, Thorne NP, Tavaré S.

Bioinformatics, 2006

doi:10.1093/bioinformatics/btl089.

A comparison of dermatologists', surgeons' and general practitioners' surgical management of cutaneous melanoma.

McKenna DB, Marioni JC, Lee RJ, Prescott RJ, Doherty VR.

Br J Dermatol, 2004

doi:10.1111/j.1365-2133.2004.06065.x.

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: A double-blind, randomized, placebo-controlled study.

Hillis GS, Pearson CV, Harding SA, Sutherland S, Ludlam CA, Marioni JC, Prescott RJ, Fox KA, Flapan AD.

Am Heart J, 2004

doi:10.1016/j.ahj.2004.01.016.