CBC-Attributed Research Publications 2011

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Adamian L, Naveed H, Liang J. Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis. Biochim Biophys Acta. 2011 Apr;1808(4):1092-102. (PubMed)

Aguirre B, Costas M, Cabrera N, Mendoza-Hernández G, Helseth DL Jr, Fernández P, Tuena de Gómez-Puyou M, Pérez-Montfort R, Torres-Larios A, Gómez-Puyou A. A Ribosomal Misincorporation of Lys for Arg in Human Triosephosphate Isomerase Expressed in Escherichia coli Gives Rise to Two Protein Populations. PLoS ONE. 2011 6(6): e21035. doi:10.1371/journal.pone.0021035 (PubMed)

Albert BJ, Yamaoka Y, Yamamoto H. Rapid total syntheses utilizing “supersilyl” chemistry. Angew Chem Int Ed Engl. 2011 Mar 7;50(11):2610-2. (PubMed)

Al-Dhaheri M, Wu J, Skliris GP, Li J, Higashimato K, Wang Y, White KP, Lambert P, Zhu Y, Murphy L, Xu W. CARM1 is an important determinant of ER{alpha}-dependent breast cancer cell differentiation and proliferation in breast cancer cells. Cancer Res. 2011 Mar 15;71(6):2118-28. (PubMed)

Ames BD, Haynes SW, Gao X, Evans BS, Kelleher NL, Tang Y, Walsh CT. Complexity Generation in Fungal Peptidyl Alkaloid Biosynthesis: Oxidation of Fumiquinazoline A to the Heptacyclic Hemiaminal Fumiquinazoline C by the Flavoenzyme Af12070 from Aspergillus fumigatus. Biochemistry. 2011 Oct 11;50(40):8756-69. (PubMed)

Arthur RK, Ruvinsky I. Evidence that purifying selection acts on promoter sequences. Genetics. 2011 Nov;189(3):1121-6. (PubMed)

Atkinson IC, Lu A, Thulborn KR. Clinically constrained optimization of flexTPI acquisition parameters for the tissue sodium concentration bioscale. Magn Reson Med. 2011 Oct;66(4):1089-99. (PubMed)

Bahadur D, Dravid VP. Hybrid nanostructures for diagnostics and therapeutics. Adv Drug Deliv Rev. 2011 Nov;63(14-15):1227. (PubMed)

Bai H, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7419-24. (PubMed)

Barrière A, Gordon KL, Ruvinsky I. Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet. 2011 Jun;7(6):e1002095. (PubMed)

Bass J, Takahashi JS. Circadian rhythms: Redox redux. (Invited Commentary). Nature. 2011 Jan 27;469(7331):476-8. (PubMed)

Bass J. Physiology: On time metabolism. (Invited Commentary). Nature. 2011 Dec 21;480(7378):466-7. (PubMed)

Bellis AD, Bernabé BP, Weiss MS, Yarrington ME, Barbolina MV, Pannier AK, Jeruss JS, Broadbelt LJ, Shea LD. Cellular arrays for large-scale analysis of transcription factor activity. Biotechnol Bioeng. 2011 Feb;108(2):395-403. (PubMed)

Below JE, Gamazon ER, Morrison JV, Konkashbaev A, Pluzhnikov A, McKeigue PM, Parra EJ, Elbein SC, Hallman DM, Nicolae DL, Bell GI, Cruz M, Cox NJ, Hanis CL. Genome-wide association and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals. Diabetologia. 2011 Aug;54(8):2047-55. (PubMed)

Bernhardt ML, Kim AM, O’Halloran TV, Woodruff TK. Zinc requirement during meiosis I-meiosis II transition in mouse oocytes is independent of the MOS-MAPK pathway. Biol Reprod. 2011 Mar;84(3):526-36. (PubMed)

Bissonnette CJ, Lyass L, Bhattacharyya BJ, Belmadani A, Miller RJ, Kessler JA. The controlled generation of functional basal forebrain cholinergic neurons from human embryonic stem cells. Stem Cells. 2011 May;29(5):802-11. (PubMed)

