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Items: 23

1.

Co-occurrence patterns of bacteria within microbiome of Moscow subway.

Klimenko NS, Tyakht AV, Toshchakov SV, Shevchenko MA, Korzhenkov AA, Afshinnekoo E, Mason CE, Alexeev DG.

Comput Struct Biotechnol J. 2020 Feb 1;18:314-322. doi: 10.1016/j.csbj.2020.01.007. eCollection 2020.

2.

The therapeutic landscape for cells engineered with chimeric antigen receptors.

MacKay M, Afshinnekoo E, Rub J, Hassan C, Khunte M, Baskaran N, Owens B, Liu L, Roboz GJ, Guzman ML, Melnick AM, Wu S, Mason CE.

Nat Biotechnol. 2020 Feb;38(2):233-244. doi: 10.1038/s41587-019-0329-2. Epub 2020 Jan 6.

PMID:
31907405
3.

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.

Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW.

Science. 2019 Apr 12;364(6436). pii: eaau8650. doi: 10.1126/science.aau8650.

PMID:
30975860
4.

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE.

Genome Biol. 2019 Apr 5;20(1):72. doi: 10.1186/s13059-019-1687-2.

5.

Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity.

Goldman SL, Hassan C, Khunte M, Soldatenko A, Jong Y, Afshinnekoo E, Mason CE.

Front Genet. 2019 Mar 1;10:133. doi: 10.3389/fgene.2019.00133. eCollection 2019. Review.

6.

The Impact of Heterogeneity on Single-Cell Sequencing.

Goldman SL, MacKay M, Afshinnekoo E, Melnick AM, Wu S, Mason CE.

Front Genet. 2019 Mar 1;10:8. doi: 10.3389/fgene.2019.00008. eCollection 2019.

7.

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters.

Fresia P, Antelo V, Salazar C, Giménez M, D'Alessandro B, Afshinnekoo E, Mason C, Gonnet GH, Iraola G.

Microbiome. 2019 Feb 28;7(1):35. doi: 10.1186/s40168-019-0648-z.

8.

The Undergraduate Training in Genomics (UTRIG) Initiative: early & active training for physicians in the genomic medicine era.

Wilcox RL, Adem PV, Afshinnekoo E, Atkinson JB, Burke LW, Cheung H, Dasgupta S, DeLaGarza J, Joseph L, LeGallo R, Lew M, Lockwood CM, Meiss A, Norman J, Markwood P, Rizvi H, Shane-Carson KP, Sobel ME, Suarez E, Tafe LJ, Wang J, Haspel RL.

Per Med. 2018 May 1;15(3):199-208. doi: 10.2217/pme-2017-0077. Epub 2018 May 30.

9.

The Microbe Directory: An annotated, searchable inventory of microbes' characteristics.

Shaaban H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE.

Gates Open Res. 2018 Jan 5;2:3. doi: 10.12688/gatesopenres.12772.1.

10.

Metagenomic characterization of ambulances across the USA.

O'Hara NB, Reed HJ, Afshinnekoo E, Harvin D, Caplan N, Rosen G, Frye B, Woloszynek S, Ounit R, Levy S, Butler E, Mason CE.

Microbiome. 2017 Sep 22;5(1):125. doi: 10.1186/s40168-017-0339-6.

11.

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE.

Genome Biol. 2017 Sep 21;18(1):182. doi: 10.1186/s13059-017-1299-7. Erratum in: Genome Biol. 2019 Apr 5;20(1):72.

12.

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing.

Tessler M, Neumann JS, Afshinnekoo E, Pineda M, Hersch R, Velho LFM, Segovia BT, Lansac-Toha FA, Lemke M, DeSalle R, Mason CE, Brugler MR.

Sci Rep. 2017 Jul 31;7(1):6589. doi: 10.1038/s41598-017-06665-3.

13.

Genetic and epigenetic heterogeneity and the impact on cancer relapse.

Hassan C, Afshinnekoo E, Li S, Wu S, Mason CE.

Exp Hematol. 2017 Oct;54:26-30. doi: 10.1016/j.exphem.2017.07.002. Epub 2017 Jul 10. Review.

14.

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications.

Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE.

J Biomol Tech. 2017 Apr;28(1):46-55. doi: 10.7171/jbt.17-2801-008. Epub 2017 Mar 21. Erratum in: J Biomol Tech. 2017 Jul;28(2):96.

15.

Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance.

Afshinnekoo E, Chou C, Alexander N, Ahsanuddin S, Schuetz AN, Mason CE.

J Biomol Tech. 2017 Apr;28(1):40-45. doi: 10.7171/jbt.17-2801-007. Epub 2017 Mar 21. Erratum in: J Biomol Tech. 2017 Jul;28(2):95.

16.

International Standards for Genomes, Transcriptomes, and Metagenomes.

Mason CE, Afshinnekoo E, Tighe S, Wu S, Levy S.

J Biomol Tech. 2017 Apr;28(1):8-18. doi: 10.7171/jbt.17-2801-006. Epub 2017 Mar 17. Review. Erratum in: J Biomol Tech. 2017 Jul;28(2):94.

17.

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE.

J Biomol Tech. 2017 Apr;28(1):31-39. doi: 10.7171/jbt.17-2801-004. Epub 2017 Mar 10. Erratum in: J Biomol Tech. 2017 Jul;28(2):93.

18.

Epigenetic therapy in a new era of medicine: creating and integrating molecular profiles of patients.

Afshinnekoo E, Mason CE.

Ann Transl Med. 2016 Nov;4(21):436. No abstract available.

19.

Globalizing and crowdsourcing biomedical research.

Afshinnekoo E, Ahsanuddin S, Mason CE.

Br Med Bull. 2016 Dec;120(1):27-33. Epub 2016 Nov 23. Review.

PMID:
27941038
20.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):97-97.e3. doi: 10.1016/j.cels.2015.07.006. Epub 2015 Jul 29. No abstract available.

21.

Modern Methods for Delineating Metagenomic Complexity.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):6-7. doi: 10.1016/j.cels.2015.07.007. Epub 2015 Jul 29. No abstract available.

22.

Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE.

Nat Commun. 2016 Feb 2;7:10164. doi: 10.1038/ncomms10164.

23.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):72-87. Epub 2015 Mar 3.

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