Recent Publications

Here are some recent publications by our faculty, postdocs, and graduate students.  These publications reflect the broad interests of our department, and collaborative environment our department and UCSF provide.

2020

Coming Soon

2019

Terren K Niethamer, Jeffrey O Bush. Getting direction(s): The Eph/ephrin signaling system in cell positioning.  Developmental Biology. 2019 Mar 1;447(1):42-57. doi: 10.1016/j.ydbio.2018.01.012. PMCID: PMC6066467.

Jeffrey van Haren, Torsten Wittmann. Microtubule Plus End Dynamics - Do We Know How Microtubules Grow?: Cells boost microtubule growth by promoting distinct structural transitions at growing microtubule ends. Bioessays. 2019 Mar;41(3):e1800194. doi: 10.1002/bies.201800194. Epub 2019 Feb 7. PMCID: PMC7021488.

Giuseppe Facchetti, Benjamin Knapp, Ignacio Flor-Parra, Fred Chang, Martin Howard. Reprogramming Cdr2-Dependent Geometry-Based Cell Size Control in Fission Yeast. Curr Biol. 2019 Jan 21;29(2):350-358.e4. doi: 10.1016/j.cub.2018.12.017. Epub 2019 Jan 10. PMCID: PMC6345630.

Erine H Budi, Ons Mamai, Steven Hoffman, Rosemary J Akhurst, Rik Derynck. Enhanced TGF-β Signaling Contributes to the Insulin-Induced Angiogenic Responses of Endothelial Cells. iScience. 2019 Jan 25;11:474-491. doi: 10.1016/j.isci.2018.12.038. Epub 2019 Jan 3. PMCID: PMC6348203.

Abigail A Kindberg, Jeffrey O Bush. Cellular organization and boundary formation in craniofacial development. Genesis. 2019 Jan;57(1):e23271. doi: 10.1002/dvg.23271. Epub 2019 Jan 12. PMCID: PMC6503678.

Jason M Peters, Byoung-Mo Koo, Ramiro Patino, Gary E Heussler, Cameron C Hearne, Jiuxin Qu, Yuki F Inclan, John S Hawkins, Candy H S Lu, Melanie R Silvis, M Michael Harden, Hendrik Osadnik, Joseph E Peters, Joanne N Engel, Rachel J Dutton, Alan D Grossman, Carol A Gross, Oren S Rosenberg. Nature Microbiology. 2019 Feb;4(2):244-250. doi: 10.1038/s41564-018-0327-z. Epub 2019 Jan 7. PMCID: PMC6424567.

Yong Chen, Kenji Ikeda, Takeshi Yoneshiro, Annarita Scaramozza, Kazuki Tajima, Qiang Wang, Kyeongkyu Kim, Kosaku Shinoda, Carlos Henrique Sponton, Zachary Brown, Andrew Brack, Shingo Kajimura. Thermal stress induces glycolytic beige fat formation via a myogenic state. Nature. 2019 Jan;565(7738):180-185. doi: 10.1038/s41586-018-0801-z. Epub 2018 Dec 19. PMCID: PMC6328316.

Moses M Obimbo, Yan Zhou, Michael T McMaster, Craig R Cohen, Zahida Qureshi, John Ong'ech, Julius A Ogeng'o, Susan J Fisher. Placental Structure in Preterm Birth Among HIV-Positive Versus HIV-Negative Women in Kenya. Journal of Acquired Immune Deficiency Syndromes. 2019 Jan 1;80(1):94-102. doi: 10.1097/QAI.0000000000001871. PMCID: PMC6289800.

Sonia Sudiwala, Sarah M Knox. The emerging role of cranial nerves in shaping craniofacial development. Genesis. 2019 Jan;57(1):e23282. doi: 10.1002/dvg.23282. PMID: 30628162.

2018

Lisa Fish, Steven Zhang, Johnny X Yu, Bruce Culbertson, Alicia Y Zhou, Andrei Goga, Hani Goodarzi. Cancer cells exploit an orphan RNA to drive metastatic progression. Nature Medicine. 2018 Nov;24(11):1743-1751. doi: 10.1038/s41591-018-0230-4. Epub 2018 Nov 5. PMCID: PMC6223318.

Feeling YuTing Chen, Eliza Gaylord, Nancy McNamara, Sarah Knox. Deciphering Molecular and Phenotypic Changes Associated with Early Autoimmune Disease in the Aire-Deficient Mouse Model of Sjögren's Syndrome. International Journal of Molecular Sciences. 2018 Nov 17;19(11):3628. doi: 10.3390/ijms19113628. PMCID: PMC6274681.

Alison J May, Noel Cruz-Pacheco, Elaine Emmerson, Eliza A Gaylord, Kerstin Seidel, Sara Nathan, Marcus O Muench, Ophir D Klein, Sarah M Knox. Diverse progenitor cells preserve salivary gland ductal architecture after radiation-induced damage. Development. 2018 Nov 5;145(21):dev166363. doi: 10.1242/dev.166363. PMCID: PMC6240316.

Katharine A White, Bree K Grillo-Hill, Mario Esquivel, Jobelle Peralta, Vivian N Bui, Ismahan Chire, Diane L Barber. β-Catenin is a pH sensor with decreased stability at higher intracellular pH. Journal of Cell Biology. 2018 Nov 5;217(11):3965-3976. doi: 10.1083/jcb.201712041. Epub 2018 Oct 12. PMCID: PMC6219716.

Pereira L. Congenital Viral Infection: Traversing the Uterine-Placental Interface. Annual Review of Virology. 2018 Sep 29;5(1):273-299. doi: 10.1146/annurev-virology-092917-043236. Epub 2018 Jul 26. PMID: 30048217.

