Advanced Search
Display options
Filter resources
Text Availability
Article type
Publication date
Species
Language
Sex
Age
Showing 1 to 12 of 37 entries
Sorted by: Best Match Show Resources per page
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Cell host & microbe

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, Xavier RJ.
PMID: 25662751
Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 05.

Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the relationship between human gut microbiome dynamics throughout infancy and type 1 diabetes (T1D), we examined a cohort...

Functional profiling of the gut microbiome in disease-associated inflammation.

Genome medicine

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C.
PMID: 23906180
Genome Med. 2013 Jul 31;5(7):65. doi: 10.1186/gm469. eCollection 2013.

The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health and...

bioBakery: a meta'omic analysis environment.

Bioinformatics (Oxford, England)

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C.
PMID: 29194469
Bioinformatics. 2018 Apr 01;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754.

SUMMARY: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured...

Embryonic vascular disruption adverse outcomes: Linking high-throughput signaling signatures with functional consequences.

Reproductive toxicology (Elmsford, N.Y.)

Ellis-Hutchings RG, Settivari RS, McCoy AT, Kleinstreuer N, Franzosa J, Knudsen TB, Carney EW.
PMID: 28414088
Reprod Toxicol. 2017 Aug;71:16-31. doi: 10.1016/j.reprotox.2017.04.003. Epub 2017 Apr 13.

Embryonic vascular disruption is an important adverse outcome pathway (AOP) as chemical disruption of cardiovascular development induces broad prenatal defects. High-throughput screening (HTS) assays aid AOP development although linking in vitro data to in vivo apical endpoints remains challenging....

Multivariable association discovery in population-scale meta-omics studies.

PLoS computational biology

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C.
PMID: 34784344
PLoS Comput Biol. 2021 Nov 16;17(11):e1009442. doi: 10.1371/journal.pcbi.1009442. eCollection 2021 Nov.

It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and...

Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men.

Genome medicine

Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT.
PMID: 34140026
Genome Med. 2021 Jun 17;13(1):102. doi: 10.1186/s13073-021-00921-y.

BACKGROUND: A higher intake of dietary fiber is associated with a decreased risk of chronic inflammatory diseases such as cardiovascular disease and inflammatory bowel disease. This may function in part due to abrogation of chronic systemic inflammation induced by...

A statistical model for describing and simulating microbial community profiles.

PLoS computational biology

Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, Tickle TL, Lu Y, Carmody RN, Franzosa EA, Janson L, Huttenhower C.
PMID: 34516542
PLoS Comput Biol. 2021 Sep 13;17(9):e1008913. doi: 10.1371/journal.pcbi.1008913. eCollection 2021 Sep.

Many methods have been developed for statistical analysis of microbial community profiles, but due to the complex nature of typical microbiome measurements (e.g. sparsity, zero-inflation, non-independence, and compositionality) and of the associated underlying biology, it is difficult to compare...

Observation of a New Excited D_{s}^{+} Meson in B^{0}→D^{-}D^{+}K^{+}π^{-} Decays.

