Manny Ares - Publications

Molecular Cell and Developmental Biology University of California, Santa Cruz, Santa Cruz, CA, United States 
Molecular Biology, Genetics, Cell Biology

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Talkish J, Igel H, Perriman RJ, Shiue L, Katzman S, Munding EM, Shelansky R, Donohue JP, Ares M. Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome. Plos Genetics. 15: e1008249. PMID 31437148 DOI: 10.1371/journal.pgen.1008249  0.32
2018 Lucas BA, Lavi E, Shiue L, Cho H, Katzman S, Miyoshi K, Siomi MC, Carmel L, Ares M, Maquat LE. Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay. Proceedings of the National Academy of Sciences of the United States of America. PMID 29339519 DOI: 10.1073/pnas.1715531115  0.32
2017 Fagg WS, Liu N, Fair JH, Shiue L, Katzman S, Donohue JP, Ares M. Autogenous cross-regulation of Quaking mRNA processing and translation balances Quaking functions in splicing and translation. Genes & Development. PMID 29021242 DOI: 10.1101/gad.302059.117  0.32
2016 Batra R, Stark TJ, Clark E, Belzile JP, Wheeler EC, Yee BA, Huang H, Gelboin-Burkhart C, Huelga SC, Aigner S, Roberts BT, Bos TJ, Sathe S, Donohue JP, Rigo F, ... Ares M, et al. RNA-binding protein CPEB1 remodels host and viral RNA landscapes. Nature Structural & Molecular Biology. PMID 27775709 DOI: 10.1038/nsmb.3310  0.32
2016 Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, Chang J, Donohue JP, Shiue L, ... ... Ares M, et al. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nature Communications. 7: 12143. PMID 27378374 DOI: 10.1038/ncomms12143  0.32
2016 Johnson TL, Ares M. SMITten by the Speed of Splicing. Cell. 165: 265-7. PMID 27058658 DOI: 10.1016/j.cell.2016.03.035  0.32
2016 de Bruin RG, Shiue L, Prins J, de Boer HC, Singh A, Fagg WS, van Gils JM, Duijs JM, Katzman S, Kraaijeveld AO, Böhringer S, Leung WY, Kielbasa SM, Donahue JP, van der Zande PH, ... ... Ares M, et al. Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. Nature Communications. 7: 10846. PMID 27029405 DOI: 10.1038/ncomms10846  0.32
2015 Ares M. Coffee with Ribohipster. Rna (New York, N.Y.). 21: 494-6. PMID 25780110 DOI: 10.1261/rna.050468.115  0.32
2014 Ares M. Methods for processing high-throughput RNA sequencing data. Cold Spring Harbor Protocols. 2014: 1139-48. PMID 25368318 DOI: 10.1101/pdb.top083352  0.32
2014 Ares M. Basic quantitative polymerase chain reaction using real-time fluorescence measurements. Cold Spring Harbor Protocols. 2014: pdb.prot080903. PMID 25275107 DOI: 10.1101/pdb.prot080903  0.32
2014 Fu XD, Ares M. Context-dependent control of alternative splicing by RNA-binding proteins. Nature Reviews. Genetics. 15: 689-701. PMID 25112293 DOI: 10.1038/nrg3778  0.32
2014 Paz I, Kosti I, Ares M, Cline M, Mandel-Gutfreund Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Research. 42: W361-7. PMID 24829458 DOI: 10.1093/nar/gku406  0.32
2014 Ares M. Methods for processing microarray data. Cold Spring Harbor Protocols. 2014: 225-9. PMID 24492782 DOI: 10.1101/pdb.prot080507  0.32
2014 Ares M. Tips on hybridizing, washing, and scanning affymetrix microarrays. Cold Spring Harbor Protocols. 2014: 219-24. PMID 24492781 DOI: 10.1101/pdb.prot080499  0.32
2014 Ares M. Scanning microarray slides. Cold Spring Harbor Protocols. 2014: 214-8. PMID 24492780 DOI: 10.1101/pdb.prot080481  0.32
2014 Ares M. Microarray slide hybridization using fluorescently labeled cDNA. Cold Spring Harbor Protocols. 2014: 124-9. PMID 24371320 DOI: 10.1101/pdb.prot080135  0.32