Elting MW, Suresh P, Dumont S. The Spindle: Integrating Architecture and Mechanics across Scales. Trends in Cell Biology. 2018 Nov;28(11):896-910. doi: 10.1016/j.tcb.2018.07.003. Epub 2018 Aug 6. PMID: 30093097.

Richardson CD, Kazane KR, Feng SJ, Zelin E, Bray NL, Schäfer AJ, Floor SN, Corn JE. CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nature Genetics. 2018 Aug;50(8):1132-1139. doi: 10.1038/s41588-018-0174-0. Epub 2018 Jul 27. PMID: 30054595.

Sponton CHKajimura S. Multifaceted Roles of Beige Fat in Energy Homeostasis Beyond UCP1. Endocrinology. 2018 Jul 1;159(7):2545-2553. doi: 10.1210/en.2018-00371. PMID: 29757365.

Rana MK, Aloisio FM, Choi C, Barber DL. Formin-dependent TGF-β signaling for epithelial to mesenchymal transition. Molecular Biology of the Cell. 2018 Jun 15;29(12):1465-1475. doi: 10.1091/mbc.E17-05-0325. Epub 2018 Apr 18. PMID: 29668357

Flor-Parra I, Iglesias-Romero AB, Chang F. The XMAP215 Ortholog Alp14 Promotes Microtubule Nucleation in Fission Yeast. Current Biology. 2018 Jun 4;28(11):1681-1691.e4. doi: 10.1016/j.cub.2018.04.008. Epub 2018 May 17. PMID: 29779879.

Katsuno Y, Qin J, Oses-Prieto JA, Wang H, Jackson-Weaver O, Zhang T, Lamouille S, Wu J, Burlingame ALL, Xu J, Derynck R. Arginine methylation of Smad7 by PRMT1 in TGF-β-induced epithelial-mesenchymal transition and epithelial stem cell generation. Journal of Biological Chemistry. 2018 Jun 15. pii: jbc.RA118.002027. doi: 10.1074/jbc.RA118.002027. [Epub ahead of print]. PMID: 29907569.

Emmerson E, Knox SM. Salivary gland stem cells: A review of development, regeneration and cancer. Genesis. 2018 May;56(5):e23211. doi: 10.1002/dvg.23211. Epub 2018 May 4. PMCID: PMC5980780.

Venkataramanan SFloor SN. The Traffic Jam: Polyamine Prevalence Pauses Protein Production. Molecular Cell. 2018 Apr 19;70(2):191-192. doi: 10.1016/j.molcel.2018.04.005. PMID: 29677487.

Zhang Y, Burkhardt DH, Rouskin S, Li GW, Weissman JS, Gross CA. A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation. Molecular Cell. 2018 Apr 19;70(2):274-286.e7. doi: 10.1016/j.molcel.2018.02.035. Epub 2018 Apr 5. PMCID: PMC5910227.

Tabata TPetitt M, Puerta-Guardo H, Michlmayr D, Harris E, Pereira L. Zika Virus Replicates in Proliferating Cells in Explants From First-Trimester Human Placentas, Potential Sites for Dissemination of Infection. Journal of Infectious Diseases. 2018 Mar 28;217(8):1202-1213. doi: 10.1093/infdis/jix552. PMID: 29106643

van Haren JCharafeddine RA, Ettinger A, Wang H, Hahn KM, Wittmann T. Local control of intracellular microtubule dynamics by EB1 photodissociation. Nature Cell Biology. 2018 Mar;20(3):252-261. doi: 10.1038/s41556-017-0028-5. Epub 2018 Jan 29. PMCID: PMC5826794.

Niethamer TK, Bush JO.Getting direction(s): The Eph/ephrin signaling system in cell positioning. Developmental Biology. 2018 Jan 30. pii: S0012-1606(17)30664-4. doi: 10.1016/j.ydbio.2018.01.012. [Epub ahead of print]. PMCID: PMC6066467.

Ikeda K, Maretich P, Kajimura S. The Common and Distinct Features of Brown and Beige Adipocytes. Trends in Endocrinology and Metabolism. 2018 Mar;29(3):191-200. doi: 10.1016/j.tem.2018.01.001. Epub 2018 Jan 20. PMCID: PMC5826798.

Du D, Katsuno Y, Meyer D, Budi EH, Chen SH, Koeppen H, Wang H, Akhurst RJ, Derynck R. Smad3-mediated recruitment of the methyltransferase SETDB1/ESET controls Snail1 expression and epithelial-mesenchymal transition. EMBO Reports. 2018 Jan;19(1):135-155. doi: 10.15252/embr.201744250. Epub 2017 Dec 12. PMCID: PMC5757214.

Emmerson EMay AJBerthoin LCruz-Pacheco NNathan SMattingly AJ, Chang JL, Ryan WR, Tward AD, Knox SM. Salivary glands regenerate after radiation injury through SOX2-mediated secretory cell replacement. EMBO Molecular Medicine. 2018 Jan 15. pii: e8051. doi: 10.15252/emmm.201708051. [Epub ahead of print]. PMID: 29335337.

