Biology Department

Recent Publications

january 2007-december 2007

Dong Cai, Cheryl A. Doughty, Terra B. Potocky, Fay J. Dufort, Zhongping Huang, Derek Blair, Krzysztof Kempa, Z. F. Ren, Thomas C. Chiles. Carbon nanotube-mediated delivery of nucleic acids does not result in non-specific activation of B lymphocytes. Nanotechnology 2007; 18, 365101.


A.R. Quinlan, G.T. Marth. Primer-site SNPs mask mutations, Nature Methods 4, 192 (Mar, 2007)

 

Asymptotic expected number of base pairs in optimal seconday structure for random RNA using the Nussinov-Jacobson energy model, P. Clote, E. Kranakis, D. Krizanc and L. Stacho, Discrete Applied Mathematics, special issue in Bioinformatics (eds S. Istrail and P. Pevzner), 157(6-7):759-787 (2007).

 

Asymptotics of RNA shapes., W.A. Lorenze, Y. Ponty and P. Clote. Journal of Computational Biology (2007) in press.


Avila RA, Tevlin BR, Lees JPB, Inouye H, and Kirschner DA (2007) Myelin structure and composition in zebrafish. Neurochem Res 32:197-209.

 

Benson L.J., Phillips J.A., Gu Y., Parthun M.R., Hoffman C.S., and Annunziato A.T. (2007) Properties of the Type B Histone Acetyltransferase Hat1: h4 tail interaction, site preference, and involvement in DNA repair. J. Biol. Chem. 282:836-842


Brian Keady, Peiwen Kuo, Susana Martinez, Lei Yuan, Laura E. Hake (2007). MAPK interacts with XGef and is required for CPEB activation during meiosis in Xenopus oocytes.  Journal of Cell Science, 120:1093-1103.

 

Boltzmann probability of RNA structural neighbors and riboswitch detection, Eva Freyhult; Vincent Moulton; Peter Clote, Bioinformatics 2007; doi: 10.1093/bioinformatics/btm314

 

Book Chapter 1. "Smart Polymers: Applications in Biotechnology and Biomedicine, Second Edition" Chapter title: Imprinting Using Smart Polymers. C. Alvarez-Lorenzo, A. Concheiro, Jeffrey Chuang and A. Yu. Grosberg. CRC Press: Boca Raton (2007).

 

Broekman ML, Baek RC, Comer LA, Fernandez JL, Seyfried TN, Sena-Esteves M.
Complete Correction of Enzymatic Deficiency and Neurochemistry in the GM1-gangliosidosis Mouse Brain by Neonatal Adeno-associated Virus-mediated Gene Delivery.
Mol Ther. 2007 Jan; 15(1):30-37.
PMID: 17164772 [PubMed-as supplied by publisher]

 

Burgess, David (2007) Taking on that first faculty job. Nature, 447:1142

 

Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model, J. Waldispuhl, P. Clote, J Comput Biol 2007 Marl 14(2):190-215


Denny CA, Alroy J, Pawlyk BS, Sandberg MA, d'Azzo A, Seyfried TN.
Neurochemical, morphological, and neurophysiological abnormalities in retinas of Sandhoff and GM1 gangliosidosis mice.
J Neurochem. 2007 Jun; 101(5):1294-302.Epub 2007 Apr 17.
PMID: 17442056 [PubMed-indexed for MEDLINE]

Desplats PA, Denny CA, Kass KE, Gilmartin T, Head SR, