CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS.

Autor: Roux de Bézieux H; Pendulum Therapeutics, Inc., San Francisco, CA 94107, USA., Lima L; European Bioinformatics Institute, Cambridge CB10 1SD, UK., Perraudeau F; Pendulum Therapeutics, Inc., San Francisco, CA 94107, USA., Mary A; Univ. Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne 69100, France., Dudoit S; Division of Biostatistics, Department of Statistics, University of California, Berkeley, CA 94704, USA., Jacob L; Univ. Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne 69100, France.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2022 Jun 24; Vol. 38 (Suppl 1), pp. i36-i44.

Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer.

Autor: Okamoto T; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan., duVerle D; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Yaginuma K; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Natsume Y; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Yamanaka H; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Kusama D; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Fukuda M; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Yamamoto M; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Perraudeau F; Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA., Srivastava U; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Kashima Y; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Suzuki A; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Kuze Y; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Takahashi Y; Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan., Ueno M; Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan., Sakai Y; Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan., Noda T; Director's Room, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan., Tsuda K; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Suzuki Y; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan., Nagayama S; Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan., Yao R; Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan. Electronic address: ryao@jfcr.or.jp.

Publikováno v: Stem cell reports [Stem Cell Reports] 2021 Apr 13; Vol. 16 (4), pp. 954-967. Date of Electronic Publication: 2021 Mar 11.

Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation.

Autor: Perraudeau F; Pendulum Therapeutics, Inc, San Francisco, California, USA., McMurdie P; Pendulum Therapeutics, Inc, San Francisco, California, USA., Bullard J; Pendulum Therapeutics, Inc, San Francisco, California, USA., Cheng A; Pendulum Therapeutics, Inc, San Francisco, California, USA., Cutcliffe C; Pendulum Therapeutics, Inc, San Francisco, California, USA., Deo A; Pendulum Therapeutics, Inc, San Francisco, California, USA., Eid J; Pendulum Therapeutics, Inc, San Francisco, California, USA., Gines J; Pendulum Therapeutics, Inc, San Francisco, California, USA., Iyer M; Pendulum Therapeutics, Inc, San Francisco, California, USA., Justice N; Pendulum Therapeutics, Inc, San Francisco, California, USA., Loo WT; Pendulum Therapeutics, Inc, San Francisco, California, USA., Nemchek M; Pendulum Therapeutics, Inc, San Francisco, California, USA., Schicklberger M; Pendulum Therapeutics, Inc, San Francisco, California, USA., Souza M; Pendulum Therapeutics, Inc, San Francisco, California, USA., Stoneburner B; Pendulum Therapeutics, Inc, San Francisco, California, USA., Tyagi S; Pendulum Therapeutics, Inc, San Francisco, California, USA., Kolterman O; Pendulum Therapeutics, Inc, San Francisco, California, USA orville.kolterman@pendulum.co.

Publikováno v: BMJ open diabetes research & care [BMJ Open Diabetes Res Care] 2020 Jul; Vol. 8 (1).

Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers.

Autor: Yao, Jun¹ (AUTHOR), Xu, Hengyi¹ (AUTHOR), Ferrick-Kiddie, Elizabeth A.¹ (AUTHOR), Nottingham, Ryan M.¹ (AUTHOR), Wu, Douglas C.¹ (AUTHOR), Ares Jr, Manuel² (AUTHOR), Lambowitz, Alan M.¹ (AUTHOR) lambowitz@austin.utexas.edu

Publikováno v: PLoS Genetics. 9/26/2024, Vol. 20 Issue 9, p1-48. 48p.

scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data.

Autor: Liu, Zhenze¹ (AUTHOR), Liang, Yingjian² (AUTHOR), Wang, Guohua^3,4 (AUTHOR) ghwang@nefu.edu.cn, Zhang, Tianjiao³ (AUTHOR) ghwang@nefu.edu.cn

Publikováno v: Briefings in Bioinformatics. Sep2024, Vol. 25 Issue 5, p1-13. 13p.