Hasegawa Y, Ikeda KChen Y, Alba DL, Stifler D, Shinoda K, Hosono T, Maretich P, Yang Y, Ishigaki Y, Chi J, Cohen P, Koliwad SK, Kajimura S. Repression of Adipose Tissue Fibrosis through a PRDM16-GTF2IRD1 Complex Improves Systemic Glucose Homeostasis. Cell Metabolism. 2018 Jan 9;27(1):180-194.e6. doi: 10.1016/j.cmet.2017.12.005. PMCID: PMC5765755

2017

Tatapudy S, Aloisio FBarber D, Nystul T. Cell fate decisions: emerging roles for metabolic signals and cell morphology. EMBO Reports. 2017 Dec;18(12):2105-2118. doi: 10.15252/embr.201744816. Epub 2017 Nov 20. PMCID: PMC5709733.

Ikeda K, Kang Q, Yoneshiro T, Camporez JP, Maki H, Homma M, Shinoda K, Chen Y, Lu X, Maretich P, Tajima K, Ajuwon KM, Soga T, Kajimura S. UCP1-independent signaling involving SERCA2b-mediated calcium cycling regulates beige fat thermogenesis and systemic glucose homeostasis. Nature Medicine. 2017 Dec;23(12):1454-1465. doi: 10.1038/nm.4429. Epub 2017 Nov 13. PMCID: PMC5727902.

Petitt MTabata T, Puerta-Guardo H, Harris E, Pereira L. Zika virus infection of first-trimester human placentas: utility of an explant model of replication to evaluate correlates of immune protection ex vivo. Current Opinion in Virology. 2017 Dec;27:48-56. doi: 10.1016/j.coviro.2017.11.008. PMCID: PMC5723543.

Hueschen C, Kenny SJ,  Xu K, Dumont S. NuMA recruits dynein activity to microtubule minus-ends at mitosis. eLife, 2017 Nov 29;6. pii: e29328. doi: 10.7554/eLife.29328.  PMCID: PMC5706958.

Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN. Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Reports. 2017 Nov 14;21(7):2005-2016. doi: 10.1016/j.celrep.2017.10.095. PMCID: PMC5759054

Shin PJ, Zhu Z, Camarda R, Bok RA, Zhou AY, Kurhanewicz J, Goga A, Vigneron DB. Cancer recurrence monitoring using hyperpolarized [1-13C]pyruvate metabolic imaging in murine breast cancer model. Magnetic Resonance Imaging, 2017 Nov;43:105-109. doi: 10.1016/j.mri.2017.07.014. Epub 2017 Jul 15. PMCID: PMC5632580.

Pereira LTabata TPetitt MFang-Hoover J. Congenital cytomegalovirus infection undermines early development and functions of the human placenta. Placenta, 2017 Nov;59 Suppl 1:S8-S16. doi: 10.1016/j.placenta.2017.04.020. PMID: 28477968

Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN. Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Reports, 2017 Nov 14;21(7):2005-2016. doi: 10.1016/j.celrep.2017.10.095. PMCID: PMC5759054.

Ikeda K, Kang Q, Yoneshiro T, Camporez JP, Maki H, Homma M, Shinoda K, Chen YLu X, Maretich P, Tajima K, Ajuwon KM, Soga T, Kajimura S. UCP1-independent signaling involving SERCA2b-mediated calcium cycling regulates beige fat thermogenesis and systemic glucose homeostasis. Nature Medicine, 2017 Nov 13. doi: 10.1038/nm.4429. PMCID: PMC5727902.

Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nature Communications, 2017 Oct 20;8(1):1077. doi: 10.1038/s41467-017-01027-z. PMCID: PMC5651823.

Wei Y, Kim TJ, Peng DH, Duan D, Gibbons DL, Yamauchi M, Jackson JR, Le Saux CJ, Calhoun C, Peters J, Derynck R, Backes BJ, Chapman HA. Fibroblast-specific inhibition of TGF-β1 signaling attenuates lung and tumor fibrosis. The Journal of Clinical Investigation,  2017 Oct 2;127(10):3675-3688. doi: 10.1172/JCI94624. PMCID: PMC5617667.

Vercoulen Y, Kondo Y, Iwig JS, Janssen AB, White KA, Amini M, Barber DL, Kuriyan J, Roose JP. A Histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1. eLife, 2017 Sep 27;6. pii: e29002. doi: 10.7554/eLife.29002. PMCID: PMC5643099

Chen FY, Lee A, Ge S, Nathan SKnox SM, McNamara NA. Aire-deficient mice provide a model of corneal and lacrimal gland neuropathy in Sjögren's syndrome. PLoS One, 2017 Sep 19;12(9):e0184916. doi: 10.1371/journal.pone.0184916. PMCID: PMC5605119.

Tran A, Tang A, O'Loughlin CT, Balistreri A, Chang E, Coto Villa D, Li J, Varshney A, Jimenez V, Pyle J, Tsujimoto B, Wellbrook C, Vargas C, Duong A, Ali N, Matthews SY, Levinson S, Woldemariam S, Khuri S, Bremer M, Eggers DK, L'Etoile N, Miller Conrad LC, VanHoven MK. C. elegans avoids toxin-producing Streptomyces using a seven transmembrane domain chemosensory receptor. eLife, 2017 Sep 5;6. pii: e23770. doi: 10.7554/eLife.23770. PMCID: PMC5584987.

White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Science Signaling, 2017 Sep 5;10(495). pii: eaam9931. doi: 10.1126/scisignal.aam9931. PMID: 28874603

Budi EHDuan DDerynck R. Transforming Growth Factor-β Receptors and Smads: Regulatory Complexity and Functional Versatility. Trends in Cell Biology, 2017 Sep;27(9):658-672. doi: 10.1016/j.tcb.2017.04.005. PMID: 28552280.

