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Items: 1 to 50 of 91

1.

Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer.

Han CM, Catoe D, Munro SA, Khnouf R, Snyder MP, Santiago JG, Salit ML, Cenik C.

Lab Chip. 2019 Aug 21;19(16):2741-2749. doi: 10.1039/c9lc00311h. Epub 2019 Jul 22.

PMID:
31328753
2.

Assessment of thyroid functions and thyroid volume in normal pregnant Egyptian females.

Elebrashy I, Kamal Eldein HA, Abd-Elstar H, Ghanem N, Mousa S, Assem M, Rashed L, Salit M, Abd-Elraoof M, Dorgham A, Mansour A, Mahmoud M, Saif A.

Gynecol Endocrinol. 2019 Jun 22:1-4. doi: 10.1080/09513590.2019.1631279. [Epub ahead of print]

PMID:
31230489
3.

High-coverage, long-read sequencing of Han Chinese trio reference samples.

Wang YC, Olson ND, Deikus G, Shah H, Wenger AM, Trow J, Xiao C, Sherry S, Salit ML, Zook JM, Smith M, Sebra R.

Sci Data. 2019 Jun 14;6(1):91. doi: 10.1038/s41597-019-0098-2.

4.

An open resource for accurately benchmarking small variant and reference calls.

Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY, De La Vega FM, Xiao C, Sherry S, Salit M.

Nat Biotechnol. 2019 May;37(5):561-566. doi: 10.1038/s41587-019-0074-6. Epub 2019 Apr 1.

PMID:
30936564
5.

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
6.

CrowdVariant: a crowdsourcing approach to classify copy number variants.

Greenside P, Zook J, Salit M, Cule M, Poplin R, DePristo M.

Pac Symp Biocomput. 2019;24:224-235.

7.

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;:.

PMID:
30858580
8.

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing.

Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS.

J Mol Diagn. 2019 Mar;21(2):318-329. doi: 10.1016/j.jmoldx.2018.10.009. Epub 2019 Jan 3.

9.

A minimum information standard for reproducing bench-scale bacterial cell growth and productivity.

Hecht A, Filliben J, Munro SA, Salit M.

Commun Biol. 2018 Dec 6;1:219. doi: 10.1038/s42003-018-0220-6. eCollection 2018.

10.

Unbiased Fitness Estimation of Pooled Barcode or Amplicon Sequencing Studies.

Li F, Salit ML, Levy SF.

Cell Syst. 2018 Nov 28;7(5):521-525.e4. doi: 10.1016/j.cels.2018.09.004. Epub 2018 Nov 1.

PMID:
30391162
11.

Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials.

Cleveland MH, Zook JM, Salit M, Vallone PM.

J Mol Diagn. 2018 Sep;20(5):583-590. doi: 10.1016/j.jmoldx.2018.04.005. Epub 2018 Jun 26.

12.

Multiplexed precision genome editing with trackable genomic barcodes in yeast.

Roy KR, Smith JD, Vonesch SC, Lin G, Tu CS, Lederer AR, Chu A, Suresh S, Nguyen M, Horecka J, Tripathi A, Burnett WT, Morgan MA, Schulz J, Orsley KM, Wei W, Aiyar RS, Davis RW, Bankaitis VA, Haber JE, Salit ML, St Onge RP, Steinmetz LM.

Nat Biotechnol. 2018 Jul;36(6):512-520. doi: 10.1038/nbt.4137. Epub 2018 May 7.

13.

Cell-based reference samples designed with specific differences in microRNA biomarkers.

Pine PS, Lund SP, Stass SA, Kukuruga D, Jiang F, Sorbara L, Srivastava S, Salit M.

BMC Biotechnol. 2018 Mar 20;18(1):17. doi: 10.1186/s12896-018-0423-4.

14.

Summarizing performance for genome scale measurement of miRNA: reference samples and metrics.

Pine PS, Lund SP, Parsons JR, Vang LK, Mahabal AA, Cinquini L, Kelly SC, Kincaid H, Crichton DJ, Spira A, Liu G, Gower AC, Pass HI, Goparaju C, Dubinett SM, Krysan K, Stass SA, Kukuruga D, Van Keuren-Jensen K, Courtright-Lim A, Thompson KL, Rosenzweig BA, Sorbara L, Srivastava S, Salit ML.

BMC Genomics. 2018 Mar 6;19(1):180. doi: 10.1186/s12864-018-4496-1.

15.

Genome-wide reconstruction of complex structural variants using read clouds.

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.

Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17.

16.

Measurements of translation initiation from all 64 codons in E. coli.

Hecht A, Glasgow J, Jaschke PR, Bawazer LA, Munson MS, Cochran JR, Endy D, Salit M.

Nucleic Acids Res. 2017 Apr 20;45(7):3615-3626. doi: 10.1093/nar/gkx070.

17.

Toward achieving harmonization in a nano-cytotoxicity assay measurement through an interlaboratory comparison study.

