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Items: 1 to 50 of 165

1.

Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation.

Zhang Z, Zhou C, Li X, Barnes SD, Deng S, Hoover E, Chen CC, Lee YS, Zhang Y, Wang C, Metang LA, Wu C, Tirado CR, Johnson NA, Wongvipat J, Navrazhina K, Cao Z, Choi D, Huang CH, Linton E, Chen X, Liang Y, Mason CE, de Stanchina E, Abida W, Lujambio A, Li S, Lowe SW, Mendell JT, Malladi VS, Sawyers CL, Mu P.

Cancer Cell. 2020 Mar 13. pii: S1535-6108(20)30101-X. doi: 10.1016/j.ccell.2020.03.001. [Epub ahead of print]

PMID:
32220301
2.

Plant Preferences of Z-Pheromone Race Ostrinia nubilalis (Lepidoptera: Crambidae) Based on Leaf Tissue Consumption Rates.

Fisher KE, Flexner JL, Mason CE.

J Econ Entomol. 2020 Mar 24. pii: toaa047. doi: 10.1093/jee/toaa047. [Epub ahead of print]

PMID:
32207824
3.

Single-cell sperm transcriptomes and variants from fathers of children with and without autism spectrum disorder.

Tomoiaga D, Aguiar-Pulido V, Shrestha S, Feinstein P, Levy SE, Mason CE, Rosenfeld JA.

NPJ Genom Med. 2020 Feb 21;5:14. doi: 10.1038/s41525-020-0117-4. eCollection 2020.

4.

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.

5.

A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.

Mische SM, Fisher NC, Meyn SM, Church KS, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL.

J Biomol Tech. 2020 Jan 13. pii: jbt.20-3101-003. doi: 10.7171/jbt.20-3101-003. [Epub ahead of print]

6.

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
7.

Translating current biomedical therapies for long duration, deep space missions.

Iosim S, MacKay M, Westover C, Mason CE.

Precis Clin Med. 2019 Dec;2(4):259-269. doi: 10.1093/pcmedi/pbz022. Epub 2019 Nov 15. Review.

8.

Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection.

Gokhale NS, McIntyre ABR, Mattocks MD, Holley CL, Lazear HM, Mason CE, Horner SM.

Mol Cell. 2020 Feb 6;77(3):542-555.e8. doi: 10.1016/j.molcel.2019.11.007. Epub 2019 Dec 3.

PMID:
31810760
9.

A comprehensive, multidisciplinary, precision medicine approach to discover effective therapy for an undiagnosed, progressive, fibroinflammatory disease.

Gochuico BR, Ziegler SG, Ten NS, Balanda NJ, Mason CE, Zumbo P, Evans CA, Van Waes C, Gahl WA, Malicdan MCV.

Transl Res. 2020 Jan;215:31-40. doi: 10.1016/j.trsl.2019.08.008. Epub 2019 Aug 28.

PMID:
31520587
10.

Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells.

Tan L, Lacko LA, Zhou T, Tomoiaga D, Hurtado R, Zhang T, Sevilla A, Zhong A, Mason CE, Noggle S, Evans T, Stuhlmann H, Schwartz RE, Chen S.

Nat Commun. 2019 Sep 13;10(1):4155. doi: 10.1038/s41467-019-12063-2.

11.

Accurate detection of m6A RNA modifications in native RNA sequences.

Liu H, Begik O, Lucas MC, Ramirez JM, Mason CE, Wiener D, Schwartz S, Mattick JS, Smith MA, Novoa EM.

Nat Commun. 2019 Sep 9;10(1):4079. doi: 10.1038/s41467-019-11713-9.

12.

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm.

Ji X, Tong W, Ning B, Mason CE, Kreil DP, Labaj PP, Chen G, Shi T.

Sci China Life Sci. 2019 Jul;62(7):937-946. doi: 10.1007/s11427-018-9433-3. Epub 2019 May 22.

