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Items: 1 to 50 of 106

1.

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL.

Nat Methods. 2019 Oct;16(10):987-990. doi: 10.1038/s41592-019-0548-y. Epub 2019 Sep 9.

PMID:
31501547
2.

Are We There Yet? How and When Specific Biotechnologies Will Improve Human Health.

O'Day E, Hosta-Rigau L, Oyarzún DA, Okano H, de Lorenzo V, von Kameke C, Alsafar H, Cao C, Chen GQ, Ji W, Roberts RJ, Ronaghi M, Yeung K, Zhang F, Lee SY.

Biotechnol J. 2019 Jan;14(1):e1800195. doi: 10.1002/biot.201800195. Epub 2018 Jun 13. Review.

3.

Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm.

Chen H, Shao J, Zhang H, Jiang M, Huang L, Zhang Z, Yang D, He M, Ronaghi M, Luo X, Sun B, Wu W, Liu C.

Front Plant Sci. 2018 Mar 14;9:324. doi: 10.3389/fpls.2018.00324. eCollection 2018.

4.

The power of synthetic biology for bioproduction, remediation and pollution control: The UN's Sustainable Development Goals will inevitably require the application of molecular biology and biotechnology on a global scale.

de Lorenzo V, Prather KL, Chen GQ, O'Day E, von Kameke C, Oyarzún DA, Hosta-Rigau L, Alsafar H, Cao C, Ji W, Okano H, Roberts RJ, Ronaghi M, Yeung K, Zhang F, Lee SY.

EMBO Rep. 2018 Apr;19(4). pii: e45658. doi: 10.15252/embr.201745658. Epub 2018 Mar 26. No abstract available.

5.

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.

Zhang F, Christiansen L, Thomas J, Pokholok D, Jackson R, Morrell N, Zhao Y, Wiley M, Welch E, Jaeger E, Granat A, Norberg SJ, Halpern A, C Rogert M, Ronaghi M, Shendure J, Gormley N, Gunderson KL, Steemers FJ.

Nat Biotechnol. 2017 Sep;35(9):852-857. doi: 10.1038/nbt.3897. Epub 2017 Jun 26.

PMID:
28650462
6.

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II.

Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce T, Wroblewski EE, Dunn T, Mann T, Alicata C, Hollenbach JA, Chang W, Shults Won M, Gunderson KL, Abi-Rached L, Ronaghi M, Parham P.

Genome Res. 2017 May;27(5):813-823. doi: 10.1101/gr.213538.116. Epub 2017 Mar 30.

7.

Standardizing the freeze-thaw preparation of growth factors from platelet lysate.

Strandberg G, Sellberg F, Sommar P, Ronaghi M, Lubenow N, Knutson F, Berglund D.

Transfusion. 2017 Apr;57(4):1058-1065. doi: 10.1111/trf.13998. Epub 2017 Feb 9.

PMID:
28182293
8.

Contiguity-Preserving Transposition Sequencing (CPT-Seq) for Genome-Wide Haplotyping, Assembly, and Single-Cell ATAC-Seq.

Christiansen L, Amini S, Zhang F, Ronaghi M, Gunderson KL, Steemers FJ.

Methods Mol Biol. 2017;1551:207-221. doi: 10.1007/978-1-4939-6750-6_12.

PMID:
28138849
9.

Inflammatory cytokines in serum samples of healthy blood donors.

Sellberg F, Ronaghi M, Knutson F, Berglund D.

Transfus Apher Sci. 2016 Oct;55(2):246-247. doi: 10.1016/j.transci.2016.07.020. Epub 2016 Jul 21. No abstract available.

PMID:
27475802
10.

Composition of growth factors and cytokines in lysates obtained from fresh versus stored pathogen-inactivated platelet units.

Sellberg F, Berglund E, Ronaghi M, Strandberg G, Löf H, Sommar P, Lubenow N, Knutson F, Berglund D.

Transfus Apher Sci. 2016 Dec;55(3):333-337. doi: 10.1016/j.transci.2016.08.004. Epub 2016 Sep 28.

PMID:
27720587
11.

Defining KIR and HLA Class I Genotypes at Highest Resolution via High-Throughput Sequencing.