2014 Ares M. Preparation of fluorescent-dye-labeled cDNA from RNA for microarray hybridization. Cold Spring Harbor Protocols. 2014: 119-23. PMID 24371319 DOI: 10.1101/pdb.prot080127  0.32
2013 Nilsen TW, Rio DC, Ares M. High-yield synthesis of RNA using T7 RNA polymerase and plasmid DNA or oligonucleotide templates. Cold Spring Harbor Protocols. 2013. PMID 24184762 DOI: 10.1101/pdb.prot078535  0.32
2013 Turner R, Shefer K, Ares M. Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7). Rna (New York, N.Y.). 19: 1857-63. PMID 24141619 DOI: 10.1261/rna.042374.113  0.32
2013 Munding EM, Shiue L, Katzman S, Donohue JP, Ares M. Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Molecular Cell. 51: 338-48. PMID 23891561 DOI: 10.1016/j.molcel.2013.06.012  0.32
2013 Effenberger KA, Perriman RJ, Bray WM, Lokey RS, Ares M, Jurica MS. A high-throughput splicing assay identifies new classes of inhibitors of human and yeast spliceosomes Journal of Biomolecular Screening. 18: 1110-1120. PMID 23771823 DOI: 10.1177/1087057113493117  0.32
2013 Ares M. Fragmentation of whole-transcriptome RNA using E. coli RNase III. Cold Spring Harbor Protocols. 2013: 479-81. PMID 23637372 DOI: 10.1101/pdb.prot074369  0.32
2013 Pandit S, Zhou Y, Shiue L, Coutinho-Mansfield G, Li H, Qiu J, Huang J, Yeo GW, Ares M, Fu XD. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Molecular Cell. 50: 223-35. PMID 23562324 DOI: 10.1016/j.molcel.2013.03.001  0.32
2013 Hall MP, Nagel RJ, Fagg WS, Shiue L, Cline MS, Perriman RJ, Donohue JP, Ares M. Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. Rna (New York, N.Y.). 19: 627-38. PMID 23525800 DOI: 10.1261/rna.038422.113  0.32
2013 Pistoni M, Shiue L, Cline MS, Bortolanza S, Neguembor MV, Xynos A, Ares M, Gabellini D. Rbfox1 downregulation and altered calpain 3 splicing by FRG1 in a mouse model of Facioscapulohumeral muscular dystrophy (FSHD). Plos Genetics. 9: e1003186. PMID 23300487 DOI: 10.1371/journal.pgen.1003186  0.32
2012 Ares M. Isolation of total RNA from yeast cell cultures. Cold Spring Harbor Protocols. 2012: 1082-6. PMID 23028070 DOI: 10.1101/pdb.prot071456  0.32
2012 Beuck C, Qu S, Fagg WS, Ares M, Williamson JR. Structural analysis of the quaking homodimerization interface. Journal of Molecular Biology. 423: 766-81. PMID 22982292 DOI: 10.1016/j.jmb.2012.08.027  0.32
2012 Ares M. Bacterial RNA isolation. Cold Spring Harbor Protocols. 2012: 1024-7. PMID 22949721 DOI: 10.1101/pdb.prot071068  0.32
2012 Charizanis K, Lee KY, Batra R, Goodwin M, Zhang C, Yuan Y, Shiue L, Cline M, Scotti MM, Xia G, Kumar A, Ashizawa T, Clark HB, Kimura T, Takahashi MP, ... ... Ares M, et al. Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron. 75: 437-50. PMID 22884328 DOI: 10.1016/j.neuron.2012.05.029  0.32
2012 Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M, Yeo GW. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Reports. 1: 167-78. PMID 22574288 DOI: 10.1016/j.celrep.2012.02.001  0.32
2012 Suenaga K, Lee KY, Nakamori M, Tatsumi Y, Takahashi MP, Fujimura H, Jinnai K, Yoshikawa H, Du H, Ares M, Swanson MS, Kimura T. Muscleblind-like 1 knockout mice reveal novel splicing defects in the myotonic dystrophy brain. Plos One. 7: e33218. PMID 22427994 DOI: 10.1371/journal.pone.0033218  0.32
2012 Gehman LT, Meera P, Stoilov P, Shiue L, O'Brien JE, Meisler MH, Ares M, Otis TS, Black DL. The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes & Development. 26: 445-60. PMID 22357600 DOI: 10.1101/gad.182477.111  0.32
2011 Anderson WA, Amasino RM, Ares M, Banerjee U, Bartel B, Corces VG, Drennan CL, Elgin SC, Epstein IR, Fanning E, Guillette LJ, Handelsman J, Hatfull GF, Hoy RR, Kelley D, et al. Competencies: a cure for pre-med curriculum. Science (New York, N.Y.). 334: 760-1. PMID 22076362 DOI: 10.1126/science.334.6057.760-b  0.32
