About Matt Shirley

PhD student at Johns Hopkins School of Medicine

Publication Spotlight: May 2013

Publication spotlight is a series designed to showcase noteworthy BCMB publications from students and faculty. Articles we showcase are newly indexed in PubMed. If you have a recent publication that you are proud of tell us about it.

May

Baile MG, Whited K, Claypool SM. Deacylation on the Matrix Side of the Mitochondrial Inner Membrane Regulates Cardiolipin Remodeling. Mol Biol Cell. 2013 May 1. PMID: 23637464.

Zhang F, Bhat S, Gabelli SB, Chen X, Miller MS, Nacev BA, Cheng YL, Meyers DJ, Tenney K, Shim JS, Crews P, Amzel LM, Ma D, Liu JO. Pyridinylquinazolines Selectively Inhibit Human Methionine Aminopeptidase-1 in Cells. J Med Chem. 2013 May 1. PMID: 23634668.

April

Stine RR, Matunis EL. Stem cell competition: finding balance in the niche. Trends Cell Biol. 2013 Apr 15. PMID: 23597843.

Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Seop Jeong J, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013 Apr 2. PMID: 23549483.

March

Huang Q, Purzycka KJ, Lusvarghi S, Li D, Legrice SF, Boeke JD. Retrotransposon Ty1 RNA contains a 5′-terminal long-range pseudoknot required for efficient reverse transcription. RNA. 2013 Mar. PMID: 23329695.

Shilagardi K, Li S, Luo F, Marikar F, Duan R, Jin P, Kim JH, Murnen K, Chen EH. Actin-Propelled Invasive Membrane Protrusions Promote Fusogenic Protein Engagement During Cell-Cell Fusion. Science. 2013 Mar 7. PMID: 23470732.

February

Han L, Ma C, Liu Q, Weng HJ, Cui Y, Tang Z, Kim Y, Nie H, Qu L, Patel KN, Li Z, McNeil B, He S, Guan Y, Xiao B, Lamotte RH, Dong X. A subpopulation of nociceptors specifically linked to itch. Nat Neurosci. 2013 Feb 16. PMID: 23263443.

If you have a publication you would like featured in this month’s Spotlight, please let us know.

Publication Spotlight: April 2013

Publication spotlight is a series designed to showcase noteworthy BCMB publications from students and faculty. Articles we showcase are newly indexed in PubMed. If you have a recent publication that you are proud of, tell us about it.

April

Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M,
Clark HM, Hu S, Hwang W, Seop Jeong J, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S,
Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S,
Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J.
Construction of human activity-based phosphorylation networks. Mol Syst Biol.
2013 Apr 2. PubMed PMID: 23549483.

March

Shilagardi K, Li S, Luo F, Marikar F, Duan R, Jin P, Kim JH, Murnen K, Chen
EH. Actin-Propelled Invasive Membrane Protrusions Promote Fusogenic Protein Engagement During Cell-Cell Fusion. Science. 2013 Mar 7. PubMed PMID: 23470732.

February

Han L, Ma C, Liu Q, Weng HJ, Cui Y, Tang Z, Kim Y, Nie H, Qu L, Patel KN, Li
Z, McNeil B, He S, Guan Y, Xiao B, Lamotte RH, Dong X. A subpopulation of
nociceptors specifically linked to itch. Nat Neurosci. 2013 Feb 16. PubMed PMID: 23263443.

January

Chan W, Schaffer TB, Pomerantz JL. A quantitative signaling screen identifies CARD11 mutations in the CARD and LATCH domains that induce Bcl10 ubiquitination and human lymphoma cell survival. Mol Cell Biol. 2013 Jan;33(2):429-43. PMID: 23149938.

October (2012)

West-Foyle H, Robinson DN. Cytokinesis mechanics and mechanosensing.
Cytoskeleton (Hoboken). 2012 Oct.  PubMed PMID: 22761196.

If you have a publication you would like featured in this month’s Spotlight, please let us know.

Publication Spotlight: March 2013

Publication spotlight is a series designed to showcase noteworthy BCMB publications from students and faculty. If you have a recent publication that you are proud of, tell us about it.

March

Shilagardi K, Li S, Luo F, Marikar F, Duan R, Jin P, Kim JH, Murnen K, Chen
EH. Actin-Propelled Invasive Membrane Protrusions Promote Fusogenic Protein Engagement During Cell-Cell Fusion. Science. 2013 Mar 7. PubMed PMID: 23470732.

January

Chan W, Schaffer TB, Pomerantz JL. A quantitative signaling screen identifies CARD11 mutations in the CARD and LATCH domains that induce Bcl10 ubiquitination and human lymphoma cell survival. Mol Cell Biol. 2013 Jan;33(2):429-43. PMID: 23149938.

November

Tamura Y, Onguka O, Itoh K, Endo T, Iijima M, Claypool SM, Sesaki H. Phosphatidylethanolamine biosynthesis in mitochondria: phosphatidylserine (PS) trafficking is independent of a PS decarboxylase and intermembrane space proteins UPS1P and UPS2P. J Biol Chem. 2012 Dec 21;287(52):43961-71. PMID: 23124206.

Hobbs RP, Lessard JC, Coulombe PA. Keratin intermediate filament proteins – novel regulators of inflammation and immunity in skin. J Cell Sci. 2012 Nov 15;125(Pt 22):5257-8. PMID: 23377656.

