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    Academic Journals

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• T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation.

  Authors:Alexandro Landshammer, Adriano Bolondi, Helene Kretzmer, Christian Much, René Buschow, Alina Rose, et al.From:eLife (Vol. 12) Peer-Reviewed

  Jan. 31, 202329,282 words Article 1440LLong non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the...

• Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.

  Authors:Alessa R. Ringel, Quentin Szabo, Andrea M. Chiariello, Konrad Chudzik, Robert Schöpflin, Patricia Rothe, et al.From:Cell (Vol. 185, Issue 20) Peer-Reviewed

  Sept. 29, 2022545 words Report

   Abstract Only

• Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

  Authors:Arie B. Brinkman, Hongcang Gu, Stefanie J.J. Bartels, Yingying Zhang, Filomena Matarese, Femke Simmer, et al.From:Genome Research (Vol. 22, Issue 6) Peer-Reviewed

  June 2012 Report

   Citation Only

• Cre-lox-regulated conditional RNA interference from transgenes

  Authors:Andrea Ventura, Alexander Meissner, Christopher P. Dillon, Michael McManus, Phillip A. Sharp, Luk Van Parijs, et al.From:Proceedings of the National Academy of Sciences of the United States (Vol. 101, Issue 28) Peer-Reviewed

  July 13, 2004129 words Author abstract

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• Targets and genomic constraints of ectopic Dnmt3b expression

  Authors:Yingying Zhang, Jocelyn Charlton, Rahul Karnik, Isabel Beerman, Zachary D Smith, Hongcang Gu, et al.From:eLife (Vol. 7) Peer-Reviewed

  Nov. 23, 201824,892 words Report 1540LDNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer...

• Dissecting direct reprogramming through integrative genomic analysis

  Authors:Tarjei S. Mikkelsen, Jacob Hanna, Xiaolan Zhang, Manching Ku, Marius Wernig, Patrick Schorderet, et al.From:Nature (Vol. 454, Issue 7205) Peer-Reviewed

  Aug. 7, 200834 words Brief article, Corre... doi:10.1038/nature07196 Nature 454, 49-55 (2008) In both the Methods Summary and the online-only Methods (cell culture section), the concentration of AZA is incorrectly listed as 0.5 mM. The correct final...

• LKB1 loss links serine metabolism to DNA methylation and tumorigenesis

  Authors:Filippos Kottakis, Brandon N. Nicolay, Ahlima Roumane, Rahul Karnik, Hongcang Gu, Julia M. Nagle, et al.From:Nature (Vol. 539, Issue 7629) Peer-Reviewed

  Nov. 17, 20169,614 words Report 1640LIntermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that...

• Dissecting neural differentiation regulatory networks through epigenetic footprinting

  Authors:Michael J. Ziller, Reuven Edri, Yakey Yaffe, Julie Donaghey, Ramona Pop, William Mallard, et al.From:Nature (Vol. 518, Issue 7539) Peer-Reviewed

  Feb. 19, 201511,314 words Report 1610LModels derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical...

• The Mammalian Epigenome

  Authors:Bradley E. Bernstein, Alexander Meissner, and Eric S. LanderFrom:Cell (Vol. 128, Issue 4) Peer-Reviewed

  Feb. 23, 2007184 words Author abstract 60L

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• Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

  Authors:Zachary D. Smith, Iftach Nachman, Aviv Regev, and Alexander MeissnerFrom:Nature Biotechnology (Vol. 28, Issue 5) Peer-Reviewed

  May 20104,540 words Report 1590LThe study of induced pluripotency often relies on experimental approaches that average measurements across a large population of cells, the majority of which do not become pluripotent. Here we used high-resolution,...

• Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade

  Authors:Sachet A. Shukla, Pavan Bachireddy, Bastian Schilling, Christina Galonska, Qian Zhan, Clyde Bango, et al.From:Cell (Vol. 173, Issue 3) Peer-Reviewed

  Apr. 19, 2018540 words Report

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• Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells

  Authors:Alexander Meissner, Marius Wernig, and Rudolf JaenischFrom:Nature Biotechnology (Vol. 25, Issue 10) Peer-Reviewed

  Oct. 20073,710 words Article Author(s): Alexander Meissner [1, 3]; Marius Wernig [1, 3]; Rudolf Jaenisch (corresponding author) [1, 2] In vitro reprogramming of somatic cells into a pluripotent embryonic stem cell-like state has been achieved...