2011 Perriman RJ, Ares M. Alternative splicing variability: exactly how similar are two identical cells? Molecular Systems Biology. 7: 505. PMID 21734644 DOI: 10.1038/msb.2011.44  0.32
2011 Gehman LT, Stoilov P, Maguire J, Damianov A, Lin CH, Shiue L, Ares M, Mody I, Black DL. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nature Genetics. 43: 706-11. PMID 21623373 DOI: 10.1038/ng.841  0.32
2011 Mishra SK, Ammon T, Popowicz GM, Krajewski M, Nagel RJ, Ares M, Holak TA, Jentsch S. Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature. 474: 173-8. PMID 21614000 DOI: 10.1038/nature10143  0.32
2010 Munding EM, Igel AH, Shiue L, Dorighi KM, Treviño LR, Ares M. Integration of a splicing regulatory network within the meiotic gene expression program of Saccharomyces cerevisiae. Genes & Development. 24: 2693-704. PMID 21123654 DOI: 10.1101/gad.1977410  0.32
2010 Perriman R, Ares M. Invariant U2 snRNA nucleotides form a stem loop to recognize the intron early in splicing. Molecular Cell. 38: 416-27. PMID 20471947 DOI: 10.1016/j.molcel.2010.02.036  0.32
2010 Du H, Cline MS, Osborne RJ, Tuttle DL, Clark TA, Donohue JP, Hall MP, Shiue L, Swanson MS, Thornton CA, Ares M. Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy. Nature Structural & Molecular Biology. 17: 187-93. PMID 20098426 DOI: 10.1038/nsmb.1720  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Determining the yield and quality of purified RNA Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.top82  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Enrichment of poly(A)+ mRNA using immobilized oligo(dT) Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5454  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Polyacrylamide gel electrophoresis of RNA Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5444  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Removal of DNA from RNA Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5443  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Removal of ribosomal subunits (and rRNA) from cytoplasmic extracts before solubilization with SDS and deproteinization Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5442  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Preparation of cytoplasmic and nuclear RNA from tissue culture cells Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5441  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Ethanol precipitation of RNA and the use of carriers Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5440  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Purification of RNA using TRIzol (TRI Reagent) Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5439  0.32
2010 Rio DC, Ares M, Hannon GJ, Nilsen TW. Purification of RNA by SDS solubilization and phenol extraction Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.prot5438  0.32
2010 Rio DC, Ares MJ, Hannon GJ, Nilsen TW. Guidelines for the use of RNA purification kits Cold Spring Harbor Protocols. 5. DOI: 10.1101/pdb.ip79  0.32
2009 Chawla G, Lin CH, Han A, Shiue L, Ares M, Black DL. Sam68 regulates a set of alternatively spliced exons during neurogenesis. Molecular and Cellular Biology. 29: 201-13. PMID 18936165 DOI: 10.1128/MCB.01349-08  0.32
2008 Ares M, Chakrabarti K. Stuttering against marginotomy. Nature Structural & Molecular Biology. 15: 18-9. PMID 18176550 DOI: 10.1038/nsmb0108-18  0.32
