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Items: 1 to 50 of 89

1.

Molecular signatures of retinal ganglion cells revealed through single cell profiling.

Laboissonniere LA, Goetz JJ, Martin GM, Bi R, Lund TJS, Ellson L, Lynch MR, Mooney B, Wickham H, Liu P, Schwartz GW, Trimarchi JM.

Sci Rep. 2019 Oct 31;9(1):15778. doi: 10.1038/s41598-019-52215-4.

2.

The Trim family of genes and the retina: Expression and functional characterization.

Chowdhury R, Laboissonniere LA, Wester AK, Muller M, Trimarchi JM.

PLoS One. 2018 Sep 12;13(9):e0202867. doi: 10.1371/journal.pone.0202867. eCollection 2018.

3.

ALS-associated genes display CNS expression in the developing zebrafish.

Laboissonniere LA, Smith CL, Mesenbrink J, Chowdhury R, Burney A, Lang M, Sierra M, Stark A, Maldonado-Casalduc G, Muller M, Trimarchi JM.

Gene Expr Patterns. 2018 Dec;30:14-31. doi: 10.1016/j.gep.2018.08.003. Epub 2018 Aug 27.

PMID:
30165106
4.

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells.

Laboissonniere LA, Sonoda T, Lee SK, Trimarchi JM, Schmidt TM.

J Vis Exp. 2017 May 22;(123). doi: 10.3791/55229.

5.

Single cell transcriptome profiling of developing chick retinal cells.

Laboissonniere LA, Martin GM, Goetz JJ, Bi R, Pope B, Weinand K, Ellson L, Fru D, Lee M, Wester AK, Liu P, Trimarchi JM.

J Comp Neurol. 2017 Aug 15;525(12):2735-2781. doi: 10.1002/cne.24241. Epub 2017 May 30.

PMID:
28510275
6.

Complementary feature selection from alternative splicing events and gene expression for phenotype prediction.

Labuzzetta CJ, Antonio ML, Watson PM, Wilson RC, Laboissonniere LA, Trimarchi JM, Genc B, Ozdinler PH, Watson DK, Anderson PE.

Bioinformatics. 2016 Sep 1;32(17):i421-i429. doi: 10.1093/bioinformatics/btw430.

7.

Disentangling neural cell diversity using single-cell transcriptomics.

Poulin JF, Tasic B, Hjerling-Leffler J, Trimarchi JM, Awatramani R.

Nat Neurosci. 2016 Aug 26;19(9):1131-41. doi: 10.1038/nn.4366. Review.

PMID:
27571192
8.

Transplantation of iPSC-derived TM cells rescues glaucoma phenotypes in vivo.

Zhu W, Gramlich OW, Laboissonniere L, Jain A, Sheffield VC, Trimarchi JM, Tucker BA, Kuehn MH.

Proc Natl Acad Sci U S A. 2016 Jun 21;113(25):E3492-500. doi: 10.1073/pnas.1604153113. Epub 2016 Jun 6.

9.

Expression Profiling of Developing Zebrafish Retinal Cells.

Mullally M, Albrecht C, Horton M, Laboissonniere LA, Goetz JJ, Chowdhury R, Manning A, Wester AK, Bose Q, Trimarchi JM.

Zebrafish. 2016 Aug;13(4):272-80. doi: 10.1089/zeb.2015.1184. Epub 2016 Mar 16.

PMID:
26982811
10.

Polo-Like Kinase 3 Appears Dispensable for Normal Retinal Development Despite Robust Embryonic Expression.

Goetz JJ, Laboissonniere LA, Wester AK, Lynch MR, Trimarchi JM.

PLoS One. 2016 Mar 7;11(3):e0150878. doi: 10.1371/journal.pone.0150878. eCollection 2016.

11.

Transcriptomic analyses of Onecut1 and Onecut2 deficient retinas.

Goetz JJ, Trimarchi JM.

Genom Data. 2015 Apr 1;4:88-9. doi: 10.1016/j.gdata.2015.03.010. eCollection 2015 Jun.

12.

Onecut1 and Onecut2 play critical roles in the development of the mouse retina.

Goetz JJ, Martin GM, Chowdhury R, Trimarchi JM.

PLoS One. 2014 Oct 14;9(10):e110194. doi: 10.1371/journal.pone.0110194. eCollection 2014. Erratum in: PLoS One. 2014;9(12):e115786.

13.

Loss of gq/11 genes does not abolish melanopsin phototransduction.

Chew KS, Schmidt TM, Rupp AC, Kofuji P, Trimarchi JM.

PLoS One. 2014 May 28;9(5):e98356. doi: 10.1371/journal.pone.0098356. eCollection 2014.

14.

Making of a retinal cell: insights into retinal cell-fate determination.

Goetz JJ, Farris C, Chowdhury R, Trimarchi JM.

Int Rev Cell Mol Biol. 2014;308:273-321. doi: 10.1016/B978-0-12-800097-7.00007-5. Review.

