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Items: 12

1.

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.

Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C.

Nat Commun. 2019 Jul 17;10(1):3136. doi: 10.1038/s41467-019-10927-1.

2.

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.

Nat Microbiol. 2019 May;4(5):898. doi: 10.1038/s41564-019-0442-5.

PMID:
30971771
3.

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.

Nat Microbiol. 2019 Feb;4(2):293-305. doi: 10.1038/s41564-018-0306-4. Epub 2018 Dec 10. Erratum in: Nat Microbiol. 2019 May;4(5):898.

4.

A role for bacterial urease in gut dysbiosis and Crohn's disease.

Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD.

Sci Transl Med. 2017 Nov 15;9(416). pii: eaah6888. doi: 10.1126/scitranslmed.aah6888.

5.

Not so simple, not so subtle: the interspecies competition between Bacillus simplex and Bacillus subtilis and its impact on the evolution of biofilms.

Rosenberg G, Steinberg N, Oppenheimer-Shaanan Y, Olender T, Doron S, Ben-Ari J, Sirota-Madi A, Bloom-Ackermann Z, Kolodkin-Gal I.

NPJ Biofilms Microbiomes. 2016 Jan 27;2:15027. doi: 10.1038/npjbiofilms.2015.27. eCollection 2016.

6.

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.

Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier R, Elinav E, Segal E.

Science. 2015 Sep 4;349(6252):1101-1106. doi: 10.1126/science.aac4812. Epub 2015 Jul 30.

7.

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C.

Nat Rev Microbiol. 2015 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27. Review.

8.

Identification and characterization of a highly motile and antibiotic refractory subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex.

Roth D, Finkelshtein A, Ingham C, Helman Y, Sirota-Madi A, Brodsky L, Ben-Jacob E.

Environ Microbiol. 2013 Sep;15(9):2532-44. doi: 10.1111/1462-2920.12160. Epub 2013 Jun 14.

9.

Genome sequence of the pattern-forming social bacterium Paenibacillus dendritiformis C454 chiral morphotype.

Sirota-Madi A, Olender T, Helman Y, Brainis I, Finkelshtein A, Roth D, Hagai E, Leshkowitz D, Brodsky L, Galatenko V, Nikolaev V, Gutnick DL, Lancet D, Ben-Jacob E.

J Bacteriol. 2012 Apr;194(8):2127-8. doi: 10.1128/JB.00158-12.

10.

Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.

Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L, Leshkowitz D, Galatenko V, Nikolaev V, Mugasimangalam RC, Bransburg-Zabary S, Gutnick DL, Lancet D, Ben-Jacob E.

BMC Genomics. 2010 Dec 17;11:710. doi: 10.1186/1471-2164-11-710.

11.

GeneCards Version 3: the human gene integrator.

Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A, Lancet D.

Database (Oxford). 2010 Aug 5;2010:baq020. doi: 10.1093/database/baq020.

12.

Lethal protein produced in response to competition between sibling bacterial colonies.

Be'er A, Ariel G, Kalisman O, Helman Y, Sirota-Madi A, Zhang HP, Florin EL, Payne SM, Ben-Jacob E, Swinney HL.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6258-63. doi: 10.1073/pnas.1001062107. Epub 2010 Mar 22.

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