James Riley Broach - Publications

1984-2012 Molecular Biology Princeton University, Princeton, NJ 
 2012- Penn State Hershey College of Medicine 
signaling pathways

58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
2018 Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, ... ... Broach JR, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/s41588-018-0195-8  1
2017 Chereji RV, Bharatula V, Elfving N, Blomberg J, Larsson M, Morozov AV, Broach JR, Björklund S. Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly. Nucleic Acids Research. PMID 28575439 DOI: 10.1093/nar/gkx491  1
2015 Rutledge MT, Russo M, Belton JM, Dekker J, Broach JR. The yeast genome undergoes significant topological reorganization in quiescence. Nucleic Acids Research. 43: 8299-313. PMID 26202961 DOI: 10.1093/nar/gkv723  1
2014 Elfving N, Chereji RV, Bharatula V, Björklund S, Morozov AV, Broach JR. A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress. Nucleic Acids Research. 42: 5468-82. PMID 24598258 DOI: 10.1093/nar/gku176  1
2014 Su XW, Broach JR, Connor JR, Gerhard GS, Simmons Z. Genetic heterogeneity of amyotrophic lateral sclerosis: implications for clinical practice and research. Muscle & Nerve. 49: 786-803. PMID 24488689 DOI: 10.1002/mus.24198  1
2013 Shor E, Fox CA, Broach JR. The yeast environmental stress response regulates mutagenesis induced by proteotoxic stress. Plos Genetics. 9: e1003680. PMID 23935537 DOI: 10.1371/journal.pgen.1003680  1
2013 Xu YF, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD. Nucleotide degradation and ribose salvage in yeast. Molecular Systems Biology. 9: 665. PMID 23670538 DOI: 10.1038/msb.2013.21  1
2013 Petrenko N, Chereji RV, McClean MN, Morozov AV, Broach JR. Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses. Molecular Biology of the Cell. 24: 2045-57. PMID 23615444 DOI: 10.1091/mbc.E12-12-0870  1
2013 Bravim F, Lippman SI, da Silva LF, Souza DT, Fernandes AA, Masuda CA, Broach JR, Fernandes PM. High hydrostatic pressure activates gene expression that leads to ethanol production enhancement in a Saccharomyces cerevisiae distillery strain. Applied Microbiology and Biotechnology. 97: 2093-107. PMID 22915193 DOI: 10.1007/s00253-012-4356-x  1
2012 Bravim F, da Silva LF, Souza DT, Lippman SI, Broach JR, Fernandes AA, Fernandes PM. High hydrostatic pressure activates transcription factors involved in Saccharomyces cerevisiae stress tolerance. Current Pharmaceutical Biotechnology. 13: 2712-20. PMID 23072392  1
2012 Xu YF, Zhao X, Glass DS, Absalan F, Perlman DH, Broach JR, Rabinowitz JD. Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation. Molecular Cell. 48: 52-62. PMID 22902555 DOI: 10.1016/j.molcel.2012.07.013  1
2011 Tsitron J, Ault AD, Broach JR, Morozov AV. Decoding complex chemical mixtures with a physical model of a sensor array. Plos Computational Biology. 7: e1002224. PMID 22046111 DOI: 10.1371/journal.pcbi.1002224  1
2011 Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR. Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters. Molecular Biology of the Cell. 22: 2106-18. PMID 21508315 DOI: 10.1091/mbc.E10-10-0826  1
2011 Klosinska MM, Crutchfield CA, Bradley PH, Rabinowitz JD, Broach JR. Yeast cells can access distinct quiescent states. Genes & Development. 25: 336-49. PMID 21289062 DOI: 10.1101/gad.2011311  1
