Publications funded by the CIRM CESCG
2020
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Bhaduri A, Andrews MG, Mancia Leon W, Jung D, Shin D, Allen D, Jung D, Schmunk G, Haeussler M, Salma
J et al.
Cell stress in cortical organoids impairs molecular subtype specification.
Nature. 2020 Jan 29;.
PMID: 31996853
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Bhaduri A, Di Lullo E, Jung D, Müller S, Crouch EE, Espinosa CS, Ozawa T, Alvarado B, Spatazza
J, Cadwell CR et al.
Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma.
Cell Stem Cell. 2020 Jan 2;26(1):48-63.e6.
PMID: 31901251
2019
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Calvanese V, Nguyen AT, Bolan TJ, Vavilina A, Su T, Lee LK, Wang Y, Lay FD, Magnusson M, Crooks GM
et al.
MLLT3 governs human haematopoietic stem-cell self-renewal and engraftment.
Nature. 2019 Dec;576(7786):281-286.
PMID: 31776511
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D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-
Chronowska A, Frazer KA.
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type
associations with disease.
Elife. 2019 Nov 20;8.
PMID: 31746734; PMC: PMC6904215
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D'Antonio-Chronowska A, Donovan MKR, Young Greenwald WW, Nguyen JP, Fujita K, Hashem S, Matsui H,
Soncin F, Parast M, Ward MC et al.
Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac
Differentiation Trajectories.
Stem Cell Reports. 2019 Nov 12;13(5):924-938.
PMID: 31668852; PMC: PMC6895695
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Kathiriya IS, Rao KS, Iacono G, Devine WP, Hota SK, Lai MH, Garay BI, Thomas R, Blair AP, Gong, HZ
et al.
A TBX5 dosage-sensitive gene regulatory network for human congenital heart disease
bioRxiv. 2019 Nov 10.
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Zanini F, Berghuis BA, Jones RC, Robilant ND, Nong RY, Clarke MF, Quake SR
Northstar: leveraging cell atlases to identify healthy and neoplastic cells in transcriptomes from human tumors.
bioRxiv. 2019 Oct 27.
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Ding H, Blair A, Yang Y, Stuart JM.
Biological process activity transformation of single cell gene expression for cross-species
alignment.
Nat Commun. 2019 Oct 25;10(1):4899.
PMID: 31653878; PMC: PMC6814736
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Benaglio P, D'Antonio-Chronowska A, Ma W, Yang F, Young Greenwald WW, Donovan MKR, DeBoever C, Li H,
Drees F, Singhal S et al.
Allele-specific NKX2-5 binding underlies multiple genetic associations with human
electrocardiographic traits.
Nat Genet. 2019 Oct;51(10):1506-1517.
PMID: 31570892; PMC: PMC6858543
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Mao X, An Q, Xi H, Yang XJ, Zhang X, Yuan S, Wang J, Hu Y, Liu Q, Fan G.
Single-Cell RNA Sequencing of hESC-Derived 3D Retinal Organoids Reveals Novel Genes Regulating RPC
Commitment in Early Human Retinogenesis.
Stem Cell Reports. 2019 Oct 8;13(4):747-760.
PMID: 31543471; PMC: PMC6829752
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Trujillo CA, Gao R, Negraes PD, Gu J, Buchanan J, Preissl S, Wang A, Wu W, Haddad GG, Chaim IA
et al.
Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network
Development.
Cell Stem Cell. 2019 Oct 3;25(4):558-569.e7.
PMID: 31474560; PMC: PMC6778040
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Lee J, Termglinchan V, Diecke S, Itzhaki I, Lam CK, Garg P, Lau E, Greenhaw M, Seeger T, Wu H et al.
Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy.
Nature. 2019 Aug;572(7769):335-340.
PMID: 31316208; PMC: PMC6779479
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Smith EN, D'Antonio-Chronowska A, Greenwald WW, Borja V, Aguiar LR, Pogue R, Matsui H, Benaglio P,
Borooah S, D'Antonio M et al.
Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally
Characterizing Causal Variants at AMD Risk Loci.
Stem Cell Reports. 2019 Jun 11;12(6):1342-1353.