PMID:
31124003
13.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
14.

Ratio-Based Method To Identify True Biomarkers by Normalizing Circulating ncRNA Sequencing and Quantitative PCR Data.

Deng Y, Zhu Y, Wang H, Khadka VS, Hu L, Ai J, Dou Y, Li Y, Dai S, Mason CE, Wang Y, Jia W, Zhang J, Huang G, Jiang B.

Anal Chem. 2019 May 21;91(10):6746-6753. doi: 10.1021/acs.analchem.9b00821. Epub 2019 Apr 30.

15.

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
16.

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.

17.

Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 May;37(5):567. doi: 10.1038/s41587-019-0108-0.

PMID:
30899106
18.

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.

19.

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.

20.

Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 May;37(5):555-560. doi: 10.1038/s41587-019-0054-x. Epub 2019 Mar 11. Erratum in: Nat Biotechnol. 2019 Mar 21;:.

21.

Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response.

Agirre X, Meydan C, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O, Mason CE, Prosper F, Melnick A.

Nat Commun. 2019 Feb 18;10(1):821. doi: 10.1038/s41467-019-08679-z.

22.

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.

McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE.

Nat Commun. 2019 Feb 4;10(1):579. doi: 10.1038/s41467-019-08289-9.

23.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

PMID:
30679363
24.

Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains.

Singh NK, Bezdan D, Checinska Sielaff A, Wheeler K, Mason CE, Venkateswaran K.

BMC Microbiol. 2018 Nov 23;18(1):175. doi: 10.1186/s12866-018-1325-2.

25.

N6-methyladenosine modification of hepatitis B virus RNA differentially regulates the viral life cycle.

Imam H, Khan M, Gokhale NS, McIntyre ABR, Kim GW, Jang JY, Kim SJ, Mason CE, Horner SM, Siddiqui A.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):8829-8834. doi: 10.1073/pnas.1808319115. Epub 2018 Aug 13.

26.

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.

27.

Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis.

Kleppe M, Spitzer MH, Li S, Hill CE, Dong L, Papalexi E, De Groote S, Bowman RL, Keller M, Koppikar P, Rapaport FT, Teruya-Feldstein J, Gandara J, Mason CE, Nolan GP, Levine RL.

Cell Stem Cell. 2018 Feb 1;22(2):277. doi: 10.1016/j.stem.2017.12.018. No abstract available.

28.

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2.

Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S.

Elife. 2018 Jan 23;7. pii: e30919. doi: 10.7554/eLife.30919.

29.

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host.

Palesch D, Bosinger SE, Tharp GK, Vanderford TH, Paiardini M, Chahroudi A, Johnson ZP, Kirchhoff F, Hahn BH, Norgren RB, Patel NB, Sodora DL, Dawoud RA, Stewart CB, Seepo SM, Harris RA, Liu Y, Raveendran M, Han Y, English A, Thomas GWC, Hahn MW, Pipes L, Mason CE, Muzny DM, Gibbs RA, Sauter D, Worley K, Rogers J, Silvestri G.

Nature. 2018 Jan 3;553(7686):77-81. doi: 10.1038/nature25140.

30.

Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

Castro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins KH, McIntyre ABR, Dworkin JP, Lupisella ML, Smith DJ, Botkin DJ, Stephenson TA, Juul S, Turner DJ, Izquierdo F, Federman S, Stryke D, Somasekar S, Alexander N, Yu G, Mason CE, Burton AS.

Sci Rep. 2017 Dec 21;7(1):18022. doi: 10.1038/s41598-017-18364-0.

31.

Cry1 Bt Susceptibilities of Fall Armyworm (Lepidoptera: Noctuidae) Host Strains.

Ingber DA, Mason CE, Flexner L.

J Econ Entomol. 2018 Feb 9;111(1):361-368. doi: 10.1093/jee/tox311.

PMID:
29240921
32.

The international MAQC Society launches to enhance reproducibility of high-throughput technologies.

