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Genetic Variants Implicate Dual Oxidase-2 in Familial and Sporadic Nonmedullary Thyroid Cancer.

Bann DV, Jin Q, Sheldon KE, Houser KR, Nguyen L, Warrick JI, Baker MJ, Broach JR, Gerhard GS, Goldenberg D.

Cancer Res. 2019 Nov 1;79(21):5490-5499. doi: 10.1158/0008-5472.CAN-19-0721. Epub 2019 Sep 9.


Genetically Modified Labeling Policies: Moving Forward or Backward?

Borges BJP, Arantes OMN, Fernandes AAR, Broach JR, Fernandes PMB.

Front Bioeng Biotechnol. 2018 Nov 27;6:181. doi: 10.3389/fbioe.2018.00181. eCollection 2018. Review.


CD4 T cells control development and maintenance of brain-resident CD8 T cells during polyomavirus infection.

Mockus TE, Shwetank, Lauver MD, Ren HM, Netherby CS, Salameh T, Kawasawa YI, Yue F, Broach JR, Lukacher AE.

PLoS Pathog. 2018 Oct 29;14(10):e1007365. doi: 10.1371/journal.ppat.1007365. eCollection 2018 Oct.


Integrative detection and analysis of structural variation in cancer genomes.

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, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Oct;50(10):1388-1398. doi: 10.1038/s41588-018-0195-8. Epub 2018 Sep 10.


Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism.

Conlon EG, Fagegaltier D, Agius P, Davis-Porada J, Gregory J, Hubbard I, Kang K, Kim D; New York Genome Center ALS Consortium, Phatnani H, Kwan J, Sareen D, Broach JR, Simmons Z, Arcila-Londono X, Lee EB, Van Deerlin VM, Shneider NA, Fraenkel E, Ostrow LW, Baas F, Zaitlen N, Berry JD, Malaspina A, Fratta P, Cox GA, Thompson LM, Finkbeiner S, Dardiotis E, Miller TM, Chandran S, Pal S, Hornstein E, MacGowan DJ, Heiman-Patterson T, Hammell MG, Patsopoulos NA, Dubnau J, Nath A, Phatnani H, Shneider NA, Manley JL.

Elife. 2018 Jul 13;7. pii: e37754. doi: 10.7554/eLife.37754.


A Possible Role for Platelet-Activating Factor Receptor in Amyotrophic Lateral Sclerosis Treatment.

Briones MRS, Snyder AM, Ferreira RC, Neely EB, Connor JR, Broach JR.

Front Neurol. 2018 Feb 6;9:39. doi: 10.3389/fneur.2018.00039. eCollection 2018.


Phosphorylation and nuclear transit modulate the balance between normal function and terminal aggregation of the yeast RNA-binding protein Ssd1.

Kurischko C, Broach JR.

Mol Biol Cell. 2017 Nov 1;28(22):3057-3069. doi: 10.1091/mbc.E17-02-0100. Epub 2017 Sep 6.


Expansion of C9ORF72 in amyotrophic lateral sclerosis correlates with brain-computer interface performance.

Geronimo A, Sheldon KE, Broach JR, Simmons Z, Schiff SJ.

Sci Rep. 2017 Aug 21;7(1):8875. doi: 10.1038/s41598-017-08857-3.


Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing.

Coble JL, Sheldon KE, Yue F, Salameh TJ, Harris LR III, Deiling S, Ruggiero FM, Eshelman MA, Yochum GS, Koltun WA, Gerhard GS, Broach JR.

Hum Mol Genet. 2017 Aug 15;26(16):3212-3220. doi: 10.1093/hmg/ddx204.


Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly.

Chereji RV, Bharatula V, Elfving N, Blomberg J, Larsson M, Morozov AV, Broach JR, Björklund S.

Nucleic Acids Res. 2017 Sep 6;45(15):8806-8821. doi: 10.1093/nar/gkx491.


Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome.

Schiff SJ, Kiwanuka J, Riggio G, Nguyen L, Mu K, Sproul E, Bazira J, Mwanga-Amumpaire J, Tumusiime D, Nyesigire E, Lwanga N, Bogale KT, Kapur V, Broach JR, Morton SU, Warf BC, Poss M.

Front Med (Lausanne). 2016 Jun 13;3:22. doi: 10.3389/fmed.2016.00022. eCollection 2016.