PMID: 31080113; PMC: PMC6565613
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Greenwald WW, Li H, Benaglio P, Jakubosky D, Matsui H, Schmitt A, Selvaraj S, D'Antonio M, D
'Antonio-Chronowska A, Smith EN et al.
Subtle changes in chromatin loop contact propensity are associated with differential gene regulation
and expression.
Nat Commun. 2019 Mar 5;10(1):1054.
PMID: 30837461; PMC: PMC6401380
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Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V,
Rosenkrantz JL, Olsen M et al.
Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical
Differentiation and Influence Cell-Type-Specific Genes.
Stem Cell Reports. 2019 Feb 12;12(2):245-257.
PMID: 30639214; PMC: PMC6372947
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Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado
B, Bedolli M, Dougherty ML et al.
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
Cell. 2019 Feb 7;176(4):743-756.e17.
PMID: 30735633; PMC: PMC6544371
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Lomova A, Clark DN, Campo-Fernandez B, Flores-Bjurström C, Kaufman ML, Fitz-Gibbon S, Wang X,
Miyahira EY, Brown D, DeWitt MA et al.
Improving Gene Editing Outcomes in Human Hematopoietic Stem and Progenitor Cells by Temporal Control
of DNA Repair.
Stem Cells. 2019 Feb;37(2):284-294.
PMID: 30372555; PMC: PMC6368869
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Yoon SJ, Elahi LS, Pașca AM, Marton RM, Gordon A, Revah O, Miura Y, Walczak EM, Holdgate GM,
Fan HC et al.
Reliability of human cortical organoid generation.
Nat Methods. 2019 Jan;16(1):75-78.
PMID: 30573846
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Chung JE, Magis W, Vu J, Heo SJ, Wartiovaara K, Walters MC, Kurita R, Nakamura Y, Boffelli D, Martin
DIK et al.
CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells.
PLoS One. 2019;14(1):e0208237.
PMID: 30645582; PMC: PMC6333401
2018
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Hsu HT, Estarás C, Huang L, Jones KA.
Specifying the Anterior Primitive Streak by Modulating YAP1 Levels in Human Pluripotent Stem
Cells.
Stem Cell Reports. 2018 Dec 11;11(6):1357-1364.
PMID: 30449705; PMC: PMC6294113
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Liu Q, Van Bortle K, Zhang Y, Zhao MT, Zhang JZ, Geller BS, Gruber JJ, Jiang C, Wu JC, Snyder MP.
Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13
-cis-retinoic acid.
Sci Rep. 2018 Aug 28;8(1):12960.
PMID: 30154523; PMC: PMC6113333
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D'Antonio M, Benaglio P, Jakubosky D, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D
'Antonio-Chronowska A, Frazer KA.
Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative
Multi-Omics Approach.
Cell Rep. 2018 Jul 24;24(4):883-894.
PMID: 30044985
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Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A,
Bishara A, Rosenkrantz JL et al.
Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.
Cell. 2018 May 31;173(6):1356-1369.e22.
PMID: 29856954; PMC: PMC5986104
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Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES,
Scheuermann RH.
Cell type discovery using single-cell transcriptomics: implications for ontological
representation.
Hum Mol Genet. 2018 May 1;27(R1):R40-R47.
PMID: 29590361; PMC: PMC5946857
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Tsunemoto R, Lee S, Szűcs A, Chubukov P, Sokolova I, Blanchard JW, Eade KT, Bruggemann J, Wu C,
Torkamani A et al.
Diverse reprogramming codes for neuronal identity.
Nature. 2018 May;557(7705):375-380.
PMID: 29743677; PMC: PMC6483730
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Larsson AJM, Stanley G, Sinha R, Weissman IL, Sandberg R.
Computational correction of index switching in multiplexed sequencing libraries.
Nat Methods. 2018 Apr 27;15(5):305-307.
PMID: 29702636
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Lee J, Shao NY, Paik DT, Wu H, Guo H, Termglinchan V, Churko JM, Kim Y, Kitani T, Zhao MT
et al.
SETD7 Drives Cardiac Lineage Commitment through Stage-Specific Transcriptional Activation.
