some of my favorite pubs throughout my academic life

PUBLICATIONS

Peer Reviewed Papers

33. Howard JM, Lin H, Wallace A, Kim G, Draper JM, Katzman S, Hauessler M, Toloue M, Liu Y and Sanford JR. hnRNP A1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome Research (2018) In Press.

32. Martinez-Nunez, Wallace A, Coyne D, Jansson L, Rush M, Ennajdaoui H, Katzman S, Bailey J, Deinhardt K, Sanchez-Elsner T, Sanford JR. Modulation of nonsense mediated decay by rapamycin. Nucleic Acids Research. 2017. 2017 Apr 7;45(6):3448-3459. doi: 10.1093/nar/gkw1109

31. Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.  Genome research. 2017; 27(5):686-696.

30. Ennajdaoui H, Howard JM, Sterne-Weiler T, Jahanbani F, Coyne DJ, Uren PJ, et al. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell reports. 2016. doi: 10.1016/j.celrep.2016.04.083.

29. Palanichamy, J.K., Tran, T.M., Howard, J.M., Contreras, J.R., Fernando, T.R., Sterne-Weiler, T., Katzman, S., Toloue, M., Yan, W., Basso, G., Pigazzi, M., Sanford, J.R. and Rao, D.S. (2016). RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. The Journal of Clinical Investigation 126, 1495-1511.

28. Martinez-Nunez, R.T., and Sanford, J.R. (2016). Studying Isoform-Specific mRNA Recruitment to Polyribosomes with Frac-seq. Methods Mol Biol 1358, 99-108.

27. Hansen, H.T., Rasmussen, S.H., Adolph, S.K., Plass, M., Krogh, A., Sanford, J., Nielsen, F.C., and Christiansen, J. (2015). Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation. Genome biology 16, 123.

26. Sterne-Weiler, T., and Sanford, J.R. (2014). Exon identity crisis: disease-causing mutations that disrupt the splicing code. Genome biology 15, 201.

25. MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD. Genome Biol. 2014 Jan 13;15(1):R19. 

24. Roberts J, Ennajdaoui H, Werth, B, Sanford JR and Chen B. Splicing factor TRA2B is required for neural progenitor survival. Journal of Comparative Neurology. 2014 Feb 1;522(2):372-92.

23. Sterne-Weiler T, Martinez-Nunez RT, Howard JM, Cvitovik I, Katzman S, Tariq MA, Pourmand N, Sanford JR. Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res. 2013; 23 (10):1615-23. PMID: 23783272

22. Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. 2012. Site identification in high-throughput RNA-protein interaction data. Bioinformatics 28(23): 3013-3020.

21. St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A et al. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 13(1): 415.

20. Wang X, Juan L, Lv J, Wang K, Sanford JR, Liu Y. 2011. Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1. BMC Genomics 12 Suppl 5: S8.

19. Teng M, Wang Y, Wang G, Jung J, Edenberg HJ, Sanford JR, Liu Y. 2011. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC Proc 5 Suppl 9: S40.

18. Sterne-Weiler, T., J. Howard, M. Mort, D.N. Cooper, and J.R. Sanford. 2011. Loss of exon identity is a common mechanism of human inherited disease. Genome Res. 21: 1563-1571.

17. Wang, X., K. Wang, M. Radovich, Y. Wang, G. Wang, W. Feng, J.R. Sanford, and Y. Liu, Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. BMC Genomics, 2009. 10 Suppl 1: p. S4.

16. Sanford, J.R.*, X. Wang, M. Mort, N. Vanduyn, D.N. Cooper, S.D. Mooney, H.J. Edenberg, and Y. Liu, Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res, 2009.

*Corresponding author

15. Henao-Mejia, J., Y. Liu, I.W. Park, J. Zhang, J. Sanford, and J.J. He, Suppression of HIV-1 Nef translation by Sam68 mutant-induced stress granules and nef mRNA sequestration. Mol Cell, 2009. 33(1): p. 87-96.

14. Butler, J.S., L.R. Palam, C.M. Tate, J.R. Sanford, R.C. Wek, and D.G. Skalnik, DNA Methyltransferase protein synthesis is reduced in CXXC finger protein 1-deficient embryonic stem cells. DNA Cell Biol, 2009. 28(5): p. 223-31.

13. Wang, X., G. Wang, C. Shen, L. Li, X. Wang, S.D. Mooney, H.J. Edenberg, J.R. Sanford, and Y. Liu, Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics, 2008. 9 Suppl 1: p. S17.

12. Sanford, J.R*., P. Coutinho, J.A. Hackett, X. Wang, W. Ranahan, and J.F. Caceres, Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF. PLoS ONE, 2008. 3(10): p. e3369.