Physical review letters

Aaij R, Abellán Beteta C, Ackernley T, Adeva B, Adinolfi M, Afsharnia H, Aidala CA, Aiola S, Ajaltouni Z, Akar S, Albrecht J, Alessio F, Alexander M, Alfonso Albero A, Aliouche Z, Alkhazov G, Alvarez Cartelle P, Amato S, Amhis Y, An L, Anderlini L, Andreianov A, Andreotti M, Archilli F, Artamonov A, Artuso M, Arzymatov K, Aslanides E, Atzeni M, Audurier B, Bachmann S, Bachmayer M, Back JJ, Baker S, Baladron Rodriguez P, Balagura V, Baldini W, Baptista Leite J, Barlow RJ, Barsuk S, Barter W, Bartolini M, Baryshnikov F, Basels JM, Bassi G, Batsukh B, Battig A, Bay A, Becker M, Bedeschi F, Bediaga I, Beiter A, Belavin V, Belin S, Bellee V, Belous K, Belov I, Belyaev I, Bencivenni G, Ben-Haim E, Berezhnoy A, Bernet R, Berninghoff D, Bernstein HC, Bertella C, Bertholet E, Bertolin A, Betancourt C, Betti F, Bettler MO, Bezshyiko I, Bhasin S, Bhom J, Bian L, Bieker MS, Bifani S, Billoir P, Birch M, Bishop FCR, Bizzeti A, Bjørn M, Blago MP, Blake T, Blanc F, Blusk S, Bobulska D, Boelhauve JA, Boente Garcia O, Boettcher T, Boldyrev A, Bondar A, Bondar N, Borghi S, Borisyak M, Borsato M, Borsuk JT, Bouchiba SA, Bowcock TJV, Boyer A, Bozzi C, Bradley MJ, Braun S, Brea Rodriguez A, Brodski M, Brodzicka J, Brossa Gonzalo A, Brundu D, Buonaura A, Burr C, Bursche A, Butkevich A, Butter JS, Buytaert J, Byczynski W, Cadeddu S, Cai H, Calabrese R, Calefice L, Calero Diaz L, Cali S, Calladine R, Calvi M, Calvo Gomez M, Camargo Magalhaes P, Camboni A, Campana P, Campora Perez DH, Campoverde Quezada AF, Capelli S, Capriotti L, Carbone A, Carboni G, Cardinale R, Cardini A, Carli I, Carniti P, Carus L, Carvalho Akiba K, Casais Vidal A, Casse G, Cattaneo M, Cavallero G, Celani S, Cerasoli J, Chadwick AJ, Chapman MG, Charles M, Charpentier P, Chatzikonstantinidis G, Chavez Barajas CA, Chefdeville M, Chen C, Chen S, Chernov A, Chitic SG, Chobanova V, Cholak S, Chrzaszcz M, Chubykin A, Chulikov V, Ciambrone P, Cicala MF, Cid Vidal X, Ciezarek G, Clarke PEL, Clemencic M, Cliff HV, Closier J, Cobbledick JL, Coco V, Coelho JAB, Cogan J, Cogneras E, Cojocariu L, Collins P, Colombo T, Congedo L, Contu A, Cooke N, Coombs G, Corti G, Costa Sobral CM, Couturier B, Craik DC, Crkovská J, Cruz Torres M, Currie R, Da Silva CL, Dall'Occo E, Dalseno J, D'Ambrosio C, Danilina A, d'Argent P, Davis A, De Aguiar Francisco O, De Bruyn K, De Capua S, De Cian M, De Miranda JM, De Paula L, De Serio M, De Simone D, De Simone P, de Vries JA, Dean CT, Dean W, Decamp D, Del Buono L, Delaney B, Dembinski HP, Dendek A, Denysenko V, Derkach D, Deschamps O, Desse F, Dettori F, Dey B, Di Nezza P, Didenko S, Dieste Maronas L, Dijkstra H, Dobishuk V, Donohoe AM, Dordei F, Dos Reis AC, Douglas L, Dovbnya A, Downes AG, Dreimanis K, Dudek MW, Dufour L, Duk V, Durante P, Durham JM, Dutta D, Dziewiecki M, Dziurda A, Dzyuba A, Easo S, Egede U, Egorychev V, Eidelman S, Eisenhardt S, Ek-In S, Eklund L, Ely S, Ene A, Epple E, Escher S, Eschle J, Esen S, Evans T, Falabella A, Fan J, Fan Y, Fang B, Farley N, Farry S, Fazzini D, Fedin P, Féo M, Fernandez Declara P, Fernandez Prieto A, Fernandez-Tenllado Arribas JM, Ferrari F, Ferreira Lopes L, Ferreira Rodrigues F, Ferreres Sole S, Ferrillo M, Ferro-Luzzi M, Filippov S, Fini RA, Fiorini M, Firlej M, Fischer KM, Fitzpatrick C, Fiutowski T, Fleuret F, Fontana M, Fontanelli F, Forty R, Franco Lima V, Franco Sevilla M, Frank M, Franzoso E, Frau G, Frei C, Friday DA, Fu J, Fuehring Q, Funk W, Gabriel E, Gaintseva T, Gallas Torreira A, Galli D, Gambetta S, Gan Y, Gandelman M, Gandini P, Gao Y, Garau M, Garcia Martin LM, Garcia Moreno P, García Pardiñas J, Garcia Plana B, Garcia Rosales FA, Garrido L, Gaspar C, Geertsema RE, Gerick D, Gerken LL, Gersabeck E, Gersabeck M, Gershon T, Gerstel D, Ghez