2010 Talarek N, Cameroni E, Jaquenoud M, Luo X, Bontron S, Lippman S, Devgan G, Snyder M, Broach JR, De Virgilio C. Initiation of the TORC1-regulated G0 program requires Igo1/2, which license specific mRNAs to evade degradation via the 5'-3' mRNA decay pathway. Molecular Cell. 38: 345-55. PMID 20471941 DOI: 10.1016/j.molcel.2010.02.039  1
2009 Shor E, Warren CL, Tietjen J, Hou Z, Müller U, Alborelli I, Gohard FH, Yemm AI, Borisov L, Broach JR, Weinreich M, Nieduszynski CA, Ansari AZ, Fox CA. The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication Plos Genetics. 5. PMID 19997491 DOI: 10.1371/journal.pgen.1000755  1
2009 Lippman SI, Broach JR. Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6. Proceedings of the National Academy of Sciences of the United States of America. 106: 19928-33. PMID 19901341 DOI: 10.1073/pnas.0907027106  1
2009 Zawadzki KA, Morozov AV, Broach JR. Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae. Molecular Biology of the Cell. 20: 3503-13. PMID 19494041 DOI: 10.1091/mbc.E09-02-0111  1
2009 Evans BJ, Wang Z, Broach JR, Oishi S, Fujii N, Peiper SC. Expression of CXCR4, a G-protein-coupled receptor for CXCL12 in yeast identification of new-generation inverse agonists. Methods in Enzymology. 460: 399-412. PMID 19446737 DOI: 10.1016/S0076-6879(09)05220-3  1
2009 Freckleton G, Lippman SI, Broach JR, Tavazoie S. Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions. Plos Genetics. 5: e1000449. PMID 19360118 DOI: 10.1371/journal.pgen.1000449  1
2009 Zaman S, Lippman SI, Schneper L, Slonim N, Broach JR. Glucose regulates transcription in yeast through a network of signaling pathways. Molecular Systems Biology. 5: 245. PMID 19225458 DOI: 10.1038/msb.2009.2  1
2009 Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. Plos Computational Biology. 5: e1000257. PMID 19119411 DOI: 10.1371/journal.pcbi.1000257  1
2008 Torti FM, Altieri D, Broach J, Fan H, Lotze M, Manfredi J, Matrisian L, Yu D, Giaccia A. Ph.D. training in cancer biology Cancer Research. 68: 9122-9124. PMID 19010881 DOI: 10.1158/0008-5472.CAN-08-2626  1
2008 Tan MP, Smith EN, Broach JR, Floudas CA. Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. Bmc Bioinformatics. 9: 268. PMID 18538024 DOI: 10.1186/1471-2105-9-268  1
2008 Zaman S, Lippman SI, Zhao X, Broach JR. How Saccharomyces responds to nutrients. Annual Review of Genetics. 42: 27-81. PMID 18303986 DOI: 10.1146/annurev.genet.41.110306.130206  1
2007 Tan MP, Broach JR, Floudas CA. Evaluation of normalization and pre-clustering issues in a novel clustering approach: global optimum search with enhanced positioning. Journal of Bioinformatics and Computational Biology. 5: 895-913. PMID 17787062 DOI: 10.1142/S0219720007002941  1
2007 Yorimitsu T, Zaman S, Broach JR, Klionsky DJ. Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae. Molecular Biology of the Cell. 18: 4180-9. PMID 17699586 DOI: 10.1091/mbc.E07-05-0485  1
2007 Urban J, Soulard A, Huber A, Lippman S, Mukhopadhyay D, Deloche O, Wanke V, Anrather D, Ammerer G, Riezman H, Broach JR, De Virgilio C, Hall MN, Loewith R. Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Molecular Cell. 26: 663-74. PMID 17560372 DOI: 10.1016/j.molcel.2007.04.020  1
2007 McClean MN, Mody A, Broach JR, Ramanathan S. Cross-talk and decision making in MAP kinase pathways. Nature Genetics. 39: 409-14. PMID 17259986 DOI: 10.1038/ng1957  1
