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.

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.

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.

Preprint, 2022

doi:10.1101/2022.09.27.509783.

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.

A reference induced pluripotent stem cell line for large-scale collaborative studies

Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D, Pratt G, Cross E, Blockwick J, Buxton P, Kinner-Bibeau L, Medura C, Tompkins C, Hughes S, Santiana M, Faghri F, Nalls MA, Vitale D, Ballard S, Qi YA, Ramos DM, Anderson KM, Stadler J, Narayan P, Papademetriou J, Reilly L, Nelson MP, Aggarwal S, Rosen LU, Kirwan P, Pisupati V, Coon SL, Scholz SW, Priebe T, Öttl M, Dong J, Meijer M, Janssen LJ, Lourenco VS, van der Kant R, Crusius D, Paquet D, Raulin A, Bu G, Held A, Wainger BJ, Gabriele RM, Casey JM, Wray S, Abu-Bonsrah D, Parish CL, Beccari MS, Cleveland DW, Li E, Rose IV, Kampmann M, Aristoy CC, Verstreken P, Heinrich L, Chen MY, Schüle B, Dou D, Holzbaur EL, Zanellati MC, Basundra R, Deshmukh M, Cohen S, Khanna R, Raman M, Nevin ZS, Matia M, Lent JV, Timmerman V, Conklin BR, Chase KJ, Zhang K, Funes S, Bosco DA, Erlebach L, Welzer M, Kronenberg-Versteeg D, Lyu G, Arenas E, Coccia E, Sarrafha L, Ahfeldt T, Marioni JC, Skarnes WC, Cookson MR, Ward ME, Merkle FT.

Preprint, 2021

doi:10.1101/2021.12.15.472643.

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.

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility

Liu Q, Hua K, Zhang X, Wong WH, Jiang R.

Preprint, 2019

doi:10.1101/610642.

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution

Strauss ME, Kirk PD, Reid JE, Wernisch L.

Preprint, 2019

doi:10.1101/567115.

A case study on the detailed reproducibility of a human cell atlas project

Hua K, Zhang X.

Preprint, 2018

doi:10.1101/467993.

Seasonal Changes in Diet and Toxicity in the Climbing Mantella Frog (<i>Mantella Laevigata</i>)

Moskowitz NA, Roland AB, Fischer EK, Ranaivorazo N, Vidoudez C, Aguilar MT, Caldera SM, Chea J, Cristus MG, Crowdis JP, DeMessie B, desJardins-Park CR, Effenberger AH, Flores F, Giles M, He EY, Izmaylov NS, Lee CC, Pagel NA, Phu KK, Rosen LU, Seda DA, Shen Y, Vargas S, Murray AW, Abebe E, Trauger SA, Donoso DA, Vences M, O’Connell LA.

Preprint, 2018

doi:10.1101/361998.

GPseudoRank: a permutation sampler for single cell orderings

Strauß ME, Reid JE, Wernisch L.

Preprint, 2017

doi:10.1101/211417.