Bonnell DA, Dravid VP, Weiss PS, Ginger D, Jackson K, Eigler D, Craighead H, Isaacs E. Enabling and Investigative Tools: Measuring Methods, Instruments, and Metrology. In: Nanotechnology Research Directions for Societal Needs in 2020: Retrospective and Outlook. 2011 71-107. (wtec.org)

Brugarolas P, Duguid EM, Zhang W, Poor CB, He C. Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus. Acta Cryst. 2011 D67, 707-715. (scripts.iucr.org)

Campanharo AS, Sirer MI, Malmgren RD, Ramos FM, Amaral LA. Duality between time series and networks. PLoS One. 2011;6(8):e23378. (PubMed)

Chaudhuri R, Tang S, Zhao G, Lu H, Case DA, Johnson ME. Comparison of SARS and NL63 Papain-Like Protease Binding Sites and Binding Site Dynamics: Inhibitor Design Implications. J Mol Biol. 2011 Nov 25;414(2):272-88. (PubMed)

Chen P, Lingen M, Sonis ST, Walsh-Reitz MM, Toback FG. Role of AMP-18 in oral mucositis. Oral Oncol. 2011 Sep;47(9):831-9. (PubMed)

Chen PR, Brugarolas P, He C. Redox signaling in human pathogens. Antioxid Redox Signal. 2011 Mar 15;14(6):1107-18. (PubMed)

Chen T, Benmohamed R, Arvanites AC, Ralay Ranaivo H, Morimoto RI, Ferrante RJ, Watterson DM, Kirsch DR, Silverman RB. Arylsulfanyl pyrazolones block mutant SOD1-G93A aggregation. Potential application for the treatment of amyotrophic lateral sclerosis. Bioorg Med Chem. 2011 Jan 1;19(1):613-22. (PubMed)

Chen ZX, Zhang YE, Vibranovski M, Luo J, Gao G, Long M. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol. 2011 Oct;28(10):2823-32. (PubMed)

Cheng J, Tiyaboonchai A, Yamashita YM, Hunt AJ. Asymmetric division of cyst stem cells in Drosophila testis is ensured by anaphase spindle repositioning. Development. 2011 Mar;138(5):831-7. (PubMed)

Cheon CH, Yamamoto H. Super Brønsted acid catalysis. Chem Commun (Camb). 2011 Mar 21;47(11):3043-56. (PubMed)

Cheung D, Miles C, Kreitman M, Ma J. Scaling of the Bicoid morphogen gradient by a volume-dependent production rate. Development. 2011 Jul;138(13):2741-9. (PubMed)

Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A, Amit I, Hacohen N. Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell. 2011 Nov 11;147(4):853-67. (PubMed)

Chow CR, Yau DM, Kozasa T. p115RhoGEF. UCSD-Nature Molecule Pages. 2011. (signaling-gateway.org)

Collier JH, Segura T. Evolving the use of peptides as components of biomaterials. Biomaterials. 2011 Jun;32(18):4198-204. (PubMed)

Colwill K; Renewable Protein Binder Working Group; In vitro Antibody Consortium, Persson H, Jarvik NE, Wyrzucki A, Wojcik J, Koide A, Kossiakoff AA, Koide S, Sidhu S, Dyson MR, Pershad K, Pavlovic JD, Karatt-Vellatt A, Schofield DJ, Kay BK, McCafferty J, Mersmann M, Meier D, Mersmann J, Helmsing S, Hust M, Dübel S; Monash Antibody Technologies Facility, Berkowicz S, Freemantle A, Spiegel M, Sawyer A, Layton D, Nice E; Pawson Laboratory, Dai A, Rocks O, Williton K, Fellouse FA, Hersi K, Pawson T; Human Protein Atlas, Nilsson P, Sundberg M, Sjöberg R, Sivertsson A, Schwenk JM, Takanen JO, Hober S, Uhlén M; Structural Genomics Consortium, Dahlgren LG, Flores A, Johansson I, Weigelt J, Crombet L, Loppnau P, Kozieradzki I, Cossar D, Arrowsmith CH, Edwards AM, Gräslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods. 2011 May 15;8(7):551-8. (PubMed)