*Co-corresponding author

11.Michlewski, G., J.R. Sanford, and J.F. Caceres, The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol Cell, 2008. 30(2): p. 179-89.

10. Liang, F., Y. Luo, Y. Dong, C.D. Walls, J. Liang, H.Y. Jiang, J.R. Sanford, R.C. Wek, and Z.Y. Zhang, Translational control of C-terminal Src kinase (Csk) expression by PRL3 phosphatase. J Biol Chem, 2008. 283(16): p. 10339-46.

9. Sanford, J.R., J.D. Ellis, D. Cazalla, and J.F. Caceres, Reversible phosphorylation differentially affects nuclear and cytoplasmic functions of splicing factor 2/alternative splicing factor. Proc Natl Acad Sci U S A, 2005. 102(42): p. 15042-7.

8. Cazalla, D., J.R. Sanford, and J.F. Caceres, A rapid and efficient protocol to purify biologically active recombinant proteins from mammalian cells. Protein Expr Purif, 2005. 42(1): p. 54-8.

7. Blaustein, M., F. Pelisch, T. Tanos, M.J. Munoz, D. Wengier, L. Quadrana, J.R. Sanford, J.P. Muschietti, A.R. Kornblihtt, J.F. Caceres, O.A. Coso, and A. Srebrow, Concerted regulation of nuclear and cytoplasmic activities of SR proteins by AKT. Nat Struct Mol Biol, 2005. 12(12): p. 1037-44.

6. Sanford, J.R., N.K. Gray, K. Beckmann, and J.F. Caceres, A novel role for shuttling SR proteins in mRNA translation. Genes Dev, 2004. 18(7): p. 755-68.

5. Niksic, M., J. Slight, J.R. Sanford, J.F. Caceres, and N.D. Hastie, The Wilms' tumour protein (WT1) shuttles between nucleus and cytoplasm and is present in functional polysomes. Hum Mol Genet, 2004. 13(4): p. 463-71.

4. Sanford, J.R. and J.P. Bruzik, Regulation of SR protein localization during development. Proc Natl Acad Sci U S A, 2001. 98(18): p. 10184-9.

3. Capellari, S., P. Parchi, C.M. Russo, J. Sanford, M.S. Sy, P. Gambetti, and R.B. Petersen, Effect of the E200K mutation on prion protein metabolism. Comparative study of a cell model and human brain. Am

J Pathol, 2000. 157(2): p. 613-22.

2. Sanford, J.R. and J.P. Bruzik, Developmental regulation of SR protein phosphorylation and activity. Genes Dev, 1999. 13(12): p. 1513-8.

1. Sanford, J.R. and J.P. Bruzik, SR proteins are required for nematode trans-splicing in vitro. Rna, 1999. 5(7): p. 918-28.

Solicited Papers

8. The 3′ end of the story: deciphering combinatorial interactions that control mRNA fate

JR Sanford, LOF Penalva. Genome biology 18 (1), 227

7. From mechanisms to therapy: RNA processing’s impact on human genetics

LO Penalva, JR Sanford. Human genetics 136 (9), 1013-1014

6. Martiniez-Nunez and Jeremy R. Sanford. Studying isoform-specific mRNA recruitment to polyribosomes with Frac-seq. Vol. 1358, Erik Dassi (Eds): Post-Transcriptional Gene Regulation, 978-1-4939-3066-1, 322984_2_En, (6) In Press

5. Howard JM and Sanford JR. The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley interdisciplinary reviews RNA. 2014. doi: 10.1002/wrna.1260.

4. Sterne-Weiler T and Sanford JR. Exon identity crisis: disease-causing mutations that disrupt the splicing code. Genome biology. 2014;15(1):201. doi: 10.1186/gb4150.

3. Sanford, J.R., J. Ellis, and J.F. Caceres, Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem Soc Trans, 2005. 33(Pt 3): p. 443-6.

2. Sanford, J.R. and J.F. Caceres, Pre-mRNA splicing: life at the centre of the central dogma. J Cell Sci, 2004. 117(Pt 26): p. 6261-3.

1. Sanford, J.R., D. Longman, and J.F. Caceres, Multiple roles of the SR protein family in splicing regulation. Prog Mol Subcell Biol, 2003. 31: p. 33-58.

PATENTS

US Patent 9,765,398

Inventors: Jeremy R Sanford, Timothy Sterne-Weiler, UC Regents

Exonic splicing enhancers (ESE) and silencers (ESS) in disease causation, methods for identification of splicing sensitive disease mutations, and functional RNA elements as targets for amelioration of aberrant pre-mRNA splicing.