Norman PJ, Hollenbach JA, Nemat-Gorgani N, Marin WM, Norberg SJ, Ashouri E, Jayaraman J, Wroblewski EE, Trowsdale J, Rajalingam R, Oksenberg JR, Chiaroni J, Guethlein LA, Traherne JA, Ronaghi M, Parham P.

Am J Hum Genet. 2016 Aug 4;99(2):375-91. doi: 10.1016/j.ajhg.2016.06.023.

12.

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.

Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K.

Science. 2016 Jun 24;352(6293):1586-90. doi: 10.1126/science.aaf1204.

13.

Subangstrom single-molecule measurements of motor proteins using a nanopore.

Derrington IM, Craig JM, Stava E, Laszlo AH, Ross BC, Brinkerhoff H, Nova IC, Doering K, Tickman BI, Ronaghi M, Mandell JG, Gunderson KL, Gundlach JH.

Nat Biotechnol. 2015 Oct;33(10):1073-5. doi: 10.1038/nbt.3357. Epub 2015 Sep 28.

14.

Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines.

Norman PJ, Norberg SJ, Nemat-Gorgani N, Royce T, Hollenbach JA, Shults Won M, Guethlein LA, Gunderson KL, Ronaghi M, Parham P.

Immunogenetics. 2015 Sep;67(9):479-85. doi: 10.1007/s00251-015-0857-y. Epub 2015 Jul 22.

15.

DNA sequencing using polymerase substrate-binding kinetics.

Previte MJ, Zhou C, Kellinger M, Pantoja R, Chen CY, Shi J, Wang B, Kia A, Etchin S, Vieceli J, Nikoomanzar A, Bomati E, Gloeckner C, Ronaghi M, He MM.

Nat Commun. 2015 Jan 23;6:5936. doi: 10.1038/ncomms6936.

16.

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J.

Genome Res. 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. Epub 2014 Oct 19.

17.

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.

Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ.

Nat Genet. 2014 Dec;46(12):1343-9. doi: 10.1038/ng.3119. Epub 2014 Oct 19.

18.

Inner ear hair cell-like cells from human embryonic stem cells.

Ronaghi M, Nasr M, Ealy M, Durruthy-Durruthy R, Waldhaus J, Diaz GH, Joubert LM, Oshima K, Heller S.

Stem Cells Dev. 2014 Jun 1;23(11):1275-84. doi: 10.1089/scd.2014.0033. Epub 2014 Mar 10.

19.

Mutation in ST6GALNAC5 identified in family with coronary artery disease.

InanlooRahatloo K, Parsa AF, Huse K, Rasooli P, Davaran S, Platzer M, Kramer M, Fan JB, Turk C, Amini S, Steemers F, Gunderson K, Ronaghi M, Elahi E.

Sci Rep. 2014 Jan 8;4:3595. doi: 10.1038/srep03595.

20.

Whole-genome haplotyping by dilution, amplification, and sequencing.

Kaper F, Swamy S, Klotzle B, Munchel S, Cottrell J, Bibikova M, Chuang HY, Kruglyak S, Ronaghi M, Eberle MA, Fan JB.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5552-7. doi: 10.1073/pnas.1218696110. Epub 2013 Mar 18.

21.

Deep sequencing of the hepatitis B virus in hepatocellular carcinoma patients reveals enriched integration events, structural alterations and sequence variations.

Toh ST, Jin Y, Liu L, Wang J, Babrzadeh F, Gharizadeh B, Ronaghi M, Toh HC, Chow PK, Chung AY, Ooi LL, Lee CG.

Carcinogenesis. 2013 Apr;34(4):787-98. doi: 10.1093/carcin/bgs406. Epub 2012 Dec 30.

PMID:
23276797
22.

mRNA-Seq of single prostate cancer circulating tumor cells reveals recapitulation of gene expression and pathways found in prostate cancer.

Cann GM, Gulzar ZG, Cooper S, Li R, Luo S, Tat M, Stuart S, Schroth G, Srinivas S, Ronaghi M, Brooks JD, Talasaz AH.

PLoS One. 2012;7(11):e49144. doi: 10.1371/journal.pone.0049144. Epub 2012 Nov 7.