Compton PD, Zamdborg L, Thomas PM, Kelleher NL. On the Scalability and Requirements of Whole Protein Mass Spectrometry. Anal Chem. 2011 Sep 1;83(17):6868-74. (PubMed)

Cui J, Hao J, Ulanovskaya OA, Dundas J, Liang J, Kozmin SA. Organic Synthesis Toward Small-Molecule Probes and Drugs Special Feature: Creation and manipulation of common functional groups en route to a skeletally diverse chemical library. Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6763-8. (PubMed)

Curtis MW, Russell B. Micromechanical regulation in cardiac myocytes and fibroblasts: implications for tissue remodeling. Pflugers Arch. 2011 Jul;462(1):105-17. (PubMed)

Cutler JI, Zhang K, Zheng D, Auyeung E, Prigodich AE, Mirkin CA. Polyvalent nucleic acid nanostructures. J Am Chem Soc. 2011 Jun 22;133(24):9254-7. (PubMed)

Dai Q, Sengupta R, Deb SK, Piccirilli JA. Synthesis of 2′-N-methylamino-2′-deoxyguanosine and 2′-N,N-dimethylamino-2′-deoxyguanosine and their incorporation into RNA by phosphoramidite chemistry. J Org Chem. 2011 Nov 4;76(21):8718-25. (PubMed)

Dai Q, Song CX, Pan T, He C. Syntheses of Two 5-Hydroxymethyl-2′-deoxycytidine Phosphoramidites with TBDMS as the 5-Hydroxymethyl Protecting Group and Their Incorporation into DNA. J Org Chem. 2011 May 20;76(10):4182-8. (PubMed)

De M, Chou SS, Dravid VP. Graphene oxide as an enzyme inhibitor: modulation of activity of α-chymotrypsin. J Am Chem Soc. 2011 Nov 9;133(44):17524-7. (PubMed)

De M, Chou SS, Joshi HM, Dravid VP. Hybrid magnetic nanostructures (MNS) for magnetic resonance imaging applications. Adv Drug Deliv Rev. 2011 Nov;63(14-15):1282-99. (PubMed)

Divoli A, Mendonça EA, Evans JA, Rzhetsky A. Conflicting biomedical assumptions for mathematical modeling: the case of cancer metastasis. PLoS Comput Biol. 2011 Oct;7(10):e1002132. (PubMed)

Dizon ML, Maa T, Kessler JA. The bone morphogenetic protein antagonist noggin protects white matter after perinatal hypoxia-ischemia. Neurobiol Dis. 2011 Jun;42(3):318-26. (PubMed)

Doré LC, Crispino JD. Transcription factor networks in erythroid cell and megakaryocyte development. Blood. 2011 Blood. 2011 Jul 14;118(2):231-9. (PubMed)

Doucette AA, Tran JC, Wall MJ, Fitzsimmons S. Intact proteome fractionation strategies compatible with mass spectrometry. Review. Expert Review of Proteomics. December 2011, Vol. 8, No. 6, Pages 787-800, DOI 10.1586/epr.11.67 (PubMed)

Dundas J, Adamian L, Liang J. Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins. J Mol Biol. 2011 Mar 11;406(5):713-29. (PubMed)

ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. (PubMed)

Evans BS, Chen Y, Metcalf WW, Zhao H, Kelleher NL. Directed Evolution of the Nonribosomal Peptide Synthetase AdmK Generates New Andrimid Derivatives In Vivo. Chem Biol. 2011 May 27;18(5):601-7. (PubMed)

Evans BS, Ntai I, Chen Y, Robinson SJ, Kelleher NL. Proteomics-Based Discovery of Koranimine, a Cyclic Imine Natural Product. J Am Chem Soc. 2011 May 18;133(19):7316-9. (PubMed)

