Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z & Kondo A Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems Science 353, aaf8729

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

duVerle DA, Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics. 2016 Sep 13;17(1):363. doi: 10.1186/s12859-016-1175-6.

Coupling CDH17 and CLDN18 markers for comprehensive membrane-targeted detection of human gastric cancer.

Matsusaka K, Ushiku T, Urabe M, Fukuyo M, Abe H, Ishikawa S, Seto Y, Aburatani H, Hamakubo T, Kaneda A, Fukayama M. Coupling CDH17 and CLDN18 markers for comprehensive membrane-targeted detection of human gastric cancer. Oncotarget. 2016 Sep 27;7(39):64168-64181. doi: 10.18632/oncotarget.11638.

Two subtypes of colorectal tumor with distinct molecular features in familial adenomatous polyposis.

Takane K, Matsusaka K, Ota S, Fukuyo M, Yue Y, Nishimura M, Sakai E, Matsushita K, Miyauchi H, Aburatani H, Nakatani Y, Takayama T, Matsubara H, Akagi K, Kaneda A. Two subtypes of colorectal tumor with distinct molecular features in familial adenomatous polyposis. Oncotarget. 2016 Dec 20;7(51):84003-84016. doi: 10.18632/oncotarget.11510.

The H3K9 methyltransferase Setdb1 regulates TLR4-mediated inflammatory responses in macrophages.

Hachiya R, Shiihashi T, Shirakawa I, Iwasaki Y, Matsumura Y, Oishi Y, Nakayama Y, Miyamoto Y, Manabe I, Ochi K, Tanaka M, Goda N, Sakai J, Suganami T, Ogawa Y. The H3K9 methyltransferase Setdb1 regulates TLR4-mediated inflammatory responses in macrophages. Sci Rep. 2016 Jun 28;6:28845. doi: 10.1038/srep28845.

Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development.

Nimura K, Yamamoto M, Takeichi M, Saga K, Takaoka K, Kawamura N, Nitta H, Nagano H, Ishino S, Tanaka T, Schwartz RJ, Aburatani H, Kaneda Y. Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development. Elife. 2016 Jun 22;5. pii: e16030. doi: 10.7554/eLife.16030.

Network-based analysis for identification of candidate genes for colorectal cancer progression.

Tsuji S, Midorikawa Y, Seki M, Takayama T, Sugiyama Y, Aburatani H. Network-based analysis for identification of candidate genes for colorectal cancer progression. Biochem Biophys Res Commun. 2016 Aug 5;476(4):534-40. doi: 10.1016/j.bbrc.2016.05.158. Epub 2016 May 30.

Transcriptional and epigenetic control of brown and beige adipose cell fate and function.

Inagaki T, Sakai J, Kajimura S. Transcriptional and epigenetic control of brown and beige adipose cell fate and function. Nat Rev Mol Cell Biol. 2016 Aug;17(8):480-95. doi: 10.1038/nrm.2016.62. Epub 2016 Jun 2. Review.

Erratum: Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.

Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano K, Maejima K, Sasaki-Oku A, et al. Erratum: Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet. 2016 May 27;48(6):700. doi: 10.1038/ng0616-700a. No abstract available.

The Effects of Cis-Regulatory Mutations in the SUL1 Gene on Sulfate-Limited Fitness in Yeast

Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ & Fields S The Effects of Cis-Regulatory Mutations in the SUL1 Gene on Sulfate-Limited Fitness in Yeast Genetics 203, 191-202

Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens.

Matsusaka K, Ishikawa S, Nakayama A, Ushiku T, Nishimoto A, Urabe M, Kaneko N, Kunita A, Kaneda A, Aburatani H, Fujishiro M, Seto Y, Fukayama M. Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens. PLoS One. 2016 Apr 27;11(4):e0154430. doi: 10.1371/journal.pone.0154430. eCollection 2016.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics

Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu Y-C, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M & Roth FP Pooled-matrix protein interaction screens using Barcode Fusion Genetics Molecular Systems Biology 12, 863

Suppression of Slit2/Robo1 mediated HUVEC migration by Robo4.

Ishibashi S, Yamashita S, Arai H, Araki E, Yokote K, Suganami H, Fruchart JC, Kodama T; K-877-04 Study Group.. Suppression of Slit2/Robo1 mediated HUVEC migration by Robo4. Atherosclerosis. 2016 Jun;249:36-43. doi: 10.1016/j.atherosclerosis.2016.02.029. Epub 2016 Feb 26.

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.

Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano K, Maejima K, Sasaki-Oku A, et al. Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet. 2016 May;48(5):500-9. doi: 10.1038/ng.3547. Epub 2016 Apr 11.

PGE2 induced in and released by dying cells functions as an inhibitory DAMP.

Hangai S, Ao T, Kimura Y, Matsuki K, Kawamura T, Negishi H, Nishio J, Kodama T, Taniguchi T, Yanai H. PGE2 induced in and released by dying cells functions as an inhibitory DAMP. Proc Natl Acad Sci U S A. 2016 Apr 5;113(14):3844-9. doi: 10.1073/pnas.1602023113.

MEIS1-mediated transactivation of synaptotagmin-like 1 promotes CXCL12/CXCR4 signaling and leukemogenesis.

Yokoyama T, Nakatake M, Kuwata T, Couzinet A, Goitsuka R, Tsutsumi S, Aburatani H, Valk PJ, Delwel R, Nakamura T. MEIS1-mediated transactivation of synaptotagmin-like 1 promotes CXCL12/CXCR4 signaling and leukemogenesis. J Clin Invest. 2016 May 2;126(5):1664-78. doi: 10.1172/JCI81516. Epub 2016 Mar 28.