Cell Stem Cell. 2018 Mar 1;22(3):428-444.e5.
PMID: 29499155; PMC: PMC5929163
2017
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Zhao MT, Chen H, Liu Q, Shao NY, Sayed N, Wo HT, Zhang JZ, Ong SG, Liu C, Kim Y et al.
Molecular and functional resemblance of differentiated cells derived from isogenic human iPSCs and
SCNT-derived ESCs.
Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):E11111-E11120.
PMID: 29203658; PMC: PMC5748177
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Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J,
Pulendran B et al.
Cell type discovery and representation in the era of high-content single cell phenotyping.
BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):559.
PMID: 29322913; PMC: PMC5763450
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Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M,
Sandoval-Espinosa C, Liu SJ, Velmeshev D et al.
Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human
cortex.
Science. 2017 Dec 8;358(6368):1318-1323.
PMID: 29217575; PMC: PMC5991609
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Estarás C, Hsu HT, Huang L, Jones KA.
YAP repression of the WNT3 gene controls hESC differentiation along the cardiac
mesoderm lineage.
Genes Dev. 2017 Nov 15;31(22):2250-2263.
PMID: 29269485; PMC: PMC5769769
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Zhao MT, Shao NY, Hu S, Ma N, Srinivasan R, Jahanbani F, Lee J, Zhang SL, Snyder MP, Wu JC.
Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced
Pluripotent Stem Cells and Somatic Cells.
Circ Res. 2017 Nov 10;121(11):1237-1250.
PMID: 29030344; PMC: PMC5773062
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Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M,
Caneda C et al.
Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human
Glioblastoma.
Cell Rep. 2017 Oct 31;21(5):1399-1410.
PMID: 29091775; PMC: PMC5810554
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Di Lullo E, Kriegstein AR.
The use of brain organoids to investigate neural development and disease.
Nat Rev Neurosci. 2017 Oct;18(10):573-584.
PMID: 28878372; PMC: PMC5667942
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Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR.
Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic
Mutation Patterns.
Cell. 2017 Oct 5;171(2):321-330.e14.
PMID: 28965763; PMC: PMC6047899
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Zarnegar MA, Reinitz F, Newman AM, Clarke MF.
Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers.
Nucleic Acids Res. 2017 Sep 29;45(17):e153.
PMID: 28973448; PMC: PMC5622369
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Sloan SA, Darmanis S, Huber N, Khan TA, Birey F, Caneda C, Reimer R, Quake SR, Barres BA,
Paşca SP.
Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from
Pluripotent Stem Cells.
Neuron. 2017 Aug 16;95(4):779-790.e6.
PMID: 28817799
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Liu Q, Jiang C, Xu J, Zhao MT, Van Bortle K, Cheng X, Wang G, Chang HY, Wu JC, Snyder MP.
Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte
Differentiation Derived From hiPSCs and hESCs.
Circ Res. 2017 Aug 4;121(4):376-391.
PMID: 28663367; PMC: PMC5576565
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Birey F, Andersen J, Makinson CD, Islam S, Wei W, Huber N, Fan HC, Metzler KRC,
Panagiotakos G, Thom N et al.
Assembly of functionally integrated human forebrain spheroids.
Nature. 2017 May 4;545(7652):54-59.
PMID: 28445465
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Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD,
Garcia M, Nelson BC et al.
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation
across a Variety of Cell Types.
Stem Cell Reports. 2017 Apr 11;8(4):1086-1100.
PMID: 28410642; PMC: PMC5390244
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D'Antonio M, Woodruff G, Nathanson JL, D'Antonio-Chronowska A, Arias A, Matsui H, Williams R,
Herrera C, Reyna SM, Yeo GW et al.
High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.
Stem Cell Reports. 2017 Apr 11;8(4):1101-1111.
PMID: 28410643; PMC: PMC5390243
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Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA.
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin
interaction data.
BMC Bioinformatics. 2017 Apr 7;18(1):207.
PMID: 28388874; PMC: PMC5384132
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Bershteyn M, Nowakowski TJ, Pollen AA, Di Lullo E, Nene A, Wynshaw-Boris A, Kriegstein AR.
Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged
Mitosis of Outer Radial Glia.
Cell Stem Cell. 2017 Apr 6;20(4):435-449.e4.
PMID: 28111201; PMC: PMC5667944
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DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E,
D'Antonio M et al.
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced
Pluripotent Stem Cells.
Cell Stem Cell. 2017 Apr 6;20(4):533-546.e7.
PMID: 28388430; PMC: PMC5444918
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Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C,
Biggs W, Sandoval E et al.
Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific
Manner Independent of Genetics.
Cell Stem Cell. 2017 Apr 6;20(4):505-517.e6.
PMID: 28388429; PMC: PMC5444384
2016
-
King AD, Huang K, Rubbi L, Liu S, Wang CY, Wang Y, Pellegrini M, Fan G.
Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse
Embryonic Stem Cells.
Cell Rep. 2016 Sep 27;17(1):289-302.
PMID: 27681438;
PMC: PMC5507178
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Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM,
Swindells S, Shen H, Ng CT et al.
Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological
Age and Epigenetic Targeting of HLA.
Mol Cell. 2016 Apr 21;62(2):157-68.
PMID: 27105112;
PMC: PMC4995115
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Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM,
Uzunangelov V, Carlin DE et al.
Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.
Cell. 2016 Aug 11;166(4):1041-1054.
PMID: 27499020;
PMC: PMC4985183
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Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO,
Wong CK
et al.
Inferring causal molecular networks: empirical assessment through a
community-based effort.
Nat Methods. 2016 Apr;13(4):310-8.
PMID: 26901648;
PMC: PMC4854847
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Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A,
Meyerowitz JG, Mathis C et al.
N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate
Epithelial Cells.
Cancer Cell. 2016 Apr 11;29(4):536-547.
PMID: 27050099;
PMC: PMC4829466
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Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM.
Pathway-Based Genomics Prediction using Generalized Elastic Net.
PLoS Comput Biol. 2016 Mar;12(3):e1004790.
PMID: 26960204;
PMC: PMC4784899
-
Sokolov A, Paull EO, Stuart JM.
One-class detection of cell states in tumor subtypes.
Pac Symp Biocomput. 2016;21:405-16.
PMID: 26776204;
PMC: PMC4856035
-
Cordero P, Stuart JM.
Tracing co-regulatory network dynamics in noisy, single-cell transcriptomr trajectories.
Pac Symp Biocomput. 2016;22:576-587.
PMID: 27897008;
PMC: PMC5203771
2015
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Blanchard JW, Eade KT, Szűcs A, Lo Sardo V, Tsunemoto RK, Williams D, Sanna PP, Baldwin KK.
Selective conversion of fibroblasts into peripheral sensory neurons.
Nat Neurosci. 2015 Jan;18(1):25-35.
PMID: 25420069; PMC: PMC4466122
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Smith BA, Sokolov A, Uzunangelov V, Baertsch R, Newton Y, Graim K, Mathis C, Cheng D, Stuart JM,
Witte ON.
A basal stem cell signature identifies aggressive prostate cancer phenotypes.
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6544-52.
PMID: 26460041;
PMC: PMC4664352
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Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L,
Szalma S et al.
NDEx, the Network Data Exchange.
Cell Syst. 2015 Oct 28;1(4):302-305.
PMID: 26594663;
PMC: PMC4649937
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Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ,
Oldham MC, Diaz A et al.
Molecular identity of human outer radial glia during cortical development.
Cell. 2015 Sep 24;163(1):55-67.
PMID: 26406371; PMC: PMC4583716
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Pietras EM, Reynaud D, Kang YA, Carlin D, Calero-Nieto FJ, Leavitt AD, Stuart JM,
Göttgens B, Passegué E.
Functionally Distinct Subsets of Lineage-Biased Multipotent Progenitors Control Blood
Production in Normal and Regenerative Conditions.
Cell Stem Cell. 2015 Jul 2;17(1):35-46.
PMID: 26095048;
PMC: PMC4542150
-
Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA,
Quake SR.
A survey of human brain transcriptome diversity at the single cell level.
Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7285-90.
PMID: 26060301;
PMC: PMC4466750
2014