2006 Zawadzki K, Broach J. A rapid technique for the visualization of live immobilized yeast cells. Journal of Visualized Experiments : Jove. 84. PMID 18704180 DOI: 10.3791/84  0.01
2006 Guldal CG, Broach J. Assay for adhesion and agar invasion in S. cerevisiae. Journal of Visualized Experiments : Jove. 64. PMID 18704175 DOI: 10.3791/64  0.01
2006 Wang ZX, Broach JR, Peiper SC. Functional expression of CXCR4 in Saccharomyces cerevisiae in the development of powerful tools for the pharmacological characterization of CXCR4. Methods in Molecular Biology (Clifton, N.J.). 332: 115-27. PMID 16878688 DOI: 10.1385/1-59745-048-0:115  1
2006 Xu EY, Zawadzki KA, Broach JR. Single-cell observations reveal intermediate transcriptional silencing states. Molecular Cell. 23: 219-29. PMID 16857588 DOI: 10.1016/j.molcel.2006.05.035  1
2006 Houston PL, Broach JR. The dynamics of homologous pairing during mating type interconversion in budding yeast. Plos Genetics. 2: e98. PMID 16789829 DOI: 10.1371/journal.pgen.0020098  1
2006 Ault AD, Broach JR. Creation of GPCR-based chemical sensors by directed evolution in yeast. Protein Engineering, Design & Selection : Peds. 19: 1-8. PMID 16263727 DOI: 10.1093/protein/gzi069  1
2006 Niida A, Wang Z, Tomita K, Oishi S, Tamamura H, Otaka A, Navenot JM, Broach JR, Peiper SC, Fujii N. Design and synthesis of downsized metastin (45-54) analogs with maintenance of high GPR54 agonistic activity. Bioorganic & Medicinal Chemistry Letters. 16: 134-7. PMID 16242330 DOI: 10.1016/j.bmcl.2005.09.054  1
2005 Xu EY, Bi X, Holland MJ, Gottschling DE, Broach JR. Mutations in the nucleosome core enhance transcriptional silencing. Molecular and Cellular Biology. 25: 1846-59. PMID 15713639 DOI: 10.1128/MCB.25.5.1846-1859.2005  1
2004 Schneper L, Düvel K, Broach JR. Sense and sensibility: nutritional response and signal integration in yeast. Current Opinion in Microbiology. 7: 624-30. PMID 15556035 DOI: 10.1016/j.mib.2004.10.002  1
2004 Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes & Development. 18: 2491-505. PMID 15466158 DOI: 10.1101/gad.1228804  1
2004 Wang Y, Pierce M, Schneper L, Güldal CG, Zhang X, Tavazoie S, Broach JR. Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. Plos Biology. 2: E128. PMID 15138498 DOI: 10.1371/journal.pbio.0020128  1
2004 Houston P, Simon PJ, Broach JR. The Saccharomyces cerevisiae recombination enhancer biases recombination during interchromosomal mating-type switching but not in interchromosomal homologous recombination. Genetics. 166: 1187-97. PMID 15082540  1
2004 Masui T, Doi R, Mori T, Toyoda E, Koizumi M, Kami K, Ito D, Peiper SC, Broach JR, Oishi S, Niida A, Fujii N, Imamura M. Metastin and its variant forms suppress migration of pancreatic cancer cells. Biochemical and Biophysical Research Communications. 315: 85-92. PMID 15013429 DOI: 10.1016/j.bbrc.2004.01.021  1
2004 Schneper L, Krauss A, Miyamoto R, Fang S, Broach JR. The Ras/protein kinase A pathway acts in parallel with the Mob2/Cbk1 pathway to effect cell cycle progression and proper bud site selection. Eukaryotic Cell. 3: 108-20. PMID 14871942  1
2003 Lin X, Floudas CA, Wang Y, Broach JR. Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data. Biotechnology and Bioengineering. 84: 864-86. PMID 14708127 DOI: 10.1002/bit.10844  1