P, Gibson V, Giovannetti M, Gioventù A, Gironella Gironell P, Giubega L, Giugliano C, Gizdov K, Gkougkousis EL, Gligorov VV, Göbel C, Golobardes E, Golubkov D, Golutvin A, Gomes A, Gomez Fernandez S, Goncalves Abrantes F, Goncerz M, Gong G, Gorbounov P, Gorelov IV, Gotti C, Govorkova E, Grabowski JP, Graciani Diaz R, Grammatico T, Granado Cardoso LA, Graugés E, Graverini E, Graziani G, Grecu A, Greeven LM, Griffith P, Grillo L, Gromov S, Gruberg Cazon BR, Gu C, Guarise M, Günther PA, Gushchin E, Guth A, Guz Y, Gys T, Hadavizadeh T, Haefeli G, Haen C, Haimberger J, Halewood-Leagas T, Hamilton PM, Han Q, Han X, Hancock TH, Hansmann-Menzemer S, Harnew N, Harrison T, Hasse C, Hatch M, He J, Hecker M, Heijhoff K, Heinicke K, Hennequin AM, Hennessy K, Henry L, Heuel J, Hicheur A, Hill D, Hilton M, Hollitt SE, Hu J, Hu J, Hu W, Huang W, Huang X, Hulsbergen W, Hunter RJ, Hushchyn M, Hutchcroft D, Hynds D, Ibis P, Idzik M, Ilin D, Ilten P, Inglessi A, Ishteev A, Ivshin K, Jacobsson R, Jakobsen S, Jans E, Jashal BK, Jawahery A, Jevtic V, Jezabek M, Jiang F, John M, Johnson D, Jones CR, Jones TP, Jost B, Jurik N, Kandybei S, Kang Y, Karacson M, Karpov M, Kazeev N, Keizer F, Kenzie M, Ketel T, Khanji B, Kharisova A, Kholodenko S, Kim KE, Kirn T, Kirsebom VS, Kitouni O, Klaver S, Klimaszewski K, Koliiev S, Kondybayeva A, Konoplyannikov A, Kopciewicz P, Kopecna R, Koppenburg P, Korolev M, Kostiuk I, Kot O, Kotriakhova S, Kravchenko P, Kravchuk L, Krawczyk RD, Kreps M, Kress F, Kretzschmar S, Krokovny P, Krupa W, Krzemien W, Kucewicz W, Kucharczyk M, Kudryavtsev V, Kuindersma HS, Kunde GJ, Kvaratskheliya T, Lacarrere D, Lafferty G, Lai A, Lampis A, Lancierini D, Lane JJ, Lane R, Lanfranchi G, Langenbruch C, Langer J, Lantwin O, Latham T, Lazzari F, Le Gac R, Lee SH, Lefèvre R, Leflat A, Legotin S, Leroy O, Lesiak T, Leverington B, Li H, Li L, Li P, Li X, Li Y, Li Y, Li Z, Liang X, Lin T, Lindner R, Lisovskyi V, Litvinov R, Liu G, Liu H, Liu S, Liu X, Loi A, Lomba Castro J, Longstaff I, Lopes JH, Loustau G, Lovell GH, Lu Y, Lucchesi D, Luchuk S, Lucio Martinez M, Lukashenko V, Luo Y, Lupato A, Luppi E, Lupton O, Lusiani A, Lyu X, Ma L, Maccolini S, Machefert F, Maciuc F, Macko V, Mackowiak P, Maddrell-Mander S, Madejczyk O, Madhan Mohan LR, Maev O, Maevskiy A, Maisuzenko D, Majewski MW, Malde S, Malecki B, Malinin A, Maltsev T, Malygina H, Manca G, Mancinelli G, Manera Escalero R, Manuzzi D, Marangotto D, Maratas J, Marchand JF, Marconi U, Mariani S, Marin Benito C, Marinangeli M, Marino P, Marks J, Marshall PJ, Martellotti G, Martinazzoli L, Martinelli M, Martinez Santos D, Martinez Vidal F, Massafferri A, Materok M, Matev R, Mathad A, Mathe Z, Matiunin V, Matteuzzi C, Mattioli KR, Mauri A, Maurice E, Mauricio J, Mazurek M, McCann M, Mcconnell L, Mcgrath TH, McNab A, McNulty R, Mead JV, Meadows B, Meaux C, Meier G, Meinert N, Melnychuk D, Meloni S, Merk M, Merli A, Meyer Garcia L, Mikhasenko M, Milanes DA, Millard E, Milovanovic M, Minard MN, Minzoni L, Mitchell SE, Mitreska B, Mitzel DS, Mödden A, Mohammed RA, Moise RD, Mombächer T, Monroy IA, Monteil S, Morandin M, Morello G, Morello MJ, Moron J, Morris AB, Morris AG, Mountain R, Mu H, Muheim F, Mukherjee M, Mulder M, Müller D, Müller K, Murphy CH, Murray D, Muzzetto P, Naik P, Nakada T, Nandakumar R, Nanut T, Nasteva I, Needham M, Neri I, Neri N, Neubert S, Neufeld N, Newcombe R, Nguyen TD, Nguyen-Mau C, Niel EM, Nieswand S, Nikitin N, Nolte NS, Nunez C, Oblakowska-Mucha A, Obraztsov V, O'Hanlon DP, Oldeman R, Olivares ME, Onderwater CJG, Ossowska A, Otalora Goicochea JM, Ovsiannikova T, Owen P, Oyanguren A, Pagare B, Pais PR, Pajero T, Palano A, Palutan M, Pan Y, Panshin G, Papanestis A, Pappagallo M, Pappalardo LL, Pappenheimer C, Parker W, Parkes C, Parkinson