PMID:
24411174
15.

Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors.

Emerson MM, Surzenko N, Goetz JJ, Trimarchi J, Cepko CL.

Dev Cell. 2013 Jul 15;26(1):59-72. doi: 10.1016/j.devcel.2013.06.005.

16.

Analysis of gene expression in wild-type and Notch1 mutant retinal cells by single cell profiling.

Mizeracka K, Trimarchi JM, Stadler MB, Cepko CL.

Dev Dyn. 2013 Oct;242(10):1147-59. doi: 10.1002/dvdy.24006. Epub 2013 Sep 2.

17.

Plasma-seq: a novel strategy for metastatic prostate cancer analysis.

Farris C, Trimarchi JM.

Genome Med. 2013 Apr 29;5(4):35. doi: 10.1186/gm439. eCollection 2013.

18.

Transcriptome sequencing of single cells with Smart-Seq.

Goetz JJ, Trimarchi JM.

Nat Biotechnol. 2012 Aug;30(8):763-5. doi: 10.1038/nbt.2325. No abstract available.

PMID:
22871714
19.

Single-cell profiling of developing and mature retinal neurons.

Goetz JJ, Trimarchi JM.

J Vis Exp. 2012 Apr 19;(62). pii: 3824. doi: 10.3791/3824.

20.

Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates.

Hafler BP, Surzenko N, Beier KT, Punzo C, Trimarchi JM, Kong JH, Cepko CL.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):7882-7. doi: 10.1073/pnas.1203138109. Epub 2012 Apr 27.

21.

Coexpression of normally incompatible developmental pathways in retinoblastoma genesis.

McEvoy J, Flores-Otero J, Zhang J, Nemeth K, Brennan R, Bradley C, Krafcik F, Rodriguez-Galindo C, Wilson M, Xiong S, Lozano G, Sage J, Fu L, Louhibi L, Trimarchi J, Pani A, Smeyne R, Johnson D, Dyer MA.

Cancer Cell. 2011 Aug 16;20(2):260-75. doi: 10.1016/j.ccr.2011.07.005.

22.

Development and diversification of retinal amacrine interneurons at single cell resolution.

Cherry TJ, Trimarchi JM, Stadler MB, Cepko CL.

Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9495-500. doi: 10.1073/pnas.0903264106. Epub 2009 May 26.

23.

Identification of genes expressed preferentially in the developing peripheral margin of the optic cup.

Trimarchi JM, Cho SH, Cepko CL.

Dev Dyn. 2009 Sep;238(9):2327-9. doi: 10.1002/dvdy.21973.

24.

Temporal requirement of the alternative-splicing factor Sfrs1 for the survival of retinal neurons.

Kanadia RN, Clark VE, Punzo C, Trimarchi JM, Cepko CL.

Development. 2008 Dec;135(23):3923-33. doi: 10.1242/dev.024620. Epub 2008 Nov 5.

25.

Second meiotic spindle integrity requires MEK/MAP kinase activity in mouse eggs.

Petrunewich MA, Trimarchi JR, Hanlan AK, Hammer MA, Baltz JM.

J Reprod Dev. 2009 Feb;55(1):30-8. Epub 2008 Oct 15.

26.

Thyroid hormone components are expressed in three sequential waves during development of the chick retina.

Trimarchi JM, Harpavat S, Billings NA, Cepko CL.

BMC Dev Biol. 2008 Oct 14;8:101. doi: 10.1186/1471-213X-8-101.

27.

Validation of oligoarrays for quantitative exploration of the transcriptome.

Nygaard V, Liu F, Holden M, Kuo WP, Trimarchi J, Ohno-Machado L, Cepko CL, Frigessi A, Glad IK, Wiel MA, Hovig E, Lyng H.

BMC Genomics. 2008 May 30;9:258. doi: 10.1186/1471-2164-9-258.

28.

The transcriptome of retinal Müller glial cells.

Roesch K, Jadhav AP, Trimarchi JM, Stadler MB, Roska B, Sun BB, Cepko CL.

J Comp Neurol. 2008 Jul 10;509(2):225-38. doi: 10.1002/cne.21730.

29.

Trace element concentrations in follicular fluid of small follicles differ from those in blood serum, and may represent long-term exposure.

Silberstein T, Saphier O, Paz-Tal O, Gonzalez L, Keefe DL, Trimarchi JR.

Fertil Steril. 2009 May;91(5):1771-4. doi: 10.1016/j.fertnstert.2008.02.007. Epub 2008 Apr 18.

PMID:
18423455
30.

Individual retinal progenitor cells display extensive heterogeneity of gene expression.

Trimarchi JM, Stadler MB, Cepko CL.

PLoS One. 2008 Feb 13;3(2):e1588. doi: 10.1371/journal.pone.0001588.

31.

Identification of molecular markers of bipolar cells in the murine retina.

Kim DS, Ross SE, Trimarchi JM, Aach J, Greenberg ME, Cepko CL.