2003 Fujii N, Oishi S, Hiramatsu K, Araki T, Ueda S, Tamamura H, Otaka A, Kusano S, Terakubo S, Nakashima H, Broach JA, Trent JO, Wang ZX, Peiper SC. Molecular-size reduction of a potent CXCR4-chemokine antagonist using orthogonal combination of conformation- and sequence-based libraries. Angewandte Chemie (International Ed. in English). 42: 3251-3. PMID 12876735 DOI: 10.1002/anie.200351024  1
2003 Alvarez Arias D, Navenot JM, Zhang WB, Broach J, Peiper SC. Constitutive activation of CCR5 and CCR2 induced by conformational changes in the conserved TXP motif in transmembrane helix 2. The Journal of Biological Chemistry. 278: 36513-21. PMID 12837756 DOI: 10.1074/jbc.M303739200  1
2003 Düvel K, Santhanam A, Garrett S, Schneper L, Broach JR. Multiple roles of Tap42 in mediating rapamycin-induced transcriptional changes in yeast. Molecular Cell. 11: 1467-78. PMID 12820961  1
2003 Schedl P, Broach JR. Making good neighbors: the right fence for the right job. Nature Structural Biology. 10: 241-3. PMID 12660719 DOI: 10.1038/nsb0403-241  1
2003 Yu Q, Qiu R, Foland TB, Griesen D, Galloway CS, Chiu YH, Sandmeier J, Broach JR, Bi X. Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression. Nucleic Acids Research. 31: 1224-33. PMID 12582242 DOI: 10.1093/nar/gkg200  1
2002 Simon P, Houston P, Broach J. Directional bias during mating type switching in Saccharomyces is independent of chromosomal architecture Embo Journal. 21: 2282-2291. PMID 11980725 DOI: 10.1093/emboj/21.9.2282  1
2002 Zhang WB, Navenot JM, Haribabu B, Tamamura H, Hiramatu K, Omagari A, Pei G, Manfredi JP, Fujii N, Broach JR, Peiper SC. A point mutation that confers constitutive activity to CXCR4 reveals that T140 is an inverse agonist and that AMD3100 and ALX40-4C are weak partial agonists. The Journal of Biological Chemistry. 277: 24515-21. PMID 11923301 DOI: 10.1074/jbc.M200889200  1
2000 Wu J, Tolstykh T, Lee J, Boyd K, Stock JB, Broach JR. Carboxyl methylation of the phosphoprotein phosphatase 2A catalytic subunit promotes its functional association with regulatory subunits in vivo. The Embo Journal. 19: 5672-81. PMID 11060018 DOI: 10.1093/emboj/19.21.5672  1
1990 Fedor-Chaiken M, Deschenes RJ, Broach JR. SRV2, a gene required for RAS activation of adenylate cyclase in yeast Cell. 61: 329-340. PMID 2158860 DOI: 10.1016/0092-8674(90)90813-T  1
1990 Broach JR, Deschenes RJ. The function of ras genes in Saccharomyces cerevisiae Advances in Cancer Research. 54: 79-139. PMID 2153328  1
1990 Deschenes RJ, Resh MD, Broach JR. Acylation and prenylation of proteins Current Opinion in Cell Biology. 2: 1108-1113. PMID 2099805 DOI: 10.1016/0955-0674(90)90164-A  1
1989 Deschenes RJ, Stimmel JB, Clarke S, Stock J, Broach JR. RAS2 protein of Saccharomyces cerevisiae is methyl-esterified at its carboxyl terminus Journal of Biological Chemistry. 264: 11865-11873. PMID 2663844  1
1987 Deschenes RJ, Broach JR. Fatty acylation is important but not essential for Saccharomyces cerevisiae RAS function Molecular and Cellular Biology. 7: 2344-2351. PMID 3302674  1
1975 Cieslà Z, Salvatore F, Broach JR, Artz SW, Ames BN. Histidine regulation in Salmonella typhimurium. XVI. A sensitive radiochemical assay for histidinol dehydrogenase. Analytical Biochemistry. 63: 44-55. PMID 1089301  0.4
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