Publications – Marioni Group

Gliomagenesis mimics an injury response orchestrated by neural crest-like cells.

Hamed AA, Hua K, Trinh QM, Simons BD, Marioni JC, Stein LD, Dirks PB.

Nature, 2025

doi:10.1038/s41586-024-08356-2.

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.

Nature genetics, 2024

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

A genome-scale single cell CRISPRi map of<i>trans</i>gene regulation across human pluripotent stem cell lines

Feng C, Peets EM, Zhou Y, Crepaldi L, Usluer S, Dunham A, Braunger JM, Su J, Strauss ME, Muraro D, Xian Cheam KA, Bonder MJ, Nogales EG, Cooper S, Bassett A, Leonard S, Gu Y, Fussing B, Burke D, Parts L, Stegle O, Velten B.

Preprint, 2024

doi:10.1101/2024.11.28.625833.

Base editing screens define the genetic landscape of cancer drug resistance mechanisms.

Coelho MA, Strauss ME, Watterson A, Cooper S, Bhosle S, Illuzzi G, Karakoc E, Dinçer C, Vieira SF, Sharma M, Moullet M, Conticelli D, Koeppel J, McCarten K, Cattaneo CM, Veninga V, Picco G, Parts L, Forment JV, Voest EE, Marioni JC, Bassett A, Garnett MJ.

Nature genetics, 2024

doi:10.1038/s41588-024-01948-8.

A spatial human thymus cell atlas mapped to a continuous tissue axis.

Yayon N, Kedlian VR, Boehme L, Suo C, Wachter BT, Beuschel RT, Amsalem O, Polanski K, Koplev S, Tuck E, Dann E, Van Hulle J, Perera S, Putteman T, Predeus AV, Dabrowska M, Richardson L, Tudor C, Kreins AY, Engelbert J, Stephenson E, Kleshchevnikov V, De Rita F, Crossland D, Bosticardo M, Pala F, Prigmore E, Chipampe NJ, Prete M, Fei L, To K, Barker RA, He X, Van Nieuwerburgh F, Bayraktar OA, Patel M, Davies EG, Haniffa MA, Uhlmann V, Notarangelo LD, Germain RN, Radtke AJ, Marioni JC, Taghon T, Teichmann SA.

Nature, 2024

doi:10.1038/s41586-024-07944-6.

Bin2cell reconstructs cells from high resolution Visium HD data.

Polański K, Bartolomé-Casado R, Sarropoulos I, Xu C, England N, Jahnsen FL, Teichmann SA, Yayon N.

Bioinformatics (Oxford, England), 2024

doi:10.1093/bioinformatics/btae546.

A multiomic atlas of human early skeletal development

To K, Fei L, Patrick Pett J, Roberts K, Polański K, Li T, Yayon N, He P, Xu C, Cranley J, Li R, Kanemaru K, Huang N, Megas S, Richardson L, Kapuge R, Perera S, Tuck E, Wilbrey-Clark A, Mulas I, Memi F, Cakir B, Predeus AV, Horsfall D, Murray S, Prete M, Mazin P, He X, Meyer KB, Haniffa M, Barker RA, Bayraktar O, Buckley CD, Teichmann SA.

Preprint, 2024

doi:10.1101/2024.07.10.602965.

Bin2cell reconstructs cells from high resolution Visium HD data

Polański K, Bartolomé-Casado R, Sarropoulos I, Xu C, England N, Jahnsen FL, Teichmann SA, Yayon N.

Preprint, 2024

doi:10.1101/2024.06.19.599766.

Knockout of the longevity gene Klotho perturbs aging and Alzheimer's disease-linked brain microRNAs and tRNA fragments.

Dubnov S, Bennett ER, Yayon N, Yakov O, Bennett DA, Seshadri S, Mufson E, Tzur Y, Greenberg D, Kuro-O M, Paldor I, Abraham CR, Soreq H.

Communications biology, 2024

doi:10.1038/s42003-024-06407-y.

Bayesian profile regression for clustering analysis involving a longitudinal response and explanatory variables.

Rouanet A, Johnson R, Strauss M, Richardson S, Tom BD, White SR, Kirk PDW.

Methodology : European journal of research methods for the behavioral & social sciences, 2023

doi:10.1093/jrsssc/qlad097.

Bespoke single cell molecular and tissue-scale analysis reveals mechanisms underpinning development and disease in complex developing cell populations

Strauss ME, Ton MN, Mason S, Bagri J, Harland LT, Imaz-Rosshandler I, Wilson NK, Nichols J, Tyser RC, Göttgens B, Marioni JC, Guibentif C.

Preprint, 2023

doi:10.1101/2023.10.11.561904.

High-throughput phenotyping of single nucleotide variants by linking transcriptomes to genotypes in single cells

Cooper SE, Coelho MA, Strauss ME, Gontarczyk AM, Wu Q, Garnett MJ, Marioni JC, Bassett AR.

Preprint, 2023

doi:10.1101/2023.05.22.541777.

Base editing screens map mutations affecting interferon-γ signaling in cancer.

Coelho MA, Cooper S, Strauss ME, Karakoc E, Bhosle S, Gonçalves E, Picco G, Burgold T, Cattaneo CM, Veninga V, Consonni S, Dinçer C, Vieira SF, Gibson F, Barthorpe S, Hardy C, Rein J, Thomas M, Marioni J, Voest EE, Bassett A, Garnett MJ.

Cancer cell, 2023

doi:10.1016/j.ccell.2022.12.009.

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 (New York, N.Y.), 2022

doi:10.1126/science.abo0510.

A human embryonic limb cell atlas resolved in space and time

Zhang B, He P, Lawrence JE, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, 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, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA.

Preprint, 2022

doi:10.1101/2022.04.27.489800.

Mapping the developing human immune system across organs

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

Preprint, 2022

doi:10.1101/2022.01.17.476665.

Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model

Gao H, Hua K, Wei L, Wu X, Chen S, Yin Q, Jiang R, Zhang X.

Preprint, 2021

doi:10.1101/2021.09.09.459281.

hECA: the cell-centric assembly of a cell atlas

Chen S, Luo Y, Gao H, Li F, Li J, Chen Y, You R, Hao M, Bian H, Xi X, Li W, Li W, Ye M, Meng Q, Zou Z, Li C, Li H, Zhang Y, Cui Y, Wei L, Chen F, Wang X, Lv H, Hua K, Jiang R, Zhang X.

Preprint, 2021

doi:10.1101/2021.07.21.453289.

NeuronMotif: Deciphering transcriptional cis-regulatory codes from deep neural networks

Wei Z, Hua K, Wei L, Ma S, Jiang R, Li Y, Wong WH, Wang X.

Preprint, 2021

doi:10.1101/2021.02.10.430606.

HGC: fast hierarchical clustering for large-scale single-cell data

Zou Z, Hua K, Zhang X.

Preprint, 2021

doi:10.1101/2021.02.07.430106.

SOMDE: A scalable method for identifying spatially variable genes with self-organizing map

Hao M, Hua K, Zhang X.

Preprint, 2020

doi:10.1101/2020.12.10.419549.

A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress.

Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen-Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S.

EMBO molecular medicine, 2020

doi:10.15252/emmm.202013551.