J Comp Neurol. 2008 Apr 10;507(5):1795-810. doi: 10.1002/cne.21639.

32.

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP.

BMC Genomics. 2007 Jun 7;8:153.

33.

Molecular heterogeneity of developing retinal ganglion and amacrine cells revealed through single cell gene expression profiling.

Trimarchi JM, Stadler MB, Roska B, Billings N, Sun B, Bartch B, Cepko CL.

J Comp Neurol. 2007 Jun 20;502(6):1047-65.

PMID:
17444492
34.

Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data.

Galante PA, Trimarchi J, Cepko CL, de Souza SJ, Ohno-Machado L, Kuo WP.

Bioinformatics. 2007 Apr 1;23(7):903-5. Epub 2007 Feb 3.

PMID:
17277333
35.

Lead concentrates in ovarian follicle compromises pregnancy.

Silberstein T, Saphier O, Paz-Tal O, Trimarchi JR, Gonzalez L, Keefe DL.

J Trace Elem Med Biol. 2006;20(3):205-7. Epub 2006 Jul 20.

PMID:
16959598
36.

The effect of female tobacco smoking on IVF outcomes.

Wright KP, Trimarchi JR, Allsworth J, Keefe D.

Hum Reprod. 2006 Nov;21(11):2930-4. Epub 2006 Jul 13.

PMID:
16840799
37.

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.

Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK.

Nat Biotechnol. 2006 Jul;24(7):832-40. Epub 2006 Jul 2.

PMID:
16823376
38.

Assessing the quality of oocytes derived from in vitro maturation: are we looking under the lamppost?

Trimarchi JR, Keefe DL.

Fertil Steril. 2006 Apr;85(4):839-40; discussion 841. Review.

PMID:
16580360
39.

Ultrasound-guided miduterine cavity embryo transfer is associated with a decreased incidence of retained embryos in the transfer catheter.

Silberstein T, Trimarchi JR, Shackelton R, Weitzen S, Frankfurter D, Plosker S.

Fertil Steril. 2005 Nov;84(5):1510-2.

PMID:
16275257
40.

Pregnancy outcome in in vitro fertilization decreases to a plateau with repeated cycles.

Silberstein T, Trimarchi JR, Gonzalez L, Keefe DL, Blazar AS.

Fertil Steril. 2005 Oct;84(4):1043-5.

PMID:
16213871
41.

Mullerian inhibiting substance levels at the time of HCG administration in IVF cycles predict both ovarian reserve and embryo morphology.

Silberstein T, MacLaughlin DT, Shai I, Trimarchi JR, Lambert-Messerlian G, Seifer DB, Keefe DL, Blazar AS.

Hum Reprod. 2006 Jan;21(1):159-63. Epub 2005 Aug 25.

PMID:
16123085
42.

Telomere length predicts embryo fragmentation after in vitro fertilization in women--toward a telomere theory of reproductive aging in women.

Keefe DL, Franco S, Liu L, Trimarchi J, Cao B, Weitzen S, Agarwal S, Blasco MA.

Am J Obstet Gynecol. 2005 Apr;192(4):1256-60; discussion 1260-1.

PMID:
15846215
43.

Noninvasive imaging of spindle dynamics during mammalian oocyte activation.

Navarro PA, Liu L, Trimarchi JR, Ferriani RA, Keefe DL.

Fertil Steril. 2005 Apr;83 Suppl 1:1197-205.

PMID:
15831293
44.

CA-125 serum levels and pregnancy outcome in in vitro fertilization.

Fish KE, Phipps M, Trimarchi J, Weitzen S, Blazar AS.

Fertil Steril. 2004 Dec;82(6):1705-7.

PMID:
15589888
45.

Cannulation of a resistant internal os with the malleable outer sheath of a coaxial soft embryo transfer catheter does not affect in vitro fertilization-embryo transfer outcome.

Silberstein T, Weitzen S, Frankfurter D, Trimarchi JR, Keefe DL, Plosker SM.

Fertil Steril. 2004 Nov;82(5):1402-6.

PMID:
15533367
46.

A primer on gene expression and microarrays for machine learning researchers.

Kuo WP, Kim EY, Trimarchi J, Jenssen TK, Vinterbo SA, Ohno-Machado L.

J Biomed Inform. 2004 Aug;37(4):293-303. Review.

47.

Monozygotic pregnancies from transfers of zona-free blastocysts.

Frankfurter D, Trimarchi J, Hackett R, Meng L, Keefe D.

Fertil Steril. 2004 Aug;82(2):483-5. No abstract available.

PMID:
15302309
48.

Genomic analysis of mouse retinal development.

Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL.

PLoS Biol. 2004 Sep;2(9):E247. Epub 2004 Jun 29.

49.

Middle to lower uterine segment embryo transfer improves implantation and pregnancy rates compared with fundal embryo transfer.

Frankfurter D, Trimarchi JB, Silva CP, Keefe DL.

Fertil Steril. 2004 May;81(5):1273-7.

PMID:
15136089
50.

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