CJ, Passalacqua B, Passaleva G, Pastore A, Patel M, Patrignani C, Pawley CJ, Pearce A, Pellegrino A, Pepe Altarelli M, Perazzini S, Pereima D, Perret P, Petridis K, Petrolini A, Petrov A, Petrucci S, Petruzzo M, Pham TTH, Philippov A, Pica L, Piccini M, Pietrzyk B, Pietrzyk G, Pili M, Pinci D, Pisani F, Piucci A, P K R, Placinta V, Plews J, Plo Casasus M, Polci F, Poli Lener M, Poliakova M, Poluektov A, Polukhina N, Polyakov I, Polycarpo E, Pomery GJ, Ponce S, Popov D, Popov S, Poslavskii S, Prasanth K, Promberger L, Prouve C, Pugatch V, Pullen H, Punzi G, Qian W, Qin J, Quagliani R, Quintana B, Raab NV, Rabadan Trejo RI, Rachwal B, Rademacker JH, Rama M, Ramos Pernas M, Rangel MS, Ratnikov F, Raven G, Reboud M, Redi F, Reiss F, Remon Alepuz C, Ren Z, Renaudin V, Ribatti R, Ricciardi S, Richards DS, Rinnert K, Robbe P, Robert A, Robertson G, Rodrigues AB, Rodrigues E, Rodriguez Lopez JA, Rollings A, Roloff P, Romanovskiy V, Romero Lamas M, Romero Vidal A, Roth JD, Rotondo M, Rudolph MS, Ruf T, Ruiz Vidal J, Ryzhikov A, Ryzka J, Saborido Silva JJ, Sagidova N, Sahoo N, Saitta B, Sanchez Gonzalo D, Sanchez Gras C, Santacesaria R, Santamarina Rios C, Santimaria M, Santovetti E, Saranin D, Sarpis G, Sarpis M, Sarti A, Satriano C, Satta A, Saur M, Savrina D, Sazak H, Scantlebury Smead LG, Schael S, Schellenberg M, Schiller M, Schindler H, Schmelling M, Schmelzer T, Schmidt B, Schneider O, Schopper A, Schubiger M, Schulte S, Schune MH, Schwemmer R, Sciascia B, Sciubba A, Sellam S, Semennikov A, Senghi Soares M, Sergi A, Serra N, Sestini L, Seuthe A, Seyfert P, Shangase DM, Shapkin M, Shchemerov I, Shchutska L, Shears T, Shekhtman L, Shen Z, Shevchenko V, Shields EB, Shmanin E, Shupperd JD, Siddi BG, Silva Coutinho R, Simi G, Simone S, Skiba I, Skidmore N, Skwarnicki T, Slater MW, Smallwood JC, Smeaton JG, Smetkina A, Smith E, Smith M, Snoch A, Soares M, Soares Lavra L, Sokoloff MD, Soler FJP, Solovev A, Solovyev I, Souza De Almeida FL, Souza De Paula B, Spaan B, Spadaro Norella E, Spradlin P, Stagni F, Stahl M, Stahl S, Stefko P, Steinkamp O, Stemmle S, Stenyakin O, Stevens H, Stone S, Stramaglia ME, Straticiuc M, Strekalina D, Strokov S, Suljik F, Sun J, Sun L, Sun Y, Svihra P, Swallow PN, Swientek K, Szabelski A, Szumlak T, Szymanski M, Taneja S, Teubert F, Thomas E, Thomson KA, Tilley MJ, Tisserand V, T'Jampens S, Tobin M, Tolk S, Tomassetti L, Torres Machado D, Tou DY, Traill M, Tran MT, Trifonova E, Trippl C, Tuci G, Tully A, Tuning N, Ukleja A, Unverzagt DJ, Usachov A, Ustyuzhanin A, Uwer U, Vagner A, Vagnoni V, Valassi A, Valenti G, Valls Canudas N, van Beuzekom M, Van Dijk M, Van Hecke H, van Herwijnen E, Van Hulse CB, van Veghel M, Vazquez Gomez R, Vazquez Regueiro P, Vázquez Sierra C, Vecchi S, Velthuis JJ, Veltri M, Venkateswaran A, Veronesi M, Vesterinen M, Vieira D, Vieites Diaz M, Viemann H, Vilasis-Cardona X, Vilella Figueras E, Vincent P, Vitali G, Vollhardt A, Vom Bruch D, Vorobyev A, Vorobyev V, Voropaev N, Waldi R, Walsh J, Wang C, Wang J, Wang J, Wang J, Wang J, Wang M, Wang R, Wang Y, Wang Z, Wark HM, Watson NK, Weber SG, Websdale D, Weisser C, Westhenry BDC, White DJ, Whitehead M, Wiedner D, Wilkinson G, Wilkinson M, Williams I, Williams M, Williams MRJ, Wilson FF, Wislicki W, Witek M, Witola L, Wormser G, Wotton SA, Wu H, Wyllie K, Xiang Z, Xiao D, Xie Y, Xu A, Xu J, Xu L, Xu M, Xu Q, Xu Z, Xu Z, Yang D, Yang Y, Yang Z, Yang Z, Yao Y, Yeomans LE, Yin H, Yu J, Yuan X, Yushchenko O, Zaffaroni E, Zarebski KA, Zavertyaev M, Zdybal M, Zenaiev O, Zeng M, Zhang D, Zhang L, Zhang S, Zhang Y, Zhang Y, Zhelezov A, Zheng Y, Zhou X, Zhou Y, Zhu X, Zhukov V, Zonneveld JB, Zucchelli S, Zuliani D, Zunica G.
PMID: 33834812
Phys Rev Lett. 2021 Mar 26;126(12):122002. doi: 10.1103/PhysRevLett.126.122002.

