Our Publications
The TUMI Genomics’ team continually publishes peer-reviewed articles to broaden the foundation of scientific knowledge
-
Katelyn Reeves, Jennifer Leibig, Antonio Feula, Tassa Saldi, Erika Lasda, William Johnson, Jacob Lilienfeld, Juniper Maggi, Kevin Pulley, Paul J. Wilkerson, Breanna Real, Gordon Zak, Jack Davis, Morgan Fink, Patrick Gonzalez, Cole Hager, Christopher Ozeroff, Kimngan Tat, Michaela Alkire, Claire Butler, Elle Coe, Jessica Darby, Nicholas Freeman, Heidi Heuer, Jeffery R. Jones, Madeline Karr, Sara Key, Kiersten Maxwell, Lauren Nelson, Emily Saldana, Rachel Shea, Lewis Salveson, Kate Tomlinson, Jorge Vargas-Barriga, Bailey Vigil, Gloria Brisson, Roy Parker, Leslie A. Leinwand, Kristen Bjorkman, Cresten Mansfeldt. High-resolution within-sewer SARS-CoV-2 surveillance facilitates informed intervention. https://doi.org/10.1101/2021.05.24.21257632
Bjorkman KK, Saldi TK, Lasda E, Bauer LC, Kovarik J, Gonzales PK, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, Larremore DB, Leinwand LA, McQueen MB, Parker R. Higher viral load drives infrequent SARS-CoV-2 transmission between asymptomatic residence hall roommates. J Infect Dis. 2021 Jul 24:jiab386.
Yang Q, Saldi TK, Gonzales PK, Lasda E, Decker CJ, Tat KL, Fink MR, Hager CR, Davis JC, Ozeroff CD, Muhlrad D, Clark SK, Fattor WT, Meyerson NR, Paige CL, Gilchrist AR, Barbachano-Guerrero A, Worden-Sapper ER, Wu SS, Brisson GR, McQueen MB, Dowell RD, Leinwand L, Parker R, Sawyer SL. Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities. Proc Natl Acad Sci U S A. 2021 May 25;118(21).
Melnick M, Gonzales P, LaRocca TJ, Song Y, Wuu J, Benatar M, Oskarsson B, Petrucelli L, Dowell RD, Link CD, Prudencio M. Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood. G3 (Bethesda). 2021 Apr 29.
Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales P, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand LA, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. Elife. 2021 Mar 29;10.
-
Saldi T, Reimondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription modify splicing outcomes. Mol Cell, 2021 Apr 15;81(8):1789-1801.
Melnick M, Gonzales P, Cabral J, Allen MA, Dowell RD, Link CD. Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA. PLoS One. 2019 Apr 8;14(4).
Zhang YJ, Guo L, Gonzales PK, Gendron TF, Wu Y, Jansen-West K, O'Raw AD, Pickles SR, Prudencio M, Carlomagno Y, Gachechiladze MA, Ludwig C, Tian R, Chew J, DeTure M, Lin WL, Tong J, Daughrity LM, Yue M, Song Y, Andersen JW, Castanedes-Casey M, Kurti A, Datta A, Antognetti G, McCampbell A, Rademakers R, Oskarsson B, Dickson DW, Kampmann M, Ward ME, Fryer JD, Link CD, Shorter J, Petrucelli L. Heterochromatin anomalies and double-stranded RNA accumulation underlie C9orf72 poly(PR) toxicity. Science. 2019 Feb 15;363(6428).
Saldi T, Gonzales P, Garrido-Lecca A, Dostal V, Roberts CM, Petrucelli L, Link CD The C. elegans ortholog of TDP-43 regulates the chromatin localization of the heterochromatin protein 1 homolog, HPL-2. Mol Cell Biol. 2018 July 16:38(15).
Gonzales PK, Roberts CM, Fonte V, Jacobsen C, Stein GH, Link CD. Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21. PLoS One. 2018 Mar 27;13(3).
Saldi T, Fong N, and Bentley DL. Transcription elongation rate affects nascent histone pre-mRNA folding and 3’ end processing. Genes and Development. 2018 Feb 1; 32(3-4):297-308.
Prudencio M, Gonzales PK, Cook CN, Gendron TF, Daughrity LM, Song Y, Ebbert MTW, van Blitterswijk M, Zhang YJ, Jansen-West K, Baker MC, DeTure M, Rademakers R, Boylan KB, Dickson DW, Petrucelli L, Link CD. Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients. Hum Mol Genet. 2017 Sep 1;26(17):3421-3431.
Fong N*, Saldi T*, Sheridan RM, Cortazar MA, Bentley DL. RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction. Mol Cell. 2017 May 18; 66(4):546-557 *First co-authors.
Garrido-Lecca A, Saldi T, Blumenthal T. Localization of RNAPII and 3' end formation factor CstF subunits on C. elegans genes and operons. Transcription. 2016 May 26; 7(3):96-110.
Saldi T, Ash PE, Wilson G, Gonzales P, Garrido-Lecca A, Roberts CM, Dostal V, Gendron TF, Stein LD, Blumenthal T, Petrucelli L, Link CD TDP-1, the TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA. EMBO J. 2014 Dec 17; 33(24):2947-66.