2008 Lauriat TL, Shiue L, Haroutunian V, Verbitsky M, Ares M, Ospina L, McInnes LA. Developmental expression profile of quaking, a candidate gene for schizophrenia, and its target genes in human prefrontal cortex and hippocampus shows regional specificity. Journal of Neuroscience Research. 86: 785-96. PMID 17918747 DOI: 10.1002/jnr.21534  0.32
2007 Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. Rna (New York, N.Y.). 13: 1923-39. PMID 17901154 DOI: 10.1261/rna.751807  0.32
2007 Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M, Black DL. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes & Development. 21: 1636-52. PMID 17606642 DOI: 10.1101/gad.1558107  0.32
2007 Perriman RJ, Ares M. Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. Genes & Development. 21: 811-20. PMID 17403781 DOI: 10.1101/gad.1524307  0.32
2007 Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes & Development. 21: 708-18. PMID 17369403 DOI: 10.1101/gad.1525507  0.32
2007 Ares M. Sing the genome electric: excited cells adjust their splicing. Plos Biology. 5: e55. PMID 17298182 DOI: 10.1371/journal.pbio.0050055  0.32
2006 Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443: 167-72. PMID 16915236 DOI: 10.1038/nature05113  0.32
2006 Li C, Kato M, Shiue L, Shively JE, Ares M, Lin RJ. Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. Cancer Research. 66: 1990-9. PMID 16488998 DOI: 10.1158/0008-5472.CAN-05-2593  0.32
2006 Davis CA, Ares M. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 103: 3262-7. PMID 16484372 DOI: 10.1073/pnas.0507783103  0.32
2006 Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. Plos Computational Biology. 2: e4. PMID 16424921 DOI: 10.1371/journal.pcbi.0020004  0.32
2006 Combs DJ, Nagel RJ, Ares M, Stevens SW. Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Molecular and Cellular Biology. 26: 523-34. PMID 16382144 DOI: 10.1128/MCB.26.2.523-534.2006  0.32
2005 Srinivasan K, Shiue L, Hayes JD, Centers R, Fitzwater S, Loewen R, Edmondson LR, Bryant J, Smith M, Rommelfanger C, Welch V, Clark TA, Sugnet CW, Howe KJ, Mandel-Gutfreund Y, ... Ares M, et al. Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods (San Diego, Calif.). 37: 345-59. PMID 16314264 DOI: 10.1016/j.ymeth.2005.09.007  0.32
2005 Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark TA, Chong JL, Chang TH, Squazzo S, Hartzog G, Ares M. Exploring functional relationships between components of the gene expression machinery. Nature Structural & Molecular Biology. 12: 175-82. PMID 15702072 DOI: 10.1038/nsmb891  0.32
2005 Ares M, Proudfoot NJ. The Spanish connection: Transcription and mRNA processing get even closer Cell. 120: 163-166. PMID 15680322 DOI: 10.1016/j.cell.2005.01.002  0.32
2005 Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. Plos Biology. 3: e5. PMID 15630477 DOI: 10.1371/journal.pbio.0030005  0.32
2003 Howe KJ, Kane CM, Ares M. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. Rna (New York, N.Y.). 9: 993-1006. PMID 12869710 DOI: 10.1261/rna.5390803  0.32
1987 Gerbi SA, Jeppesen C, Stebbins-Boaz B, Ares M. Evolution of eukaryotic rRNA: constraints imposed by RNA interactions. Cold Spring Harbor Symposia On Quantitative Biology. 52: 709-19. PMID 3454284 DOI: 10.1101/SQB.1987.052.01.080  0.32
1985 Lindgren V, Ares M, Weiner AM, Francke U. Human genes for U2 small nuclear RNA map to a major adenovirus 12 modification site on chromosome 17 Nature. 314: 115-116. PMID 2579339 DOI: 10.1038/314115a0  0.32
1985 Yuo CY, Ares M, Weiner AM. Sequences required for 3′ end formation of human U2 small nuclear RNA Cell. 42: 193-202. PMID 2410138 DOI: 10.1016/S0092-8674(85)80115-X  0.32
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