Elliott JT, Rösslein M, Song NW, Toman B, Kinsner-Ovaskainen A, Maniratanachote R, Salit ML, Petersen EJ, Sequeira F, Romsos EL, Kim SJ, Lee J, von Moos NR, Rossi F, Hirsch C, Krug HF, Suchaoin W, Wick P.

ALTEX. 2017;34(2):201-218. doi: 10.14573/altex.1605021. Epub 2016 Sep 29.

18.

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships.

Kalman LV, Datta V, Williams M, Zook JM, Salit ML, Han JY.

Ann Lab Med. 2016 Nov;36(6):513-20. doi: 10.3343/alm.2016.36.6.513. Review.

19.

External RNA Controls Consortium Beta Version Update.

Lee H, Pine PS, McDaniel J, Salit M, Oliver B.

J Genomics. 2016 Jul 26;4:19-22. doi: 10.7150/jgen.16082. eCollection 2016.

20.

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

Pine PS, Munro SA, Parsons JR, McDaniel J, Lucas AB, Lozach J, Myers TG, Su Q, Jacobs-Helber SM, Salit M.

BMC Biotechnol. 2016 Jun 24;16(1):54. doi: 10.1186/s12896-016-0281-x.

21.

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1.

Devonshire AS, Sanders R, Whale AS, Nixon GJ, Cowen S, Ellison SL, Parkes H, Pine PS, Salit M, McDaniel J, Munro S, Lund S, Matsukura S, Sekiguchi Y, Kawaharasaki M, Granjeiro JM, Falagan-Lotsch P, Saraiva AM, Couto P, Yang I, Kwon H, Park SR, Demšar T, Žel J, Blejec A, Milavec M, Dong L, Zhang L, Sui Z, Wang J, Viroonudomphol D, Prawettongsopon C, Partis L, Baoutina A, Emslie K, Takatsu A, Akyurek S, Akgoz M, Vonsky M, Konopelko LA, Cundapi EM, Urquiza MP, Huggett JF, Foy CA.

Biomol Detect Quantif. 2016 Jun 6;8:15-28. doi: 10.1016/j.bdq.2016.05.003. eCollection 2016 Jun.

22.

In Vivo Site-Specific Protein Tagging with Diverse Amines Using an Engineered Sortase Variant.

Glasgow JE, Salit ML, Cochran JR.

J Am Chem Soc. 2016 Jun 22;138(24):7496-9. doi: 10.1021/jacs.6b03836. Epub 2016 Jun 9.

PMID:
27280683
23.

Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.

24.

When Wavelengths Collide: Bias in Cell Abundance Measurements Due to Expressed Fluorescent Proteins.

Hecht A, Endy D, Salit M, Munson MS.

ACS Synth Biol. 2016 Sep 16;5(9):1024-7. doi: 10.1021/acssynbio.6b00072. Epub 2016 Jun 6.

25.

Advancing Benchmarks for Genome Sequencing.

Zook JM, Salit M.

Cell Syst. 2015 Sep 23;1(3):176-7. doi: 10.1016/j.cels.2015.09.004. Epub 2015 Sep 23.

26.

A research roadmap for next-generation sequencing informatics.

Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante CD, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T.

Sci Transl Med. 2016 Apr 20;8(335):335ps10. doi: 10.1126/scitranslmed.aaf7314. Review.

27.

Evaluation of microbial qPCR workflows using engineered Saccharomyces cerevisiae.

Da Silva SM, Vang LK, Olson ND, Lund SP, Downey AS, Kelman Z, Salit ML, Lin NJ, Morrow JB.

Biomol Detect Quantif. 2016 Feb 19;7:27-33. doi: 10.1016/j.bdq.2016.01.001. eCollection 2016 Mar.

28.

PEPR: pipelines for evaluating prokaryotic references.

Olson ND, Zook JM, Samarov DV, Jackson SA, Salit ML.

Anal Bioanal Chem. 2016 Apr;408(11):2975-83. doi: 10.1007/s00216-015-9299-5. Epub 2016 Mar 2.

29.

Medical implications of technical accuracy in genome sequencing.

Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT, Salit M, Ashley EA.

Genome Med. 2016 Mar 2;8(1):24. doi: 10.1186/s13073-016-0269-0.

30.

svclassify: a method to establish benchmark structural variant calls.

Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M.

BMC Genomics. 2016 Jan 16;17:64. doi: 10.1186/s12864-016-2366-2.

31.

Unmet needs: Research helps regulators do their jobs.

Altman RB, Khuri N, Salit M, Giacomini KM.

Sci Transl Med. 2015 Nov 25;7(315):315ps22. doi: 10.1126/scitranslmed.aac4369. Review.

PMID:
26606966
32.

Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing.

Mack SJ, Milius RP, Gifford BD, Sauter J, Hofmann J, Osoegawa K, Robinson J, Groeneweg M, Turenchalk GS, Adai A, Holcomb C, Rozemuller EH, Penning MT, Heuer ML, Wang C, Salit ML, Schmidt AH, Parham PR, Müller C, Hague T, Fischer G, Fernandez-Viňa M, Hollenbach JA, Norman PJ, Maiers M.

Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25.

33.

Using mixtures of biological samples as process controls for RNA-sequencing experiments.

Parsons J, Munro S, Pine PS, McDaniel J, Mehaffey M, Salit M.

BMC Genomics. 2015 Sep 17;16:708. doi: 10.1186/s12864-015-1912-7.

34.

svviz: a read viewer for validating structural variants.

Spies N, Zook JM, Salit M, Sidow A.

Bioinformatics. 2015 Dec 15;31(24):3994-6. doi: 10.1093/bioinformatics/btv478. Epub 2015 Aug 18.

PMID:
26286809
35.

Achieving high-sensitivity for clinical applications using augmented exome sequencing.

Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R.

Genome Med. 2015 Jul 16;7:71. doi: 10.1186/s13073-015-0197-4. eCollection 2015.

36.

Best practices for evaluating single nucleotide variant calling methods for microbial genomics.

Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW, Schupp JM, Keim P, Morrow JB, Salit ML, Zook JM.

Front Genet. 2015 Jul 7;6:235. doi: 10.3389/fgene.2015.00235. eCollection 2015. Review.

37.

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM.

Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. No abstract available.

38.

Applicability and efficacy of a model for prevention of perinatal transmission of hepatitis B virus infection: single center study in Egypt.

El-Karaksy HM, Mohsen LM, Saleh DA, Hamdy MS, Yassin NA, Farouk M, Salit ME, El-Shabrawi MH.

World J Gastroenterol. 2014 Dec 7;20(45):17075-83. doi: 10.3748/wjg.v20.i45.17075.

39.

Use of Cause-and-Effect Analysis to Design a High-Quality Nanocytotoxicology Assay.

Rösslein M, Elliott JT, Salit M, Petersen EJ, Hirsch C, Krug HF, Wick P.

Chem Res Toxicol. 2015 Jan 20;28(1):21-30. doi: 10.1021/tx500327y. Epub 2015 Jan 6.

PMID:
25473822
40.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M.

Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125.

PMID:
25254650
41.

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films.

Baker BA, Pine PS, Chatterjee K, Kumar G, Lin NJ, McDaniel JH, Salit ML, Simon CG Jr.

Biomaterials. 2014 Aug;35(25):6716-26. doi: 10.1016/j.biomaterials.2014.04.075. Epub 2014 May 17.

PMID:
24840613
42.

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M.

Nat Biotechnol. 2014 Mar;32(3):246-51. doi: 10.1038/nbt.2835. Epub 2014 Feb 16.

PMID:
24531798
43.

Evaluation of motorcyclist's discomfort during prolonged riding process with and without lumbar support.

Karuppiah K, Salit MS, Ismail MY, Ismail N, Tamrin SB.

An Acad Bras Cienc. 2012 Dec;84(4):1169-88.

44.

Characterization of in vitro transcription amplification linearity and variability in the low copy number regime using External RNA Control Consortium (ERCC) spike-ins.

Kralj JG, Salit ML.

Anal Bioanal Chem. 2013 Jan;405(1):315-20. doi: 10.1007/s00216-012-6445-1. Epub 2012 Oct 20.

PMID:
23086083
45.

Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing.

Zook JM, Samarov D, McDaniel J, Sen SK, Salit M.

PLoS One. 2012;7(7):e41356. doi: 10.1371/journal.pone.0041356. Epub 2012 Jul 31.

46.

Preparation, characterization and thermal degradation of polyimide (4-APS/BTDA)/SiO(2) composite films.

Ahmad MB, Gharayebi Y, Salit MS, Hussein MZ, Ebrahimiasl S, Dehzangi A.

Int J Mol Sci. 2012;13(4):4860-72. doi: 10.3390/ijms13044860. Epub 2012 Apr 17.

47.

Mediation of Drosophila autosomal dosage effects and compensation by network interactions.

Malone JH, Cho DY, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM, Oliver B.

Genome Biol. 2012 Apr 24;13(4):r28. doi: 10.1186/gb-2012-13-4-r28.

48.

Prospects for enhancement of Ring Laser Gyroscopes using gaseous media.

Salit M, Salit K, Bauhahn P.

Opt Express. 2011 Dec 5;19(25):25312-9. doi: 10.1364/OE.19.025312.

PMID:
22273921
49.

Anthropometry of Malaysian young adults.

Karmegam, Karuppiah, Salit MS, Ismail MY, Ismail N, Tamrin SB, Gobalakrishnan K, Palanimuthu S, Palaniandy T.

J Hum Ergol (Tokyo). 2011 Dec;40(1-2):37-46.

PMID:
25665206
50.

Ultra-low power, Zeno effect based optical modulation in a degenerate V-system with a tapered nano fiber in atomic vapor.

Salit K, Salit M, Krishnamurthy S, Wang Y, Kumar P, Shahriar MS.

Opt Express. 2011 Nov 7;19(23):22874-81. doi: 10.1364/OE.19.022874.

PMID:
22109165

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