Szpiech ZA, Strauli NB, White KA, Garrido Ruiz D, Jacobson MP, Barber DL, Hernandez RD. Prominent Features Of The Amino Acid Mutation Landscape In Cancer. PLoS One. 2017 Aug 24;12(8):e0183273. doi: 10.1371/journal.pone.0183273. eCollection 2017. PMCID: PMC5570307.

Inagaki T, Sakai J, Kajimura S. Transcriptional and epigenetic control of brown and beige adipose cell fate and function. Nature Reviews-Molecular Cell Biology, 2017 Aug;18(8):527. doi: 10.1038/nrm.2017.72. PMID: 28698600.

Hussmann JAOsadnik HGross CA. Ribosomal Architecture: Constraints Imposed by the Need for Self-Production. Current Biology, 2017 Aug 21;27(16):R798-R800. doi: 10.1016/j.cub.2017.06.080. PMID: 28829964

Sponton CHKajimura S. Burning Fat and Building Bone by FSH Blockade. Cell Metabolism, 2017 Aug 1;26(2):285-287. doi: 10.1016/j.cmet.2017.07.018. PMID: 28768167

Kim S, Prochazka J, Bush JO. Live Imaging of Mouse Secondary Palate Fusion. JoVE, 2017 Jul 27;(125). doi: 10.3791/56041. PMID: 28784960.

Makhijani K, Alexander B, Rao D, Petraki S, Herboso LKukar KBatool I, Wachner S, Gold KS, Wong C, O'Connor MB, Brückner K. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications, 2017 Jul 27;8:15990. doi: 10.1038/ncomms15990. PMCID: PMC5537569.

Chang F. Forces that shape fission yeast cells. Molecular Biology of the Cell, 2017 Jul 7;28(14):1819-1824. doi: 10.1091/mbc.E16-09-0671. PMCID: PMC5541833

Guild J, Ginzberg MB, Hueschen CL, Mitchison TJ, Dumont S. Increased lateral microtubule contact at the cell cortex is sufficient to drive mammalian spindle elongation. Molecular Biology of the Cell, 2017 Jul 7;28(14):1975-1983. doi: 10.1091/mbc.E17-03-0171. PMCID: PMC5541847.

Farmer DT, Finley JK, Chen FY, Tarifeño-Saldivia E, McNamara NA, Knox SM, McManus MT. miR-205 is a critical regulator of lacrimal gland development. Developmental Biology, 2017 Jul 1;427(1):12-20. doi: 10.1016/j.ydbio.2017.05.012. PMID: 28511845.

Elting MW, Prakash M, Udy DBDumont S.  Mapping Load-Bearing in the Mammalian Spindle Reveals Local Kinetochore Fiber Anchorage that Provides Mechanical Isolation and Redundancy.  Current Biology, 2017 Jun 29. pii: S0960-9822(17)30720-0. doi: 10.1016/j.cub.2017.06.018.  PMID: 28690110bioRxiv doi: 10.1101/103572 (2017).  

Webb, BA, Dosey AM, Wittmann T, Killman JM, Barber DL.  The glycolytic enzyme phosphofructokinase-1 assembles into filaments.  The Journal of Cell Biology, 2017 Jun 23. pii: jcb.201701084. doi: 10.1083/jcb.201701084.  PMID: 28646105.  

Emmerson E, May AJNathan SCruz-Pacheco N, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM.  SOX2 regulates acinar cell development in the salivary gland.  eLife, 2017 Jun 17;6. pii: e26620. doi: 10.7554/eLife.26620.  PMCID: PMC5498133.  

Long AFUdy DBDumont S. Hec1 Tail Phosphorylation Differentially Regulates Mammalian Kinetochore Coupling to Polymerizing and Depolymerizing Microtubules. Current Biology, 2017 Jun 5;27(11):1692-1699.e3. doi: 10.1016/j.cub.2017.04.058. PMCID: PMC5502739bioRxiv doi: 10.1101/105916 (2017).

Kuhn JDumont S. Spindle assembly checkpoint satisfaction occurs via end-on but not lateral attachments under tension. The Journal of Cell Biology, 2017 Jun 5;216(6):1533-1542. doi: 10.1083/jcb.201611104. PMCID: PMC5461026bioRxiv doi: 10.1101/105460 (2017).

Karg T, Elting MW, Vicars H, Dumont S, Sullivan W. The chromokinesin Klp3a and microtubules facilitate acentric chromosome segregation. The Journal of Cell Biology, 2017 Jun 5;216(6):1597-1608. doi: 10.1083/jcb.201604079. PMCID: PMC5461011

Farmer D, Nathan SFinley J, Yu KS, Emmerson E, Byrnes L, Sneddon J, McManus M, Tward A, Knox S. Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland. Development, 2017 Jun 2. pii: dev.150789. doi: 10.1242/dev.150789. PMCID: PMC5536870.

Budi EHDuan DDerynck R. Transforming Growth Factor-β Receptors and Smads: Regulatory Complexity and Functional Versatility. Trends in Cell Biology, 2017 May 25. pii: S0962-8924(17)30063-6. doi: 10.1016/j.tcb.2017.04.005. PMID: 28552280.

Anderton BCamarda R, Balakrishnan S, Balakrishnan A, Kohnz RA, Lim L, Evason KJMomcilovic OKruttwig K, Huang Q, Xu G, Nomura DK, Goga A. MYC-driven inhibition of the glutamate-cysteine ligase promotes glutathione depletion in liver cancer. EMBO Reports, 2017 Apr;18(4):569-585. doi: 10.15252/embr.201643068.  PMCID: PMC5376764.