Evans BS, Robinson SJ, Kelleher NL. Surveys of non-ribosomal peptide and polyketide assembly lines in fungi and prospects for their analysis in vitro and in vivo. Fungal Genet Biol. 2011 Jan;48(1):49-61. (PubMed)

Evans JA, Rzhetsky A. Advancing science through mining libraries, ontologies, and communities. J Biol Chem. 2011 Jul 8;286(27):23659-66. (PubMed)

Fajans SS, Bell GI. MODY: history, genetics, pathophysiology, and clinical decision making. Diabetes Care. 2011 Aug;34(8):1878-84. (PubMed)

Feng X, Grossman R, Stein L. PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics. 2011 May 9;12:139. (PubMed)

Fenner D, Odili S, Hong HK, Kobayashi Y, Kohsaka A, Siepka SM, Vitaterna MH, Chen P, Zelent B, Grimsby J, Takahashi JS, Matschinsky FM, Bass J. Generation of ENU diabetes models in the mouse demostrates genotype-specific action of glucokinase activators. J Biol Chem. 2011 Nov 11;286(45):39560-72. (PubMed)

Ferreira A, Bigio EH. Calpain-mediated tau cleavage: a mechanism leading to neurodegeneration shared by multiple tauopathies. Mol Med. 2011;17(7-8):676-85. (PubMed)

Fu H, Chen H, Zhang X, Qu Y, Marko JF, Yan J. Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching. Nucleic Acids Res. 2011 Apr 1;39(8):3473-81. (PubMed)

Fushimi K, Long C, Jayaram N, Chen X, Li L, Wu JY. Expression of human FUS/TLS in yeast leads to protein aggregation and cytotoxicity, recapitulating key features of FUS proteinopathy. Protein Cell. 2011 Feb;2(2):141-9. (PubMed)

García J. The calcium channel α2/δ1 subunit interacts with ATP5b in the plasma membrane of developing muscle cells. Am J Physiol Cell Physiol. 2011 Jul;301(1):C44-52. (PubMed)

Gasiorowski JZ, Collier JH. Directed Intermixing in Multicomponent Self-Assembling Biomaterials. Biomacromolecules. 2011 Oct 10;12(10):3549-58. (PubMed)

Gerbasi VR, Preall JB, Golden DE, Powell DW, Cummins TD, Sontheimer EJ. Blanks, a nuclear siRNA/dsRNA-binding complex component, is required for Drosophila spermiogenesis. Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3204-9. (PubMed)

Gessmann D, Mager F, Naveed H, Arnold T, Weirich S, Linke D, Liang J, Nussberger S. Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations. J Mol Biol. 2011 Oct 14;413(1):150-61. (PubMed)

Gidalevitz T, Prahlad V, Morimoto RI. The stress of protein misfolding: from single cells to multicellular organisms. Cold Spring Harb Perspect Biol. 2011 Jun 1;3(6). (PubMed)

Godley LA, Cunningham J, Dolan ME, Huang RS, Gurbuxani S, McNerney ME, Larson RA, Leong H, Lussier Y, Onel K, Odenike O, Stock W, White KP, Le Beau MM. An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol. 2011 Apr;38(2):215-24. (PubMed)

Graham JS, Johnson RC, Marko JF. Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res. 2011 Mar 1;39(6):2249-59. (PubMed)

Graham JS, Johnson RC, Marko JF. Counting proteins bound to a single DNA molecule. Biochem Biophys Res Commun. 2011 Nov 11;415(1):131-4. (PubMed)

Greeley SA, John PM, Winn AN, Ornelas J, Lipton RB, Philipson LH, Bell GI, Huang ES. The cost-effectiveness of personalized genetic medicine: the case of genetic testing in neonatal diabetes. Diabetes Care. 2011 Mar;34(3):622-7. (PubMed)

Greeley SA, Naylor RN, Philipson LH, Bell GI. Neonatal diabetes: an expanding list of genes allows for improved diagnosis and treatment. Curr Diab Rep. 2011 Dec;11(6):519-32. (PubMed)