If you have a publication you would like featured in this month’s Spotlight, please let us know.

Publication Spotlight: December 2012

Publication spotlight is a series designed to showcase noteworthy BCMB publications from students and faculty. If you have a recent publication that you are proud of, tell us about it.

January

Wang JT, Seydoux G. Germ cell specification. Adv Exp Med Biol. 2013;757:17-39. Review. PMID: 22872473.

Baile MG, Claypool SM. The power of yeast to model diseases of the powerhouse of the cell. Front Biosci. 2013 Jan 1;18:241-78. PMID: 23276920.

December

Wang Y, Rattner A, Zhou Y, Williams J, Smallwood PM, Nathans J. Norrin/Frizzled4 signaling in retinal vascular development and blood brain barrier plasticity. Cell. 2012 Dec 7;151(6):1332-44. PMID: 23217714.

Han L, Ma C, Liu Q, Weng HJ, Cui Y, Tang Z, Kim Y, Nie H, Qu L, Patel KN, Li Z, McNeil B, He S, Guan Y, Xiao B, Lamotte RH, Dong X. A subpopulation of nociceptors specifically linked to itch. Nat Neurosci. 2012 Dec 23. PMID: 23263443.

September

Tu-Sekine B, Goldschmidt H, Petro E, Raben DM. Diacylglycerol kinase θ: Regulation and stability. Adv Biol Regul. 2012 Sep 20. PMID: 23266086.

Sisk JM, Clements JE, Witwer KW. miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction. Viruses. 2012 Sep 25;4(10):1844-64. PMID: 23202444.

October

Deng K, Zink MC, Clements JE, Siliciano RF. A quantitative measurement of antiviral activity of anti-human immunodeficiency virus type 1 drugs against simian immunodeficiency virus infection: dose-response curve slope strongly influences class-specific inhibitory potential. J Virol. 2012 Oct;86(20):11368-72. PMID: 22875968.

Nalayanda DD, Puleo C, Fulton WB, Sharpe LM, Wang TH, Abdullah F. An open-access microfluidic model for lung-specific functional studies at an air-liquid interface. Biomed Microdevices. 2009 Oct;11(5):1081-9. PMID: 19484389.

If you have publication you would like featured in this month’s Spotlight, please let us know.

Alumni Profile: Seth Zonies, Technology Commercialization Specialist

Seth Zonies

I like to observe the world and know how it works. The thing that always fired me up was how incredible it is that mothers and daughters and fathers and sons could look and act so alike. This is where my fascination with genetics began.

Seth Zonies completed his graduate work in the lab of Geraldine Seydoux in 2011. Before he was a BCMB student, Seth worked at the National Human Genome Research Institute (NHGRI) at the NIH in Bethesda, studying the development of hearing in zebrafish. Even before graduate school Seth was thinking about his future:

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Publication Spotlight: November 2012

November

Chan W, Schaffer TB, Pomerantz JL. A quantitative signaling screen identifies CARD11 mutations in the CARD and LATCH Domains that induce Bcl10 ubiquitination
and human lymphoma cell survival. Mol Cell Biol. 2012 Nov 12. PubMed PMID: 23149938.

Stevens EL, Baugher JD, Shirley MD, Frelin LP, Pevsner J. Unexpected Relationships and Inbreeding in HapMap Phase III Populations. PLoS One. 2012;7(11):e49575. doi: 10.1371/journal.pone.0049575. Epub 2012 Nov 19. PubMed PMID: 23185369.

Clayton AM, Cirimotich CM, Dong Y, Dimopoulos G. Caudal is a negative regulator of the Anopheles IMD Pathway that controls resistance to P. falciparum infection. Dev Comp Immunol. 2012 Nov 22. doi:pii: S0145-305X(12)00220-0. 10.1016/j.dci.2012.10.009. [Epub ahead of print] PubMed PMID: 23178401.

October

Zhu H, Cox E, Qian J. Functional protein microarray as molecular decathlete: A
versatile player in clinical proteomics. Proteomics Clin Appl. 2012 Oct 2. doi:
10.1002/prca.201200041. PubMed PMID: 23027439.

August

Hatori Y, Clasen S, Hasan NM, Barry AN, Lutsenko S. Functional partnership of
the copper export machinery and glutathione balance in human cells. J Biol Chem.
2012 Aug 3;287(32):26678-87. doi: 10.1074/jbc.M112.381178. Epub 2012 May 30.
PubMed PMID: 22648419.

If you have publication you would like featured in this month’s Spotlight, please let us know.

November Lab Spotlight – Pevsner Lab

Lab Stats

PI Name: Jonathan Pevsner
Number of Years in BCMB: >12
Model System(s): Human genome, mammalian cell culture
Research Area: Genomics of childhood and rare diseases, relatedness and inbreeding within human populations.
Lab Website
Lab Personnel:
Joseph Baugher – BCMB student
Eric Stevens – Human Genetics student
Matt Shirley – BCMB student
Larry Frelin – Research Technician

Dr. Pevsner splits his work day between the lab and his office.

BCMBNews (BN): You wrote a very successful bioinformatics textbook. What motivated you to do this?

JP: I’m dedicated to teaching—including a BCMB core course—and the book is an extension of the teaching. Writing it has helped me become a better teacher.

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