• Saturation analysis for whole-genome bisulfite sequencing data

  Authors:Emanuele Libertini, Simon C. Heath, Rifat A. Hamoudi, Marta Gut, Michael J. Ziller, Javier Herrero, et al.From:Nature Biotechnology (Vol. 34, Issue 7) Peer-Reviewed

  July 20161,581 words Report 1540LTo the Editor: Whole-genome bisulfite sequencing (WGBS) has become an integral part of basic and clinical research and has been widely used to generate reference methylomes since 2010 (refs. 1,2). However, because of...

• A unique regulatory phase of DNA methylation in the early mammalian embryo

  Authors:Zachary D. Smith, Michelle M. Chan, Tarjei S. Mikkelsen, Hongcang Gu, Andreas Gnirke, Aviv Regev, et al.From:Nature (Vol. 484, Issue 7394) Peer-Reviewed

  Apr. 19, 20126,724 words Report 1510LDNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of 5-methylcytosine at fertilization, followed by passive loss that reaches a...

• Epigenetic modifications in pluripotent and differentiated cells

  Author:Alexander MeissnerFrom:Nature Biotechnology (Vol. 28, Issue 10) Peer-Reviewed

  Oct. 201010,060 words Report 1350LEpigenetic modifications constitute a complex regulatory layer on top of the genome sequence. Pluripotent and differentiated cells provide a powerful system for investigating how the epigenetic code influences cellular...

• Sprouty-2 regulates oncogenic K-ras in lung development and tumorigenesis

  Authors:Alice T. Shaw, Alexander Meissner, James A. Dowdle, Denise Crowley, Margaret Magendantz, Chensi Ouyang, et al.From:Genes & Development (Vol. 21, Issue 6) Peer-Reviewed

  Mar. 15, 200747 words Article

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• Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells

  Authors:Weida Li, Claudia Cavelti-Weder, Yinying Zhang, Kendell Clement, Scott Donovan, Gabriel Gonzalez, et al.From:Nature Biotechnology (Vol. 32, Issue 12) Peer-Reviewed

  Dec. 20147,451 words Report 1430LDirect lineage conversion is a promising approach to generate therapeutically important cell types for disease modeling and tissue repair. However, the survival and function of lineage-reprogrammed cells in vivo over...

• Genome-scale DNA methylation maps of pluripotent and differentiated cells

  Authors:Alexander Meissner, Tarjei S. Mikkelsen, Hongcang Gu, Marius Wernig, Jacob Hanna, Andrey Sivachenko, et al.From:Nature (Vol. 454, Issue 7205) Peer-Reviewed

  Aug. 7, 20084,836 words Report 1460LDNA methylation is essential for normal development (1-3) and has been implicated in many pathologies including cancer (4, 5). Our knowledge about the genome-wide distribution of DNA methylation, how it changes during...

• A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells

  Authors:Alexander M. Tsankov, Veronika Akopian, Ramona Pop, Sundari Chetty, Casey A. Gifford, Laurence Daheron, et al.From:Nature Biotechnology (Vol. 33, Issue 11) Peer-Reviewed

  Nov. 201510,775 words Report 1560LResearch on human pluripotent stem cells has been hampered by the lack of a standardized, quantitative, scalable assay of pluripotency. We previously described an assay called ScoreCard that used gene expression...

• Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2

  Authors:Wen G. Chen, Qiang Chang, Yingxi Lin, Alexander Meissner, Anne E. West, Eric C. Griffith, et al.From:Science (Vol. 302, Issue 5646) Peer-Reviewed

  Oct. 31, 20033,695 words Article Mutations in MeCP2, which encodes a protein that has been proposed to function as a global transcriptional repressor, are the cause of Rett syndrome (RTT), an X-linked progressive neurological disorder. Although the...