The yeast genome undergoes significant topological reorganization in quiescence.

Rutledge MT, Russo M, Belton JM, Dekker J, Broach JR.

Nucleic Acids Res. 2015 Sep 30;43(17):8299-313. doi: 10.1093/nar/gkv723. Epub 2015 Jul 21.


A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress.

Elfving N, Chereji RV, Bharatula V, Björklund S, Morozov AV, Broach JR.

Nucleic Acids Res. 2014 May;42(9):5468-82. doi: 10.1093/nar/gku176. Epub 2014 Mar 5.


Genetic heterogeneity of amyotrophic lateral sclerosis: implications for clinical practice and research.

Su XW, Broach JR, Connor JR, Gerhard GS, Simmons Z.

Muscle Nerve. 2014 Jun;49(6):786-803. doi: 10.1002/mus.24198. Epub 2014 Apr 8. Review.


The yeast environmental stress response regulates mutagenesis induced by proteotoxic stress.

Shor E, Fox CA, Broach JR.

PLoS Genet. 2013;9(8):e1003680. doi: 10.1371/journal.pgen.1003680. Epub 2013 Aug 1.


Nucleotide degradation and ribose salvage in yeast.

Xu YF, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD.

Mol Syst Biol. 2013 May 14;9:665. doi: 10.1038/msb.2013.21.


Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses.

Petrenko N, Chereji RV, McClean MN, Morozov AV, Broach JR.

Mol Biol Cell. 2013 Jun;24(12):2045-57. doi: 10.1091/mbc.E12-12-0870. Epub 2013 Apr 24.


High hydrostatic pressure activates transcription factors involved in Saccharomyces cerevisiae stress tolerance.

Bravim F, da Silva LF, Souza DT, Lippman SI, Broach JR, Fernandes AA, Fernandes PM.

Curr Pharm Biotechnol. 2012 Dec;13(15):2712-20.


Nutritional control of growth and development in yeast.

Broach JR.

Genetics. 2012 Sep;192(1):73-105. doi: 10.1534/genetics.111.135731. Review.


High hydrostatic pressure activates gene expression that leads to ethanol production enhancement in a Saccharomyces cerevisiae distillery strain.

Bravim F, Lippman SI, da Silva LF, Souza DT, Fernandes AA, Masuda CA, Broach JR, Fernandes PM.

Appl Microbiol Biotechnol. 2013 Mar;97(5):2093-107. doi: 10.1007/s00253-012-4356-x. Epub 2012 Aug 23.


Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.

Xu YF, Zhao X, Glass DS, Absalan F, Perlman DH, Broach JR, Rabinowitz JD.

Mol Cell. 2012 Oct 12;48(1):52-62. doi: 10.1016/j.molcel.2012.07.013. Epub 2012 Aug 16.


Decoding complex chemical mixtures with a physical model of a sensor array.

Tsitron J, Ault AD, Broach JR, Morozov AV.

PLoS Comput Biol. 2011 Oct;7(10):e1002224. doi: 10.1371/journal.pcbi.1002224. Epub 2011 Oct 20.


Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters.

Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR.

Mol Biol Cell. 2011 Jun 15;22(12):2106-18. doi: 10.1091/mbc.E10-10-0826. Epub 2011 Apr 20.


Yeast cells can access distinct quiescent states.

Klosinska MM, Crutchfield CA, Bradley PH, Rabinowitz JD, Broach JR.

Genes Dev. 2011 Feb 15;25(4):336-49. doi: 10.1101/gad.2011311. Epub 2011 Feb 2.


Initiation of the TORC1-regulated G0 program requires Igo1/2, which license specific mRNAs to evade degradation via the 5'-3' mRNA decay pathway.

Talarek N, Cameroni E, Jaquenoud M, Luo X, Bontron S, Lippman S, Devgan G, Snyder M, Broach JR, De Virgilio C.

Mol Cell. 2010 May 14;38(3):345-55. doi: 10.1016/j.molcel.2010.02.039.


The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication.

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.

PLoS Genet. 2009 Dec;5(12):e1000755. doi: 10.1371/journal.pgen.1000755. Epub 2009 Dec 4.


Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6.

Lippman SI, Broach JR.

Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19928-33. doi: 10.1073/pnas.0907027106. Epub 2009 Nov 9.


Expression of CXCR4, a G-protein-coupled receptor for CXCL12 in yeast identification of new-generation inverse agonists.