Pemble H, Kumar P, van Haren JWittmann T. GSK3-mediated CLASP2 phosphorylation modulates kinetochore dynamics. Journal of Cell Science, 2017 Apr 15;130(8):1404-1412. doi: 10.1242/jcs.194662.  PMCID: PMC5399784.

Camarda R, Williams J, Goga A. In vivo Reprogramming of Cancer Metabolism by MYC. Frontiers in Cell and Developmental Biology, 2017 Apr 11;5:35. doi: 10.3389/fcell.2017.00035. PMCID: PMC5386977.

Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. Cell Systems, 2017 Mar 22;4(3):291-305.e7. doi: 10.1016/j.cels.2016.12.013. PMCID: PMC5400513

Baggett NE, Zhang Y, Gross CA. Global analysis of translation termination in E. coli. PLoS Genetics, 2017 Mar 16;13(3):e1006676. doi: 10.1371/journal.pgen.1006676. PMCID: PMC5373646.

Niethamer TKLarson AR, O'Neill AK, Bershteyn M, Hsiao EC, Klein OD, Pomerantz JH, Bush JO. EPHRIN-B1 Mosaicism Drives Cell Segregation in Craniofrontonasal Syndrome hiPSC-Derived Neuroepithelial Cells. Stem Cell Reports, 2017 Mar 14;8(3):529-537. doi: 10.1016/j.stemcr.2017.01.017. PMCID: PMC5355632.

O'Halloran DM, Altshuler-Keylin S, Zhang XD, He C, Morales-Phan C, Yu Y, Kaye JA, Brueggemann C, Chen TY, L'Etoile ND. Contribution of the cyclic nucleotide gated channel subunit, CNG-3, to olfactory plasticity in Caenorhabditis elegans. Scientific Reports, Epub 2017 Mar 13. 2017 Dec;7(1):169. doi: 10.1038/s41598-017-00126-7. PMCID: PMC5427828.

Altshuler-Keylin SKajimura S. Mitochondrial homeostasis in adipose tissue remodeling. Science Signaling, 2017 Feb 28;10(468). pii: eaai9248. doi: 10.1126/scisignal.aai9248. PMCID: PMC5465966.

White KA, Grillo-Hill BK, Barber DL. Cancer cell behaviors mediated by dysregulated pH dynamics at a glance. Journal of Cell Science, 2017 Feb 15;130(4):663-669. doi: 10.1242/jcs.195297. PMCID: PMC5339414.

Kajimura S. Adipose tissue in 2016: Advances in understanding of adipose tissue biology. Nature Reviews Endocrinology, 2017 Feb;13(2):69-70. doi: 10.1038/nrendo.2016.211. Epub 2017 Jan 4. PMCID: PMC5465959.

Burkhardt DH, Rouskin S, Zhang Y, Li GW, Weissman JS, Gross CA. Operon mRNAs are organized into ORF-centric structures that predict translation efficiency. eLife, 2017 Jan 31;6. pii: e22037. doi: 10.7554/eLife.22037. PMCID: PMC5318159.

van Haren J, Ettinger A, Wang H, Hahn K, Wittmann T. Local Control of Intracellular Microtubule Dynamics by End Binding Protein 1 (EB1) Photo-Dissociation. bioRxiv doi: 10.1101/099598 (2017).

2016

Webb BA, White KA, Grillo-Hill BK, Schonichen A, Cho C, Barber DL. A histidine cluster in the cytoplasmic domain of the Na-H exchanger NHE1 confers pH-sensitive phospholipid binding and regulates transporter activity. Journal of Biological Chemistry, 2016 Nov 11;291(46):24096-24104. PMCID: PMC5104935.

Ulmschneider B, Grillo-Hill BK, Benitez M, Azimova D, Barber DL, Nystul TG. Increased intracellular pH is necessary for adult epithelial and embryonic stem cell differentiation. Journal of Cell Biology, 2016 Nov 7;215(3):345-355. PMCID: PMC51000294.

Tabata TPetitt MFang-Hoover J, Zydek M, Pereira L. Persistent cytomegalovirus infection in amniotic membranes of the human placenta. American Journal of Pathology, 2016 Nov;186(11):2970-2986. PMCID: PMC5222962.

Horiuchi DCamarda RZhou AY, Yau C, Momcilovic O, Balakrishnan S, Corella AN, Eyob HKessenbrock K, Lawson DA, Marsh LA, Anderton BNRohrberg J, Kunder R, Bazarov AV, Yaswen P, McManus MT, Rugo HS, Werb Z, Goga A. PIM1 kinase inhibition as a targeted therapy against triple-negative breast tumors with elevated MYC expression. Nature Medicine 2016 Nov;22(11):1321-1329. doi: 10.1038/nm.4213. PMCID: PMC5341692.

O'Neill AK, Kindberg AA, Neithamer TK, Larson AR, Ho HH, Greenberg ME, Bush JO. Unidirectional Eph/ephrin signaling creates a cortical actomyosin differential to drive cell segregation. Journal of Cell Biology, 2016 Oct 24;215(2):217-229. PMCID: PMC5084648.

He C, Altshuler-Keylin S, Daniel D, L'Etoile ND, O'Halloran D. The cyclic nucleotide gated channel subunit CNG-1 instructs behavioral outputs in Caenorhabditis elegans by coincidence detection of nutritional status and olfactory input. Neuroscience Letters, 2016 Oct 6;632:71-78. doi: 10.1016/j.neulet.2016.08.037.  PMID: 27561605.

Altshuler-Keylin SShinoda KHasegawa YIkeda KHong HKang QYang Y, Perera RM, Debnath J, Kajimura S. Beige adipocyte maintenance is regulated by autophagy-induced mitochondrial clearance. Cell Metabolism, 2016 Aug 24;24(3):402-19. PMID: 27568548.

Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK. Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity. ACS Chemical Biology, 2016 Aug 19;11(8):2131-9. doi: 10.1021/acschembio.6b00433. PMCID: PMC4994060.

Ingaki T, Sakai J, Kajimura S. Transcriptional and epigenetic control of brown and beige adipose cell fate function. Nature Review Molecular Cell Biology, 2016 Aug;17(8): 480-95. PMCID: PMC4956538.

Tabata TPetitt M, Puerta-Guardo H, Michlmayr D, Wang C, Fang-Hoover J, Harris E, Pereira L. Zika virus targets different primary human placental cells, suggesting two routes of vertical transmission. Cell Host & Microbe, 2016 Jul 18;20(2):155-66. PMID: 27443522.

Cho CE, Brueggermann CL'Eotile ND, Bargmann CI. Parallel encoding of sensory history and behavioral preference during Caenorhabdities elegans olfactory learning. elife, 2016 Jul 6; doi:10.7554/eLife.14000. PMCID: PMC4935464.

Moses HL, Roberts AB, Derynck R. The discovery and early days of TGF-β: a historical perspective. Cold Spring Harbor Perspectives in Biology, 2016 July 1:8(7) doi:10.1101/cshperspect.a021865. PMID: 27328871.

Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA. A chemical-genomic screen of neglected antibiotics reveals illicit transport of Kasugamycin and Blasticidin S. PLoS Genetics, 2016 Jun 29:12(6): e1006124. PMCID: PMC4927156.

Iwasaki S, Floor SN, Ingolia NT. Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature, 2016 Jun 23;534(7608):558-61. doi: 10.1038/nature17978. PMCID: PMC4946961

Ettinger Avan Haren J, Ribeiro S, Wittmann T. Doublecortin is excluded from growing microtubule ends and recognizes the GDP-Microtubule lattice. Current Biology, 2016 Jun 20;26(20): 1549-55. PMCID: PMC5023073.

Chondronikola M, Volp E, Børsheim E, Porter C, Saraf MK, Annamalai P, Yafanti C, Chao T, Wong DShinoda K, Labbė SM, Hurren NM, Cesani F, Kajimura S, Sidossis LS. Brown adipose tissue activation is linked to distinct systemic effects on lipid metabolism in humans. Cell Metabolism, 2016 Jun 14;23(6): 1200-6. PMID: 27238638.

Peters JM, Colavin A, Shi H, Czamy TL, Larson MH, Wong S, Hawkins JS, Lu CH, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell, 2016 Jun 2;165(6): 1493-506. PMCID: PMC4894308.

Louie SM, Grossman EA, Crawford LA, Ding L, Camarda R, Huffman TR, Miyamoto DK, Goga A, Weerapana E, Nomura DK. GSTP1 Is a Driver of Triple-Negative Breast Cancer Cell Metabolism and Pathogenicity. Cell Chemical Biology, 2016 May 19;23(5):567-78. doi: 10.1016/j.chembiol.2016.03.017. PMCID: PMC4876719.

Ohyama K, Nogusa Y, Shinoda K, Suzuki K, Bannai M, Kajimura S. A synergistic antiobesity effect by a combination of capsinoids and cold temperature through promoting beige adipocyte biogenesis. Diabetes, 2016 May;65(5): 1410-23. PMCID: PMC4839206.

Humtsoe JO, Pham E, Louie RJ, Chan DA, Kramer RH. ErbB3 upregulation by the HNSCC 3D microenvironment modulates cell survival and growth. Oncogene, 2016 Mar 24;35(12): 1554-64. PMID: 26073080.

Camarda R, Zhou AY, Kohnz RA, Balakrishnan S, Mahieu C, Anderton B, Eyob H, Kajimura S, Tward A, Krings G, Nomura DK, Goga A. Inhibition of fatty acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer. Nature Medicine, 2016 Mar 7; doi:10.1038/nm.4055. PMCID: PMC4892846.

Budi EHXu JDerynck R. Regulation of TGF-β receptors. Method in Molecular Biology, 2016;1344:1-33. PMID: 26520115.

2015

Prochazka J, Prochazkova M, Du W, Spoutil F, Tureckova J, Hoch R, Shimogori T, Sedlacek R, Rubenstein JL, Wittmann T, Klein OD. Migration of founder epithelial cells drives proper molar tooth positioning and morphogenesis. Developmental Cell, 2015 Dec 21;35(6):713-24. PMCID: PMC4710359.

Muthusamy BPBudi EHKatsuno Y, Lee MK, Smith SM, Mirza AM, Akhurst RJ, Derynck R. ShcA protects against epithlial-mesenchymal transition through compartmentalized inhibition of TGF-β induce Smad activation. PLoS Biology, 2015 Dec 17;13(12):e1002325. PMCID: PMC4682977.

Parshin A, Shiver AL, Lee J, Ozerova M, Schneidman-Duhovny D, Gross CA, Borukhov S. DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes sequence insertion 1. PNAS, 2015 Dec 15;112(50): E6862-71. PMCID: PMC4687573.

Shinoda KOhyama KHasegawa Y, Chang HY, Ogura M, Sato A, Hong HHosono TSharp LZScheel DW, Graham M, Ishihama Y, Kajimura S. Phosphoproteomics identifies CK2 as a negative regulator of beige adipocyte thermogenesis and energy expenditures. Cell Metabolism, 2015 Dec 1;22(6): 997-1008. PMCID: PMC4670581.