Shi L, Kusko R, Wolfinger RD, Haibe-Kains B, Fischer M, Sansone SA, Mason CE, Furlanello C, Jones WD, Ning B, Tong W.

Nat Biotechnol. 2017 Dec 8;35(12):1127-1128. doi: 10.1038/nbt.4029. No abstract available.

PMID:
29220036
33.

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research.

Shamarina D, Stoyantcheva I, Mason CE, Bibby K, Elhaik E.

Microbiome. 2017 Oct 4;5(1):132. doi: 10.1186/s40168-017-0349-4.

34.

Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis.

Kleppe M, Spitzer MH, Li S, Hill CE, Dong L, Papalexi E, De Groote S, Bowman RL, Keller M, Koppikar P, Rapaport FT, Teruya-Feldstein J, Gandara J, Mason CE, Nolan GP, Levine RL.

Cell Stem Cell. 2017 Oct 5;21(4):489-501.e7. doi: 10.1016/j.stem.2017.08.011. Epub 2017 Sep 28. Erratum in: Cell Stem Cell. 2018 Feb 1;22(2):277.

35.

Erratum: PGBD5 promotes site-specific oncogenic mutations in human tumors.

Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A.

Nat Genet. 2017 Sep 27;49(10):1558. doi: 10.1038/ng1017-1558b. No abstract available.

PMID:
28951624
36.

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.

37.

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.

38.

The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells.

Vu LP, Pickering BF, Cheng Y, Zaccara S, Nguyen D, Minuesa G, Chou T, Chow A, Saletore Y, MacKay M, Schulman J, Famulare C, Patel M, Klimek VM, Garrett-Bakelman FE, Melnick A, Carroll M, Mason CE, Jaffrey SR, Kharas MG.

Nat Med. 2017 Nov;23(11):1369-1376. doi: 10.1038/nm.4416. Epub 2017 Sep 18.

39.

rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline.

Jain D, Meydan C, Lange J, Claeys Bouuaert C, Lailler N, Mason CE, Anderson KV, Keeney S.

PLoS Genet. 2017 Aug 30;13(8):e1006964. doi: 10.1371/journal.pgen.1006964. eCollection 2017 Aug.

40.

Chromosome End Repair and Genome Stability in Plasmodium falciparum.

Calhoun SF, Reed J, Alexander N, Mason CE, Deitsch KW, Kirkman LA.

mBio. 2017 Aug 8;8(4). pii: e00547-17. doi: 10.1128/mBio.00547-17.

41.

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.

42.

Nanopore sequencing in microgravity.

McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE.

NPJ Microgravity. 2016 Oct 20;2:16035. doi: 10.1038/npjmgrav.2016.35. eCollection 2016.

43.

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.

44.

PGBD5 promotes site-specific oncogenic mutations in human tumors.

Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A.

Nat Genet. 2017 Jul;49(7):1005-1014. doi: 10.1038/ng.3866. Epub 2017 May 15. Erratum in: Nat Genet. 2017 Sep 27;49(10 ):1558.

45.

Charting the unknown epitranscriptome.

Novoa EM, Mason CE, Mattick JS.

Nat Rev Mol Cell Biol. 2017 Jun;18(6):339-340. doi: 10.1038/nrm.2017.49. Epub 2017 May 10.

PMID:
28488699
46.

Daily Rhythm in Plasma N-acetyltryptamine.

Backlund PS, Urbanski HF, Doll MA, Hein DW, Bozinoski M, Mason CE, Coon SL, Klein DC.

J Biol Rhythms. 2017 Jun;32(3):195-211. doi: 10.1177/0748730417700458. Epub 2017 May 3.

47.

Focus on Metagenomics.

Mason CE, Tighe S.

J Biomol Tech. 2017 Apr;28(1):1. doi: 10.7171/jbt.17-2801-010. Epub 2017 Mar 29. No abstract available.

48.

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.

49.

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.

50.

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.

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