Evans BJ, Wang Z, Broach JR, Oishi S, Fujii N, Peiper SC.

Methods Enzymol. 2009;460:399-412. doi: 10.1016/S0076-6879(09)05220-3.


Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions.

Freckleton G, Lippman SI, Broach JR, Tavazoie S.

PLoS Genet. 2009 Apr;5(4):e1000449. doi: 10.1371/journal.pgen.1000449. Epub 2009 Apr 10.


Glucose regulates transcription in yeast through a network of signaling pathways.

Zaman S, Lippman SI, Schneper L, Slonim N, Broach JR.

Mol Syst Biol. 2009;5:245. doi: 10.1038/msb.2009.2. Epub 2009 Feb 17. Erratum in: Mol Syst Biol. 2009;5:257.


Predicting cellular growth from gene expression signatures.

Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.

PLoS Comput Biol. 2009 Jan;5(1):e1000257. doi: 10.1371/journal.pcbi.1000257. Epub 2009 Jan 2.


Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures.

Tan MP, Smith EN, Broach JR, Floudas CA.

BMC Bioinformatics. 2008 Jun 6;9:268. doi: 10.1186/1471-2105-9-268.


How Saccharomyces responds to nutrients.

Zaman S, Lippman SI, Zhao X, Broach JR.

Annu Rev Genet. 2008;42:27-81. doi: 10.1146/annurev.genet.41.110306.130206. Review.


Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae.

Yorimitsu T, Zaman S, Broach JR, Klionsky DJ.

Mol Biol Cell. 2007 Oct;18(10):4180-9. Epub 2007 Aug 15.


Sch9 is a major target of TORC1 in Saccharomyces cerevisiae.

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.

Mol Cell. 2007 Jun 8;26(5):663-74.


Do cells think?

Ramanathan S, Broach JR.

Cell Mol Life Sci. 2007 Jul;64(14):1801-4. Review.


Cross-talk and decision making in MAP kinase pathways.

McClean MN, Mody A, Broach JR, Ramanathan S.

Nat Genet. 2007 Mar;39(3):409-14. Epub 2007 Jan 28. Erratum in: Nat Genet. 2007 Apr;39(4):567.


Single-cell observations reveal intermediate transcriptional silencing states.

Xu EY, Zawadzki KA, Broach JR.

Mol Cell. 2006 Jul 21;23(2):219-29.


The dynamics of homologous pairing during mating type interconversion in budding yeast.

Houston PL, Broach JR.

PLoS Genet. 2006 Jun;2(6):e98. Epub 2006 Jun 23.


Creation of GPCR-based chemical sensors by directed evolution in yeast.

Ault AD, Broach JR.

Protein Eng Des Sel. 2006 Jan;19(1):1-8. Epub 2005 Nov 1.


Design and synthesis of downsized metastin (45-54) analogs with maintenance of high GPR54 agonistic activity.

Niida A, Wang Z, Tomita K, Oishi S, Tamamura H, Otaka A, Navenot JM, Broach JR, Peiper SC, Fujii N.

Bioorg Med Chem Lett. 2006 Jan 1;16(1):134-7. Epub 2005 Oct 18.


Mutations in the nucleosome core enhance transcriptional silencing.

Xu EY, Bi X, Holland MJ, Gottschling DE, Broach JR.

Mol Cell Biol. 2005 Mar;25(5):1846-59.


Sense and sensibility: nutritional response and signal integration in yeast.

Schneper L, Düvel K, Broach JR.

Curr Opin Microbiol. 2004 Dec;7(6):624-30. Review.


Making the right choice--long-range chromosomal interactions in development.

Broach JR.

Cell. 2004 Nov 24;119(5):583-6. Review. Erratum in: Cell. 2004 Dec 29;119(7):1057.


PP2A phosphatase activity is required for stress and Tor kinase regulation of yeast stress response factor Msn2p.

Santhanam A, Hartley A, Düvel K, Broach JR, Garrett S.

Eukaryot Cell. 2004 Oct;3(5):1261-71.


A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size.

Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M.

Genes Dev. 2004 Oct 15;18(20):2491-505. Epub 2004 Oct 1.


Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast.

Wang Y, Pierce M, Schneper L, Güldal CG, Zhang X, Tavazoie S, Broach JR.

PLoS Biol. 2004 May;2(5):E128. Epub 2004 May 11.

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