Gu Y, Grossman R. Toward Efficient and Simplified Distributed Data Intensive Computing. IEEE Transactions on Parallel and Distributed Systems. 2011 Volume 22, Issue 6, pages 974-984. (ieeexplore.ieee.org)

Guan W, Ban L, Cai L, Li L, Chen W, Liu X, Mrksich M, Wang PG. Combining carbochips and mass spectrometry to study the donor specificity for the Neisseria meningitidis β1,3-N-acetylglucosaminyltransferase LgtA. Bioorg Med Chem Lett. 2011 Sep 1;21(17):5025-8. (PubMed)

Gurard-Levin ZA, Scholle MD, Eisenberg AH, Mrksich M. High-throughput screening of small molecule libraries using SAMDI mass spectrometry. ACS Comb Sci. 2011 Jul 11;13(4):347-50. (PubMed)

Hajicek N, Kukimoto-Niino M, Mishima-Tsumagari C, Chow CR, Shirouzu M, Terada T, Patel M, Yokoyama S, Kozasa T. Identification of critical residues in Galpha13 for stimulation of p115RhoGEF activity and the structure of the Galpha13-p115RhoGEF RH domain complex. J Biol Chem. 2011 Jun 10;286(23):20625-36. (PubMed)

Han TH, Huang YK, Tan AT, Dravid VP, Huang J. Steam etched porous graphene oxide network for chemical sensing. J Am Chem Soc. 2011 Oct 5;133(39):15264-7. (PubMed)

Han Y, Khodr CE, Sapru MK, Pedapati J, Bohn MC. A microRNA embedded AAV alpha-synuclein gene silencing vector for dopaminergic neurons. Brain Res. 2011 Apr 22;1386:15-24. (PubMed)

Hao L, Patel PC, Alhasan AH, Giljohann DA, Mirkin CA. Nucleic acid-gold nanoparticle conjugates as mimics of microRNA. Small. 2011 Nov 18;7(22):3158-62. (PubMed)

Hause RJ, Kim HD, Leung KK, Jones RB. Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches. Expert Rev Proteomics. 2011 Oct;8(5):565-75. (PubMed)

Hay N. Akt isoforms and glucose homeostasis – the leptin connection. Trends Endocrinol Metab. 2011 Feb;22(2):66-73. (PubMed)

Hay N. Interplay between FOXO, TOR, and Akt. Biochim Biophys Acta. 2011 Nov;1813(11):1965-70. (PubMed)

He BZ, Holloway AK, Maerkl SJ, Kreitman M. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet. 2011 Apr;7(4):e1002053. (PubMed)

He Z, Eichel K, Ruvinsky I. Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances. PLoS One. 2011;6(7):e22677. (PubMed)

Ho JW, Bishop E, Kharchenko PV, Negre N, White KP, Park PJ. ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis. BMC Genomics. 2011 Feb 28;12(1):134. (PubMed)

Hollenhorst MA, Ntai I, Badet B, Kelleher NL, Walsh CT. A Head-to-Head Comparison of Eneamide and Epoxyamide Inhibitors of Glucosamine-6-Phosphate Synthase from the Dapdiamide Biosynthetic Pathway. Biochemistry. 2011 May 17;50(19):3859-61. (PubMed)

Hu C, Eggler AL, Mesecar AD, van Breemen RB. Modification of Keap1 Cysteine Residues by Sulforaphane. Chem Res Toxicol. 2011 Apr 18;24(4):515-21. (PubMed)

Huang L, Roqueiro D, Dai Y. Analyzing mRNA and microRNA co-expression profiles to identify pathways and their potential regulators in ER+ and ER- breast tumors. Proceedings of 2011 IEEE Engineering in Medicine and Biology Society (EMBC’11). (PubMed)

Huang L, Zhao S, Frasor JM, Dai Y. An Integrated Bioinformatics Approach Identifies Elevated Cyclin E2 Expression and E2F Activity as Distinct Features of Tamoxifen Resistant Breast Tumors. PLoS ONE 2011 6(7): e22274. (PubMed)

Huang W, Ramsey KM, Marcheva B, Bass J. Circadian rhythms, sleep, and metabolism. J Clin Invest. 2011 Jun 1;121(6):2133-41. (PubMed)