Fong N, Kim H, Zhou Y, Ji X, Qiu J, Saldi T, Diener K, Jones K, Fu XD, Bentley DL. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev. 2014 Dec 1; 28(23):2663-76.
Garrido-Lecca A, Blumenthal T. RNA polymerase II C-terminal domain phosphorylation patterns in Caenorhabditis elegans operons, polycistronic gene clusters with only one promoter. Mol Cell Biol. 2010 Aug;30(15). Mol Cell Biol. 2010 Aug;30(15):3887-93.
-
Cook SG, Bourke AM, O'Leary H, Zaegel V, Lasda E, Mize-Berge J, Quillinan N, Tucker CL, Coultrap SJ, Herson PS, Bayer KU. Analysis of the CaMKIIα and β splice-variant distribution among brain regions reveals isoform-specific differences in holoenzyme formation. Sci Rep. 2018 Apr 3;8(1):5448.
Lasda E, Parker R. Circular RNAs Co-Precipitate with Extracellular Vesicles: A Possible Mechanism for circRNA Clearance. PLoS One. 2016 Feb 5;11(2):e0148407.
Lasda EL, Kuersten S, Blumenthal T. SL trans-splicing in a Caenorhabditis elegans in vitro extract. Cold Spring Harb Protoc. 2011 Feb 1;2011(2).
Lasda EL, Allen MA, Blumenthal T. Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing. Genes Dev. 2010 Aug 1;24(15):1645-58.
Seth, P., Miller, H.B., Lasda, E.L., Pearson, J.L., and Garcia-Blanco, M.A. 2008. Identification of an intronic splicing enhancer essential for the inclusion of FGFR2 exon IIIc. J. Biol. Chem 283: 10058-10067. PMID: 18256031
MacMorris, M., Kumar, M., Lasda, E., Larsen, A., Kraemer, B., and Blumenthal, T. 2007. A novel family of C. elegans snRNPs contains proteins associated with trans-splicing. RNA 13: 511-520. PMID: 17283210.
O'Leary, H., Lasda, E., and Bayer, K.U. 2006. CaMKIIbeta association with the actin cytoskeleton is regulated by alternative splicing. Mol. Biol. Cell 17: 4656-4665. PMID: 16928958.
Baraniak, A.P., Lasda, E.L., Wagner, E.J., and Garcia-Blanco, M.A. 2003. A stem structure in fibroblast growth factor receptor 2 transcripts mediates cell-type-specific splicing by approximating intronic control elements. Mol. Cell. Biol 23: 9327-9337. PMID: 14645542.
-
Ash PE, Zhang YJ, Roberts CM, Saldi T, Hutter H, Buratti E, Petrucelli L, Link CD. Neurotoxic effects of TDP-43 overexpression in C. elegans. Hum Mol Genet. 2010 Aug 15; 19(16):3206-18
Saldi T, Wilusz C, MacMorris M, Blumenthal T. Functional Redundance of Worm Spliceosomal Proteins U1A and U2B. Proc Natl Acad Sci USA. 2007 Jun 5; 104(23):9753-7.
Van Auken K, Weaver D, Robertson B, Sundaram M, Saldi T, Edgar L, Elling U, Lee M, Boese Q, Wood WB. Roles of Homothorax/Meis/Prep homolog UNC-62 and Exd/Pbx homologs CEH-20 and CEH-40 in C. elegans embrogenesis. Development. 2002 Nov; 129(22):5255-68.
Novak, A.E., Taylor, A.D., Pineda, R.H., Lasda, E.L., Wright, M.A., and Ribera, A.B. 2006. Embryonic and larval expression of zebrafish voltage-gated sodium channel alpha-subunit genes. Dev. Dyn 235: 1962-1973. PMID: 16615064.
-
Saldi T, Gonzales P, LaRocca T, Link CD. Neurodegeneration, heterochromatin, and double-stranded RNA. Journal of Experimental Neuroscience. 2019 Feb 14;13.
Saldi T*, Cortazar MA*, Sheridan RM*, Bentley DL. Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol. 2016 Jun 19; 428(12):2623-35. *First co-authors.
Blumenthal T, Davis P, Garrido-Lecca A. Operon and non-operon gene clusters in the C. elegans genome. WormBook. 2015 Apr 28:1-20.
Lasda E, Parker R. Circular RNAs: diversity of form and function. RNA. 2014 Dec;20(12):1829-42.
Link CD, Saldi T. Cell death by glutamate repeats. Science. 2012 Feb 24; 335(6071):926-7.
Lasda EL, Blumenthal T. Trans-splicing. Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):417-34.
Garcia-Blanco, M.A., Baraniak, A.P., and Lasda, E.L. 2004. Alternative splicing in disease and therapy. Nat. Biotechnol 22: 535-546. PMID: 15122293.
Mistry, N., Harrington, W., Lasda, E., Wagner, E.J., and Garcia-Blanco, M.A. 2003. Of urchins and men: evolution of an alternative splicing unit in fibroblast growth factor receptor genes. RNA 9: 209-217. PMID: 12554864.
Niranjanakumari, S., Lasda, E., Brazas, R., and Garcia-Blanco, M.A. 2002. Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo. Methods 26: 182-190. PMID: 12054895.