Gold KBrückner K. Macrophages and cellular immunity in Drosophila melanogaster. Seminars in Immunology, 2015 Dec; 27(6): 357-368. PMID: 27117654.

Mattingly AFinley JKKnox SM. Salivary gland development and disease. Wiley Interdisciplinary Reviews: Developmental Biology, 2015 Nov/Dec;4(6): 573-590. PMID: 25970268.

Petraki S, Alexander BBrückner K. Assaying blood cell populations of the Drosophila melanogaster larva. Journal of Visualized Experiments, 2015 Nov 11;(105). PMCID: PMC4692709.

Shinoda K, Ohyama K, Hasegawa Y, Chang HY, Ogura M, Sato A, Hong H, Hosono T, Sharp LZ, Scheel DW, Graham M, Ishihama Y, Kajimura S. Phosphoproteomics identifies CK2 as a negative regulator of beige adipocyte thermogenesis and energy expenditure. Cell Metabolism, 2015 Oct 29;S1550-4131(15)00516-1. PMCID: PMC4670581.

Lewis AE, Hwa J, Wang R, Soriano P, Bush JO. Neural crest defects in ephrin-B2 mutant mice are non-autonomous and originate from defects in the vasculature. Developmental Biology, 2015 Oct 15;406(2):186-95. PMCID: PMC4639416.

Kajimura S, Spiegelman BM, Seale P. Brown and beige fat: physiological roles beyond heat generation. Cell Metabolism, 2015 Oct 6;22(4):546-59. PMCID: PMC4613812.

Lawson DA, Bhakta NR, Kessenbrock K, Prummel KD, Yu Y, Takai K, Zhou AEyob HBalakrishnan S, Wang CY, Yaswen P, Goga* A, Werb* Z. Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells. Nature, 2015 Oct 1;526(7571):131-5. PMCID: PMC4648562.

Peters JM, SIlvis MR, Zhao D, Hawkins JS, Gross CA, Qi LS. Bacterial CRISPR: accomplishments and prospects. Current Opinion in Microbiology, 2015 Oct;27:121-6. PMCID: PMC4659716.

Gray AN, Koo BM, Shiver AL, Peters JM, Osadnik H, Gross CA. High-throughput bacterial functional genomics in the sequencing era. Current Opinion in Microbiology, 2015 Oct;27:86-95. PMCID: PMC4659725.

Budi EH, Muthusamy BP, Derynck R. The insulin response integrates increased TGF-β signaling through Akt-induced enhancement of cell surface delivery of TGF-β receptors. Science Signaling, 2015 Sept 29;RA96. PMCID: PMC4669960.   

Atilgan E, Magidson V, Khodjakov A, Chang F. Morphogenesis of the fission yeast cell through cell wall expansion. Current Biology, 2015 Aug 17;25(16):2150-7. PMCID: PMC4627367.

Lane AB, Strzelecka M, Ettinger A, Grenfell AW, Wittmann T, Heald R. Enzymatically generated CRISPR libraries of genome labeling and screening. Developmental Cell, 2015 Aug 10;34(3):373-8. PMCID: PMC4536113.

Udy DB, Voorhies M, Chan PP, Lowe TM, Dumont S. Draft de novo transcriptome of the rat kangaroo potorous tridactylus as a tool for cell biology. PLoS One, 2015 Aug 7;10(8):e0134738. PMCID: PMC4529305.

Webb* BA, Forouhar* F, Szu FE, Seetharaman J, Tong* L, Barber* DL. Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations. Nature, 2015 May 18;523(7558):111-4. PMCID: PMC4510984

Gray AN, Egan AJ, Van't Veer IL, Verheul J, Colavin A, Koumoutsi A, Biboy J, Altelaar AF, Damen MJ, Huang KC, Simorre JP, Breukink E, den Blaauwen T, Typas A, Gross CA, Vollmer W. Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division. eLife, 2015 May 7;4. PMCID: PMC4458516.

Tabata TPetitt M, Zydek M, Fang-Hoover J, Larocque N, Tsuge M, Gormley M, Kauvar LM, Pereira L. Human cytomegalovirus infection interferes with the maintenance and differentiation of trophoblast progenitor cells of the human placenta. Journal of Virology, 2015 May;89(9):5134-47. PMCID: PMC4403461.

Shinoda K, Luijten IH, Hasegawa Y, Hong H, Sonne SB, Kim M, Xue R, Chondronikola M, Cypess AM, Tseng YH, Nedergaard J, Sidossis LS, Kajimura S. Genetic and functional characterization of clonally derived adult human brown adipocytes. Nature Medicine, 2015 Apr;21(4):389-94. PMCID: PMC4427356

Kim SLewis AE, Singh V, Ma X, Adelstein R, Bush JO. Convergence and extrusion are require for normal fusion of the mammalian secondary palate. PLOS Biology, 2015 Apr;13(4), e1002122. PMCID: PMC4388528.

Knosp WM, Knox SM, Lombaert IM, Haddox CL, Patel VN, Hoffman MP. Submandibular parasympathetic gangliogenesis requires sprouty-dependent Wnt signals from epithelial progenitors. Develomental Cell, 2015 Mar 23;32(6):667-77. PMCID: PMC4374127.

Grillo-Hill BK, Choi C, Jiminez-Vidal M, Barber DL. Increased H+ efflux is sufficient to induce dysplasia and necessary for viability with oncogene expression. eLife, 2015 Mar 20;4. PMCID: PMC4392478

Rana* MKSrivastava* J, Yang M, Chen CS, Barber DL. Hypoxia increases the abundance but not the assembly of extracellular fibronectin during epithelial cell transdifferentiation. Journal of Cell Science, 2015 Mar 15;128(6):1083-9. PMCID: PMC4359919.