Jalali A, Bassuk AG, Kan L, Israsena N, Mukhopadhyay A, McGuire T, Kessler JA. HeyL promotes neuronal differentiation of neural progenitor cells. J Neurosci Res. 2011 Mar;89(3):299-309. (PubMed)

Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, He C. N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011 Oct 16;7(12):885-7. (PubMed)

Jimenez-Morales D, Liang J. Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria. PLoS One. 2011;6(11):e26400. (PubMed)

Jung JP, Moyano JV, Collier JH. Multifactorial optimization of endothelial cell growth using modular synthetic extracellular matrices. Integr Biol (Camb). 2011 Mar;3(3):185-96. (PubMed)

Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, Victorsen A, White KP, Kellis M. Evidence of abundant stop codon readthrough in Drosophila and other Metazoa. Genome Res. 2011 Dec;21(12):2096-113. (PubMed)

Kan L, Lounev VY, Pignolo RJ, Duan L, Liu Y, Stock SR, McGuire TL, Lu B, Gerard NP, Shore EM, Kaplan FS, Kessler JA. Substance P signaling mediates BMP-dependent heterotopic ossification. J Cell Biochem. 2011 Oct;112(10):2759-72. (PubMed)

Kar A, Fushimi K, Zhou X, Ray P, Shi C, Chen X, Liu Z, Chen S, Wu JY. RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5’ splice site. Mol Cell Biol. 2011 May;31(9):1812-21. (PubMed)

Karfeld-Sulzer LS, Waters EA, Kohlmeir EK, Kissler H, Zhang X, Kaufman DB, Barron AE, Meade TJ. Protein polymer MRI contrast agents: Longitudinal analysis of biomaterials in vivo. Magn Reson Med. 2011 Jan;65(1):220-8. (PubMed)

Khodr CE, Sapru MK, Pedapati J, Han Y, West NC, Kells AP, Bankiewicz KS, Bohn MC. An alpha- synuclein AAV gene silencing vector ameliorates a behavioral deficit in a rat model of Parkinson’s disease, but displays toxicity in dopamine neurons. Brain Research. 2011 Jun 13;1395:94-107. (PubMed)

Kim AM, Bernhardt ML, Kong BY, Ahn RW, Vogt S, Woodruff TK, O’Halloran TV. Zinc Sparks Are Triggered by Fertilization and Facilitate Cell Cycle Resumption in Mammalian Eggs. ACS Chem Biol. 2011 Jul 15;6(7):716-23. (PubMed)

Kim HJ, Du W, Ismagilov RF. Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(ii). Integr Biol (Camb). 2011 Feb;3(2):126-33. (PubMed)

Klaić L, Trippier PC, Mishra RK, Morimoto RI, Silverman RB. Remarkable Stereospecific Conjugate Additions to the Hsp90 Inhibitor Celastrol. J Am Chem Soc. 2011 Dec 14;133(49):19634-7. (PubMed)

Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol. 2011 Jan;18(1):100-6. (PubMed)

Kording KP. Of toasters and molecular ticker tapes. PLoS Comput Biol. 2011 Dec;7(12):e1002291. Review. (PubMed)

Kowal AS, Chisholm RL. Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion. Eukaryot Cell. 2011 May;10(5):662-71. (PubMed)

Kozasa T, Hajicek N, Chow CR, Suzuki N. Signalling mechanisms of RhoGTPase regulation by the heterotrimeric G proteins G12 and G13. J Biochem. 2011 Oct;150(4):357-69. (PubMed)

Krantz SB, Shields MA, Dangi-Garimella S, Cheon EC, Barron MR, Hwang RF, Rao MS, Grippo PJ, Bentrem DJ, Munshi HG. MT1-MMP cooperates with Kras(G12D) to promote pancreatic fibrosis through increased TGF-β signaling. Mol Cancer Res. 2011 Oct;9(10):1294-304. (PubMed)

