Biblio

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Journal Article

Pigoni M, Uzquiano A, Paulsen B, Kedaigle A, Yang SMin, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, et al. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Hum Mol Genet. 2023.

Ludwig L, Lareau CA, Bao EL, Liu N, Utsugisawa T, Tseng AM, Myers SA, Verboon JM, Ulirsch JC, Luo W, et al. A Congenital Anemia Reveals Distinct Targeting Mechanisms for Master Transcription Factor GATA1. Blood. 2022.

Puram RV, Kowalczyk MS, de Boer CG, Schneider RK, Miller PG, McConkey M, Tothova Z, Tejero H, Heckl D, Järås M, et al. Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML. Cell. 2016;165(2):303-316.

Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, et al. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021.

Chen B, Scurrah C'R, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, et al. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell. 2021.

Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev, iv A, Eggan K, Meissner A. DNA methylation dynamics of the human preimplantation embryo. Nature. 2014;511(7511):611-615.

Kumar RM, Cahan P, Shalek AK, Satija R, A DaleyKeyser J, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, et al. Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2015.

Voit RA, Tao L, Yu F, Cato LD, Cohen B, Fleming TJ, Antoszewski M, Liao X, Fiorini C, Nandakumar SK, et al. A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia. Nat Immunol. 2022.

Ximerakis M, Holton KM, Giadone RM, Ozek C, Saxena M, Santiago S, Adiconis X, Dionne D, Nguyen L, Shah KM, et al. Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nat Aging. 2023;3(3):327-345.

Mann M, Mehta A, de Boer CG, Kowalczyk MS, Lee K, Haldeman P, Rogel N, Knecht AR, Farouq D, Regev, iv A, et al. Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age. Cell Rep. 2018;25(11):2992-3005.e5.

Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Braga FVieira, Timens W, Koppelman GH, Budinger GRScott, et al. The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease. Am J Respir Cell Mol Biol. 2019.

Bolton C, Smillie CS, Pandey S, Elmentaite R, Wei G, Argmann C, Aschenbrenner D, James KR, McGovern DPB, Macchi M, et al. An integrated taxonomy for monogenic inflammatory bowel disease. Gastroenterology. 2021.

Cheng C-W, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, et al. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell. 2019;178(5):1115-1131.e15.

Mehta A, Zhao JL, Sinha N, Marinov GK, Mann M, Kowalczyk MS, Galimidi RP, Du X, Erikci E, Regev, iv A, et al. The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression. Immunity. 2015;42(6):1021-1032.

Kobayashi-Kirschvink KJ, Comiter CS, Gaddam S, Joren T, Grody EI, Ounadjela JR, Zhang K, Ge B, Kang JWoong, Xavier RJ, et al. Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nat Biotechnol. 2024.

Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, et al. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 2022;185(20):3770-3788.e27.

Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, et al. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol. 2023.

Gojo J, Englinger B, Jiang L, Hübner JM, Shaw MKL, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, et al. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma. Cancer Cell. 2020;38(1):44-59.e9.

Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016.

Satija R, Farrell JA, Gennert D, Schier AF, Regev, iv A. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015.

De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CBravo, Marchese D, Caratù G, Poovathingal S, et al. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol. 2023.

Mages S, Moriel N, Avraham-Davidi I, Murray E, Watter J, Chen F, Rozenblatt-Rosen O, Klughammer J, Regev, iv A, Nitzan M. TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics. Nat Biotechnol. 2023.

Ludwig LS, Lareau CA, Bao EL, Nandakumar SK, Muus C, Ulirsch JC, Chowdhary K, Buenrostro JD, Mohandas N, An X, et al. Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis. Cell Rep. 2019;27(11):3228-3240.e7.

Gazit R, Garrison BS, Rao TNageswara, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev, iv A, Wagers AJ, et al. Transcriptome Analysis Identifies Regulators of Hematopoietic Stem and Progenitor Cells. Stem Cell Reports. 2013;1(3):266-280.

Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, et al. Voices of biotech. Nat Biotechnol. 2016;34(3):270-275.