Huskey NE, Guo T, Evason KJ, Momcilovic O, Pardo D, Creasman KJ, Judson RL, Blelloch R, Oakes SA, Hebrok M, Goga A. CDK1 inhibition targets the p53-NOXA-MCL1 axis, selectively kills embryonic stem cells, and prevents teratoma formation. Stem Cell Reports, 2015 Mar 10;4(3):374-89. PMCID: PMC4375943.

Sopko R, Lin YB, Makhijani K, Alexander B, Perrimon N, Brückner K. A systems-level interrogation identifies regulators of Drosophila blood cell number and survival. PLOS Genetics, 2015 Mar 6;11(3):e1005056. PMCID: PMC4352040.

Kauvar LM, Liu K, Park M, DeChene N, Stephenson R, Tenorio E, Ellsworth SL, Tabata TPetitt M, Tsuge M, Fang-Hoover J, Adler SP, Cui X, McVoy MA, Pereira L. A high-affinity native human antibody neutralizes human cytomegalovirus infection of diverse cell types. Antimicrobial Agents and Chemotherapy, 2015 Mar;59(3):1558-68. PMCID: PMC4325823.

Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga* A, Bandyopadhyay* S. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Cancer Discovery, 2015 Feb;5(2):154-67. PMCID: PMC4407699

LeClaire LL, Rana M, Baumgartner M, Barber DL. The Nck-interacting kinase NIK increases Arp2/3 complex activity by phosphorylating the Arp2 subunit. Journal of Cell Biology, 2015 Jan 19;208(2):161-70. PMCID: PMC4298681.

Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F. The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokineses. Molecular Biology of the Cell, 2015 Jan 1;26(1):78-90. PMCID: PMC4279231.

2014

Xu P, Bailey-Bucktrout S, Xi Y, Xu D, Du D, Zhang Q, Xhang W, Liu J, Melton A, Sheppard D, Chapman HA, Bluestone JA, Derynck R. Innate antiviral host defense attenuates TGF-β Function through IRF3-mediated suppression of smad signaling. Molecular Cell, 2014 Dec 18;56(6):723-37. PMCID: PMC4273650

Galmozzi A, Sonne SB, Altshuler-Keylin S, Hasegawa Y, Shinoda K, Luijten IH, Chang JW, Sharp LZ, Cravatt BF, Saez E, Kajimura S. ThermoMouse: an in vivo model to identify modulators of UCP1 expression in brown adipose tissue. Cell Reports, 2014 Dec 11;9(5):1584-93. PMCID: PMC4268417.

Agrawal P, Wang M, Kim S, Lewis AE, Bush JO. Embryonic expression of EphA receptor genes in mice supports their candidacy for involvement in cleft lip and palate. Developmental Dynamics, 2014 Nov;243(11):1470-6. PMCID: PMC4404412.

Juang BT, Ludwig A, Benedetti KGu C, Collins K, Morales C, Asundi AWittmann T, L'Etoile N, Hagerman PJ. Expression of an expanded CCG-repeat RNA in a single pair of primary senesory neurons impairs olfactory adaptation in Caenorhabditis elegans. Human Molecular Genetics, 2014 Sept 15;23(18):4945-59. PMCID: PMC4140470.

Gold KS, Brückner K. Drosophila as a model for the two myeloid blood cell systems in vertebrates. Experimental Hematology, 2014 Aug;42(8):717-27. PMID: 24946019.

Nevedsky* PI, Emmerson* E, Finley JK, Ettinger ACruz-Pacheco N, Prochazka J, Haddox CL, Northrup E, Hodges C, Mostov KE, Hoffmann M, Knox S. Parasympathetic Innervation Regulates Tubulogenesis in the Developing Salivary Gland. Developmental Cell, 2014 Aug 25;30(4):449-62. PMCID: PMC4155578.

Elting MW*, Hueschen CL*, Udy DB, Dumont S. Force on spindle microtubule minus-ends moves chromosomes. The Journal of Cell Biology, 2014 Jul 21;206(2):245-56. PMCID: PMC4107791.

Stehbens SJ, Paszek M, Pemble H, Ettinger A, Gierke S, Wittmann T. CLASPs link focal-adhesion-associated microtubule capture to localized exocytosis and adhesion site turnover. Nature Cell Biology, 2014 Jun;16(6):561-73. PMCID: PMC4108447.

Guo MS, Gross CA. Stress-induced remodeling of the bacterial proteome. Current Biology, 2014 May 19;24(10):R424-34. PMCID: PMC4089988.

Ozeki N, Mogi M, Yamaguchi H, Hiyama T, Kawai R, Hase N, Nakata K, Nakamura H, Kramer RH. Differentiation of human skeletal muscle stem cells into odontoblasts is dependent on induction of alpha-1 intergrin expression. Journal of Biological Chemistry, 2014 May 16;289(20):14380-91. PMCID: PMC4022904.

Lamouille S, Xu J, Derynck R. Molecular mechanisms of epithelial-mesenchymal transition. Nature Reviews Molecular Cell Biology, 2014 Mar;15(3):178-96. PMCID: PMC4240281.

Lim L, Balakrishnan A, Huskey N, Jones KD, Jodari M, Ng R, Song G, Riordan J, Anderton B, Cheung ST, Willenbring H, Dupuy A, Chen X, Brown D, Chang AN, Goga A. MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancer. Hepatology, 2014 Jan;59(1):202-15. PMCID: PMC3877416.