Kuzmis A, Lim SB, Desai E, Jeon E, Lee BS, Rubinstein I, Onyüksel H. Micellar nanomedicine of human neuropeptide Y. Nanomedicine. 2011 Aug;7(4):464-71. (PubMed)

Lahn BT. The "occlusis" model of cell fate restriction. Bioessays. 2011 Jan;33(1):13-20. (PubMed)

Lee BS, Jayathilaka GD, Huang JS, Vida LN, Honig GR, Gupta S. Analyses of in vitro nonenzymatic glycation of normal and variant hemoglobins by maldi-tof mass spectrometry. J Biomol Tech. 2011 Sep;22(3):90-4. (PubMed)

Lee SM, Lee OS, O’Halloran TV, Schatz GC, Nguyen ST. Triggered release of pharmacophores from [Ni(HAsO₃)]-loaded polymer-caged nanobin enhances pro-apoptotic activity: a combined experimental and theoretical study. ACS Nano. 2011 May 24;5(5):3961-9. (PubMed)

Li Q, Singh CR, Ma S, Price ND, Jagannath C. Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages. J Proteome Res. 2011 May 6;10(5):2425-39. (PubMed)

Li Q. Precision Quantitative Proteomics with Fourier-Transform Mass Spectrometry. (Chapter) In: Fourier Transforms – New Analytical Approaches and FTIR Strategies). Publisher: InTech, April 2011. (intechopen.com)

Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanical forces mediate localized topological change in epithelia. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:178-81. (PubMed)

Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M. Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta. 2012 Apr;1818(4):927-41. Review. (PubMed)

Loor G, Kondapalli J, Iwase H, Chandel NS, Waypa GB, Guzy RD, Vanden Hoek TL, Schumacker PT. Mitochondrial oxidant stress triggers cell death in simulated ischemia-reperfusion. Biochim Biophys Acta. 2011 Jul;1813(7):1382-94. (PubMed)

Lott SE, Ludwig MZ, Kreitman M. Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia. Evolution. 2011 May;65(5):1388-99. (PubMed)

Lu A, Atkinson IC, Vaughn JT, Thulborn KR. Impact of gradient timing error on the tissue sodium concentration bioscale measured using flexible twisted projection imaging. J Magn Reson. 2011 Dec;213(1):176-81. (PubMed)

Ludwig MZ, Manu, Kittler R, White KP, Kreitman M. Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness. PLoS Genet. 2011 Nov;7(11):e1002364. (PubMed)

Maggioni M, Santambrogio MD, Liang J. GPU-accelerated Chemical Similarity Assessment for Large Scale Databases. Procedia Computer Science Volume 4, 2011, Pages 2007-2016. Proceedings of the International Conference on Computational Science, ICCS 2011. (sciencedirect.com)

Mandal M, Powers SE, Maienschein-Cline M, Bartom ET, Hamel KM, Kee BL, Dinner AR, Clark MR. Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nat Immunol. 2011 Oct 30;12(12):1212-20. (PubMed)

Mao Y, Zamdborg L, Kelleher NL, Hendrickson CL, Marshall AG. Identification of Phosphorylated Human Peptides by Accurate Mass Measurement Alone. Int. J. Mass Spectrom. 2011 308, 357-361. (PubMed)

Marcheva B, Ramsey KM, Bass J. Circadian genes and insulin exocytosis. Cell Logist. 2011 Jan;1(1):32-36. (PubMed)

Marko JF. The mitotic chromosome: structure and mechanics. (Book Chapter.) In: Genome Organization and Function in the Cell Nucleus. Ed. K. Rippe, Wiley-VCH. 2012 Ch. 18, 449-485. (onlinelibrary.wiley.com)

Martinez-Garcia E, Popovic R, Min DJ, Sweet SM, Thomas PM, Zamdborg L, Heffner A, Will C, Lamy L, Staudt LM, Levens DL, Kelleher NL, Licht JD. The MMSET histone methyl transferase switches global histone methylation and alters gene expression in t(4;14) multiple myeloma cells. Blood. 2011 Jan 6;117(1):211-20. (PubMed)

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