Publications of PI. Costea

Publications of PI. Costea

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2022 1 publication(s).
21.
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Van Rossum T, Costea PI, Paoli L, Alves RJ, Thielemann R, Sunagawa S, Bork P
2022 Jan 27; 38(4): 1162-1164. PubMed: 34791031.
Abstract + PDF
2019 3 publication(s).
20.
Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Huerta-Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P
Gut.
2019 Oct 18; 68(10): 1781-1790. PubMed: 30658995.
Abstract + PDF
19.
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves RJ, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S
2019 Mar 4; 10(1): 1014. PubMed: 30833550.
Abstract + PDF
18.
Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P
2019 Feb 12; 8: . PubMed: 30747106.
Abstract + PDF
2018 5 publication(s).
17.
Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P
2018 Apr 19; 6(1): 72. PubMed: 29669589.
Abstract + PDF
16.
Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
2018 Jan; 3(1): 8-16. PubMed: 29255284.
Abstract + PDF
15.
Publisher Correction: Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
2018 Mar 13; 3(3): 388. PubMed: 29440750.
Abstract + PDF
14.
Selective maternal seeding and environment shape the human gut microbiome.
Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P
2018 Apr 1; 28(4): 561-568. PubMed: 29496731.
Abstract + PDF
13.
Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P
2018 Jul 28; 8(7): e021682. PubMed: 30056386.
Abstract + PDF
2017 6 publication(s).
12.
Subspecies in the global human gut microbiome.
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P
2017 Dec 14; 13(12): 960. PubMed: 29242367.
Abstract + PDF
11.
metaSNV: A tool for metagenomic strain level analysis.
Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P
2017; 12(7): e0182392. PubMed: 28753663.
Abstract + PDF
10.
Towards standards for human fecal sample processing in metagenomic studies.
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P
2017 Nov 2; 35(11): 1069-1076. PubMed: 28967887.
Abstract + PDF
9.
Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHit-Consortium , Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
2017 May 3; 545(7652): 116. PubMed: 28470190.
PDF
8.
The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.
Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC
2017 Nov 24; 7(1): 16324. PubMed: 29176730.
Abstract + PDF
7.
Salt-responsive gut commensal modulates TH17 axis and disease.
Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN
2017 Nov 30; 551(7682): 585-589. PubMed: 29143823.
Abstract + PDF
2016 1 publication(s).
6.
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P
2016 Apr 29; 352(6285): 586-9. PubMed: 27126044.
Abstract + PDF
2015 3 publication(s).
5.
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT C, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
2015 Dec 10; 528(7581): 262-266. Epub 2015 Dec 2; PubMed: 26633628.
Abstract + PDF
4.
Structure and function of the global ocean microbiome.
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, De Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
2015 May 22; 348(6237): 1261359. PubMed: 25999513.
Abstract + PDF
3.
Temporal and technical variability of human gut metagenomes.
2015 Apr 8; 16(1): 73. Epub 2015 Apr 8; PubMed: 25888008.
Abstract + PDF
2014 2 publication(s).
2.
A fair comparison.
2014 Apr 28; 11(4): 359. PubMed: 24681719.
PDF
1.
Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P
2014 Nov 28; 10(11): 766. PubMed: 25432777.
Abstract + PDF