Publications by authors named "Davide Albanese"

35Publications

Large scale genome reconstructions illuminate Wolbachia evolution.

Nat Commun 2020 10 16;11(1):5235. Epub 2020 Oct 16.

Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.

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http://dx.doi.org/10.1038/s41467-020-19016-0DOI Listing
October 2020

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance.

mSystems 2020 May 26;5(3). Epub 2020 May 26.

Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1128/mSystems.00061-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253362PMC
May 2020

Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.

Microbiol Resour Announc 2020 Mar 5;9(10). Epub 2020 Mar 5.

Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.

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http://dx.doi.org/10.1128/MRA.01599-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171226PMC
March 2020

Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees.

Environ Microbiol 2020 Jun 6;22(6):2080-2093. Epub 2020 Mar 6.

Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1111/1462-2920.14963DOI Listing
June 2020

Alpine headwaters emerging from glaciers and rock glaciers host different bacterial communities: Ecological implications for the future.

Sci Total Environ 2020 May 4;717:137101. Epub 2020 Feb 4.

Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, Italy.

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http://dx.doi.org/10.1016/j.scitotenv.2020.137101DOI Listing
May 2020

Microbiome of vineyard soils is shaped by geography and management.

Microbiome 2019 11 8;7(1):140. Epub 2019 Nov 8.

Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1186/s40168-019-0758-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839268PMC
November 2019

Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions.

Sci Rep 2018 11 15;8(1):16893. Epub 2018 Nov 15.

Department of Ecological and Biological Sciences (DEB), Tuscia University, Largo dell'Università, 01100, Viterbo, Italy.

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http://dx.doi.org/10.1038/s41598-018-35329-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237987PMC
November 2018

Host: Microbiome co-metabolic processing of dietary polyphenols - An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects.

Food Res Int 2018 10 8;112:108-128. Epub 2018 Jun 8.

Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all'Adige, TN, Italy; Center Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09639969183046
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http://dx.doi.org/10.1016/j.foodres.2018.06.016DOI Listing
October 2018

A practical tool for maximal information coefficient analysis.

Gigascience 2018 04;7(4):1-8

Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy.

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http://dx.doi.org/10.1093/gigascience/giy032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893960PMC
April 2018

Strain profiling and epidemiology of bacterial species from metagenomic sequencing.

Nat Commun 2017 12 22;8(1):2260. Epub 2017 Dec 22.

Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1038/s41467-017-02209-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741664PMC
December 2017

Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake.

Microb Ecol 2018 Jul 1;76(1):125-143. Epub 2017 Dec 1.

Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1007/s00248-017-1120-xDOI Listing
July 2018

SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns.

Sci Rep 2017 11 10;7(1):15343. Epub 2017 Nov 10.

Computational Biology Unit, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy.

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http://dx.doi.org/10.1038/s41598-017-15729-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681646PMC
November 2017

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy.

Front Microbiol 2017 13;8:1979. Epub 2017 Oct 13.

Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Meyer Children Hospital, Florence, Italy.

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http://dx.doi.org/10.3389/fmicb.2017.01979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645538PMC
October 2017

Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout (Oncorhynchus mykiss).

Int J Food Sci Nutr 2018 May 31;69(3):318-333. Epub 2017 Aug 31.

f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy.

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http://dx.doi.org/10.1080/09637486.2017.1370699DOI Listing
May 2018

Temperature drives the assembly of endophytic communities' seasonal succession.

Environ Microbiol 2017 08 24;19(8):3353-3364. Epub 2017 Jul 24.

Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, TN, 38010, Italy.

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http://dx.doi.org/10.1111/1462-2920.13843DOI Listing
August 2017

New evidences on the altered gut microbiota in autism spectrum disorders.

Microbiome 2017 02 22;5(1):24. Epub 2017 Feb 22.

Institute of Agriculture Biology and Biotechnology, National Research Council (CNR), Via Moruzzi 1, 56124, Pisa, Italy.

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http://dx.doi.org/10.1186/s40168-017-0242-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320696PMC
February 2017

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status.

Front Microbiol 2016 26;7:1703. Epub 2016 Oct 26.

Department of Neuroscience, Psychology, Drug Research and Child Health, Meyer Children's Hospital, University of FlorenceFlorence, Italy; Rheumatology Unit, Anna Meyer Children's Hospital, University of FlorenceFlorence, Italy.

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http://dx.doi.org/10.3389/fmicb.2016.01703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080347PMC
October 2016

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Nat Microbiol 2016 05 27;1(7):16070. Epub 2016 May 27.

Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy.

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http://dx.doi.org/10.1038/nmicrobiol.2016.70DOI Listing
May 2016

Altered gut microbiota in Rett syndrome.

Microbiome 2016 07 30;4(1):41. Epub 2016 Jul 30.

Institute of Biometeorology (IBIMET), National Research Council (CNR), Via Giovanni Caproni 8, I-50145, Florence, Italy.

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http://dx.doi.org/10.1186/s40168-016-0185-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967335PMC
July 2016

Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation.

Microb Biotechnol 2016 Mar 18;9(2):195-208. Epub 2016 Jan 18.

Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.

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http://dx.doi.org/10.1111/1751-7915.12337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767281PMC
March 2016

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation.

Sci Rep 2015 Oct 7;5:14862. Epub 2015 Oct 7.

Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy.

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http://www.nature.com/articles/srep14862
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http://dx.doi.org/10.1038/srep14862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595646PMC
October 2015

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

Sci Rep 2015 May 19;5:9743. Epub 2015 May 19.

Fondazione Edmund Mach, Research and Innovation Centre, Computational Biology Department, Via E. Mach 1, 38010 - S. Michele all'Adige (TN), Italy.

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http://www.nature.com/articles/srep09743
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http://dx.doi.org/10.1038/srep09743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649890PMC
May 2015

Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting.

PLoS Comput Biol 2015 Mar 27;11(3):e1004186. Epub 2015 Mar 27.

Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1004186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376673PMC
March 2015

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.

Bioinformatics 2013 Feb 14;29(3):407-8. Epub 2012 Dec 14.

Fondazione Bruno Kessler, via Sommarive 18, I-38123 Povo (Trento), Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts707DOI Listing
February 2013

TOFwave: reproducibility in biomarker discovery from time-of-flight mass spectrometry data.

Mol Biosyst 2012 Nov 9;8(11):2845-9. Epub 2012 Aug 9.

Fondazione Bruno Kessler, Trento, Italy.

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http://dx.doi.org/10.1039/c2mb25223fDOI Listing
November 2012