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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.Breast cancer is characterized by both genetic and epigenetic alterations (Sjoblom et al. 2006; Esteller 2007, 2008...
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Resource: Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear
- Henriëtte van Beijnum,
- Tim Koopmans,
- Antonio Tomasso,
- Vanessa Disela,
- Severin te Lindert,
- Jeroen Bakkers,
- Anna Alemany,
- Eugene Berezikov,
- and Kerstin Bartscherer
Genome Res. August 2023 33: 1424-1437; Published in Advance September 19, 2023, doi:10.1101/gr.277538.122
...with the tomo-seq data, we found muscles to be exclusively present in the proximal part of the ear (Fig. 3E,F). In addition, we found asymmetric expression of genes related to epidermal differentiation and hair follicles, such as filaggrin (Flg), desmocollin 3 (Dsc3), and cystatin E/M (Cst6) (Fig. 3C...
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Method: A model-based constrained deep learning clustering approach for spatially resolved single-cell data
- Xiang Lin,
- Le Gao,
- Nathan Whitener,
- Ashley Ahmed,
- and Zhi Wei
Genome Res. October 2022 32: 1906-1917; Published in Advance October 5, 2022, doi:10.1101/gr.276477.121
...variable genes by graph convolutional network. Nat Methods 18: 1342–1351. doi:10.1038/s41592-021-01255-8 ↵Hubert L, Arabie P. 1985. Comparing partitions. J Classif 2: 193–218. doi:10.1007/BF01908075 ↵Kaur G, Levy E. 2012. Cystatin C in Alzheimer's disease. Front Mol Neurosci 5: 79. doi:10.3389/fnmol.2012...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a -wide catalog of 9537 spl-TRs with a total of 58,290 significant TR–splicing associations across 49...
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RESOURCE: An atlas of human gene expression from massively parallel signature sequencing (MPSS)
- C. Victor Jongeneel,
- Mauro Delorenzi,
- Christian Iseli,
- Daixing Zhou,
- Christian D. Haudenschild,
- Irina Khrebtukova,
- Dmitry Kuznetsov,
- Brian J. Stevenson,
- Robert L. Strausberg,
- Andrew J.G. Simpson,
- and Thomas J. Vasicek
Genome Res. July 2005 15: 1007-1014; doi:10.1101/gr.4041005
...reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the idea that most human genes have been mapped, if not functionally characterized. This data set should prove useful for the identification of tissue...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
...An analysis of the gene complement of a marsupial, Monodelphis domestica : Evolution of lineage-specific genes and giant chromosomes Leo Goodstadt 1 , Andreas Heger , Caleb Webber , and Chris P. Ponting MRC Functional Genetics Unit...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...These authors contributed equally to this review. Corresponding author: christopher.pearson@sickkids.caAbstractExpansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans...
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RESOURCE: BodyMap: A Collection of 3′ ESTs for Analysis of Human Gene Expression Information
- Shoko Kawamoto,
- Junji Yoshii,
- Katsuya Mizuno,
- Kouichi Ito,
- Yasuhide Miyamoto,
- Tadashi Ohnishi,
- Ryo Matoba,
- Naohiro Hori,
- Yuhiko Matsumoto,
- Toshiyuki Okumura,
- Yuko Nakao,
- Hisae Yoshii,
- Junko Arimoto,
- Hiroko Ohashi,
- Hiroko Nakanishi,
- Ikko Ohno,
- Jun Hashimoto,
- Kota Shimizu,
- Kazuhisa Maeda,
- Hiroshi Kuriyama,
- Koji Nishida,
- Akiyo Shimizu-Matsumoto,
- Wakako Adachi,
- Reiko Ito,
- Satoshi Kawasaki,
- K.S. Chae,
- Katsuji Murakawa,
- Masahiro Yokoyama,
- Atsushi Fukushima,
- Teruyoshi Hishiki,
- Akihiko Nakaya,
- Jun Sese,
- Norikazu Monma,
- Hitoshi Nikaido,
- Shinichi Morishita,
- Kenichi Matsubara,
- and Kousaku Okubo
Genome Res. November 1, 2000 10: 1817-1827; doi:10.1101/gr.151500
...). BodyMap has been used in the isolation and characterization of tissue-specific transcripts ( Nishida et al 1996 ; Ohno et al. 1996 ; Maeda et al. 1997 ; Shimizu-Matsumoto et al. 1997 ) and in disease gene identification ( Irvine et al. 1997 ; Nishida et al. 1997 ). Here we describe the structure...
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ARTICLES: A nonsense mutation in the cathepsin K gene observed in a family with pycnodysostosis.
- M R Johnson,
- M H Polymeropoulos,
- H L Vos,
- R I Ortiz de Luna,
- and C A Francomano
Genome Res. November 1996 6: 1050-1055; doi:10.1101/gr.6.11.1050
..., Bethesda, Maryland 20892-1852, USA. Abstract Pycnodysostosis (MIM 265800) is a rare, autosomal recessive skeletal dysplasia characterized by short stature, wide cranial sutures, and increased bone density and fragility. Linkage analysis localized the disease gene to human chromosome 1q21...
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LETTER: The Mouse Brain Transcriptome by SAGE: Differences in Gene Expression between P30 Brains of the Partial Trisomy 16 Mouse Model of Down Syndrome (Ts65Dn) and Normals
- Roman Chrast,
- Hamish S. Scott,
- Marie Pierre Papasavvas,
- Colette Rossier,
- Emmanuel S. Antonarakis,
- Christine Barras,
- Muriel T. Davisson,
- Cecilia Schmidt,
- Xavier Estivill,
- Mara Dierssen,
- Melanie Pritchard,
- and Stylianos E. Antonarakis
Genome Res. December 1, 2000 10: 2006-2021; doi:10.1101/gr.158500
...and increased generation of reactive oxygen species in Down's syndrome neurons in vitro. Nature 378 : 776 – 779 . ↵ Chen H. , Centola M. , Altschul S.F. , Metzger H. ( 1998 ) Characterization of gene expression in resting and activated mast cells J. Exp. Med. 188 : 1657 – 1668 . ↵ Cramton S.E. , Laski F...

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