Using pp collision data corresponding to an integrated luminosity of 5.4  fb^{-1} collected with the LHCb detector at a center-of-mass energy of 13 TeV, the B^{0}→D^{-}D^{+}K^{+}π^{-} decay is studied. A new excited D_{s}^{+} meson is observed decaying into the...

Multivariable association discovery in population-scale meta-omics studies.

PLoS computational biology

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C.
PMID: 34784344
PLoS Comput Biol. 2021 Nov 16;17(11):e1009442. doi: 10.1371/journal.pcbi.1009442. eCollection 2021 Nov.

It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and...

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice.

mSystems

Yasuda K, Hsu T, Gallini CA, Mclver LJ, Schwager E, Shi A, DuLong CR, Schwager RN, Abu-Ali GS, Franzosa EA, Garrett WS, Huttenhower C, Morgan XC.
PMID: 28808691
mSystems. 2017 Aug 08;2(4). doi: 10.1128/mSystems.00047-17. eCollection 2017.

Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Cell

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.
PMID: 27984736
Cell. 2016 Dec 15;167(7):1897. doi: 10.1016/j.cell.2016.11.046.

No abstract available.

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project.

Nature

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.
PMID: 29022944
Nature. 2017 Nov 09;551(7679):256. doi: 10.1038/nature24485. Epub 2017 Oct 12.

This corrects the article DOI: 10.1038/nature23889.

Showing 1 to 12 of 37 entries