23.

Genetic analysis and SOD1 mutation screening in Iranian amyotrophic lateral sclerosis patients.

Alavi A, Nafissi S, Rohani M, Zamani B, Sedighi B, Shamshiri H, Fan JB, Ronaghi M, Elahi E.

Neurobiol Aging. 2013 May;34(5):1516.e1-8. doi: 10.1016/j.neurobiolaging.2012.09.006. Epub 2012 Oct 9.

PMID:
23062701
24.

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1.

Babrzadeh F, Jalili R, Wang C, Shokralla S, Pierce S, Robinson-Mosher A, Nyren P, Shafer RW, Basso LC, de Amorim HV, de Oliveira AJ, Davis RW, Ronaghi M, Gharizadeh B, Stambuk BU.

Mol Genet Genomics. 2012 Jun;287(6):485-94. doi: 10.1007/s00438-012-0695-7. Epub 2012 May 6.

PMID:
22562254
25.

LTBP2 mutations cause Weill-Marchesani and Weill-Marchesani-like syndrome and affect disruptions in the extracellular matrix.

Haji-Seyed-Javadi R, Jelodari-Mamaghani S, Paylakhi SH, Yazdani S, Nilforushan N, Fan JB, Klotzle B, Mahmoudi MJ, Ebrahimian MJ, Chelich N, Taghiabadi E, Kamyab K, Boileau C, Paisan-Ruiz C, Ronaghi M, Elahi E.

Hum Mutat. 2012 Aug;33(8):1182-7. doi: 10.1002/humu.22105. Epub 2012 May 29.

PMID:
22539340
26.

Highly parallel genome-wide expression analysis of single mammalian cells.

Fan JB, Chen J, April CS, Fisher JS, Klotzle B, Bibikova M, Kaper F, Ronaghi M, Linnarsson S, Ota T, Chien J, Laurent LC, Loring JF, Nisperos SV, Chen GY, Zhong JF.

PLoS One. 2012;7(2):e30794. doi: 10.1371/journal.pone.0030794. Epub 2012 Feb 8. Erratum in: PLoS One. 2012;7(2). doi: 10.1371/annotation/3f0ddf41-2e7a-4b56-93c2-2731f2890b19. Loring, Jeanne F [added].

27.

Non-housekeeping genes expressed in human trabecular meshwork cell cultures.

Paylakhi SH, Yazdani S, April C, Fan JB, Moazzeni H, Ronaghi M, Elahi E.

Mol Vis. 2012;18:241-54. Epub 2012 Jan 28.

28.

Concise review: Inner ear stem cells--an oxymoron, but why?

Ronaghi M, Nasr M, Heller S.

Stem Cells. 2012 Jan;30(1):69-74. doi: 10.1002/stem.785. Review.

29.

Manifestation of diffuse yellowish keratoderma on the palms and soles in autosomal recessive congenital ichthyosis patients may be indicative of mutations in NIPAL4.

Alavi A, Shahshahani MM, Klotzle B, Fan JB, Ronaghi M, Elahi E.

J Dermatol. 2012 Apr;39(4):375-81. doi: 10.1111/j.1346-8138.2011.01412.x. Epub 2011 Nov 21.

PMID:
22098531
30.

Highly parallel oligonucleotide purification and functionalization using reversible chemistry.

York KT, Smith RC, Yang R, Melnyk PC, Wiley MM, Turk CM, Ronaghi M, Gunderson KL, Steemers FJ.

Nucleic Acids Res. 2012 Jan;40(1):e4. doi: 10.1093/nar/gkr910. Epub 2011 Oct 29.

31.

Effect of PITX2 knockdown on transcriptome of primary human trabecular meshwork cell cultures.

Paylakhi SH, Fan JB, Mehrabian M, Sadeghizadeh M, Yazdani S, Katanforoush A, Kanavi MR, Ronaghi M, Elahi E.

Mol Vis. 2011;17:1209-21. Epub 2011 May 5.

32.

PRKN, DJ-1, and PINK1 screening identifies novel splice site mutation in PRKN and two novel DJ-1 mutations.

Ghazavi F, Fazlali Z, Banihosseini SS, Hosseini SR, Kazemi MH, Shojaee S, Parsa K, Sadeghi H, Sina F, Rohani M, Shahidi GA, Ghaemi N, Ronaghi M, Elahi E.

Mov Disord. 2011 Jan;26(1):80-9. doi: 10.1002/mds.23417. Epub 2010 Nov 8.

PMID:
21322020
33.

Although divergent in residues of the peptide binding site, conserved chimpanzee Patr-AL and polymorphic human HLA-A*02 have overlapping peptide-binding repertoires.

Gleimer M, Wahl AR, Hickman HD, Abi-Rached L, Norman PJ, Guethlein LA, Hammond JA, Draghi M, Adams EJ, Juo S, Jalili R, Gharizadeh B, Ronaghi M, Garcia KC, Hildebrand WH, Parham P.

J Immunol. 2011 Feb 1;186(3):1575-88. doi: 10.4049/jimmunol.1002990. Epub 2011 Jan 5.

34.

Ontology-based meta-analysis of global collections of high-throughput public data.

Kupershmidt I, Su QJ, Grewal A, Sundaresh S, Halperin I, Flynn J, Shekar M, Wang H, Park J, Cui W, Wall GD, Wisotzkey R, Alag S, Akhtari S, Ronaghi M.

PLoS One. 2010 Sep 29;5(9). pii: e13066. doi: 10.1371/journal.pone.0013066.

35.

pfSNP: An integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses.

Wang J, Ronaghi M, Chong SS, Lee CG.

Hum Mutat. 2011 Jan;32(1):19-24. doi: 10.1002/humu.21331.

PMID:
20672376
36.

Transplanted oligodendrocytes and motoneuron progenitors generated from human embryonic stem cells promote locomotor recovery after spinal cord transection.

Erceg S, Ronaghi M, Oria M, Roselló MG, Aragó MA, Lopez MG, Radojevic I, Moreno-Manzano V, Rodríguez-Jiménez FJ, Bhattacharya SS, Cordoba J, Stojkovic M.

Stem Cells. 2010 Sep;28(9):1541-9. doi: 10.1002/stem.489.

37.

Efficient differentiation of human embryonic stem cells into functional cerebellar-like cells.

Erceg S, Ronaghi M, Zipancic I, Lainez S, Roselló MG, Xiong C, Moreno-Manzano V, Rodríguez-Jiménez FJ, Planells R, Alvarez-Dolado M, Bhattacharya SS, Stojkovic M.

Stem Cells Dev. 2010 Nov;19(11):1745-56. doi: 10.1089/scd.2009.0498. Epub 2010 Oct 7.

PMID:
20521974
38.

A Microfluidic Platform for Characterization of Protein-Protein Interactions.

Javanmard M, Talasaz AH, Nemat-Gorgani M, Huber DE, Pease F, Ronaghi M, Davis RW.

IEEE Sens J. 2009 Aug;9(8):883-891.

39.

ROPS performance during field upset and static testing.

Harris JR, McKenzie EA Jr, Etherton JR, Cantis DM, Ronaghi M.

J Agric Saf Health. 2010 Jan;16(1):5-18.

PMID:
20222267
40.

Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems.

Parameswaran P, Sklan E, Wilkins C, Burgon T, Samuel MA, Lu R, Ansel KM, Heissmeyer V, Einav S, Jackson W, Doukas T, Paranjape S, Polacek C, dos Santos FB, Jalili R, Babrzadeh F, Gharizadeh B, Grimm D, Kay M, Koike S, Sarnow P, Ronaghi M, Ding SW, Harris E, Chow M, Diamond MS, Kirkegaard K, Glenn JS, Fire AZ.

PLoS Pathog. 2010 Feb 12;6(2):e1000764. doi: 10.1371/journal.ppat.1000764.

41.

Challenges of stem cell therapy for spinal cord injury: human embryonic stem cells, endogenous neural stem cells, or induced pluripotent stem cells?

Ronaghi M, Erceg S, Moreno-Manzano V, Stojkovic M.

Stem Cells. 2010 Jan;28(1):93-9. doi: 10.1002/stem.253. Review.

42.

CD24 gene polymorphism is associated with the disease progression and susceptibility to multiple sclerosis in the Iranian population.

Ronaghi M, Vallian S, Etemadifar M.

Psychiatry Res. 2009 Dec 30;170(2-3):271-2. doi: 10.1016/j.psychres.2009.01.002. Epub 2009 Nov 5.

PMID:
19896210
43.

Identification of four novel potentially Parkinson's disease associated LRRK2 variations among Iranian patients.

Shojaee S, Fazlali Z, Ghazavi F, Banihosseini SS, Kazemi MH, Parsa K, Sadeghi H, Sina F, Shahidi GA, Ronaghi M, Elahi E.

Neurosci Lett. 2009 Dec 25;467(2):53-7. doi: 10.1016/j.neulet.2009.09.058. Epub 2009 Oct 1.

PMID:
19800393
44.

Loss of function mutations in the gene encoding latent transforming growth factor beta binding protein 2, LTBP2, cause primary congenital glaucoma.

Narooie-Nejad M, Paylakhi SH, Shojaee S, Fazlali Z, Rezaei Kanavi M, Nilforushan N, Yazdani S, Babrzadeh F, Suri F, Ronaghi M, Elahi E, Paisán-Ruiz C.

Hum Mol Genet. 2009 Oct 15;18(20):3969-77. doi: 10.1093/hmg/ddp338. Epub 2009 Aug 4.

PMID:
19656777
45.

Rapid and selective extraction, isolation, preconcentration, and quantitation of small RNAs from cell lysate using on-chip isotachophoresis.

Schoch RB, Ronaghi M, Santiago JG.

Lab Chip. 2009 Aug 7;9(15):2145-52. doi: 10.1039/b903542g. Epub 2009 Apr 28.

PMID:
19606290
46.

Deregulated direct targets of the hepatitis B virus (HBV) protein, HBx, identified through chromatin immunoprecipitation and expression microarray profiling.

Sung WK, Lu Y, Lee CW, Zhang D, Ronaghi M, Lee CG.

J Biol Chem. 2009 Aug 14;284(33):21941-54. doi: 10.1074/jbc.M109.014563. Epub 2009 May 13.

47.

Electrical detection of protein biomarkers using bioactivated microfluidic channels.

Javanmard M, Talasaz AH, Nemat-Gorgani M, Pease F, Ronaghi M, Davis RW.

Lab Chip. 2009 May 21;9(10):1429-34. doi: 10.1039/b818872f. Epub 2009 Mar 2.

48.

Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes.

Norman PJ, Abi-Rached L, Gendzekhadze K, Hammond JA, Moesta AK, Sharma D, Graef T, McQueen KL, Guethlein LA, Carrington CV, Chandanayingyong D, Chang YH, Crespí C, Saruhan-Direskeneli G, Hameed K, Kamkamidze G, Koram KA, Layrisse Z, Matamoros N, Milà J, Park MH, Pitchappan RM, Ramdath DD, Shiau MY, Stephens HA, Struik S, Tyan D, Verity DH, Vaughan RW, Davis RW, Fraser PA, Riley EM, Ronaghi M, Parham P.

Genome Res. 2009 May;19(5):757-69. doi: 10.1101/gr.085738.108.

49.

A clinic-based screening of mutations in exons 31, 34, 35, 41, and 48 of LRRK2 in Iranian Parkinson's disease patients.

Shojaee S, Sina F, Farboodi N, Fazlali Z, Ghazavi F, Ghorashi SA, Parsa K, Sadeghi H, Shahidi GA, Ronaghi M, Elahi E.

Mov Disord. 2009 May 15;24(7):1023-7. doi: 10.1002/mds.22503.

PMID:
19353692
50.

Activated spinal cord ependymal stem cells rescue neurological function.

Moreno-Manzano V, Rodríguez-Jiménez FJ, García-Roselló M, Laínez S, Erceg S, Calvo MT, Ronaghi M, Lloret M, Planells-Cases R, Sánchez-Puelles JM, Stojkovic M.

Stem Cells. 2009 Mar;27(3):733-43. doi: 10.1002/stem.24.

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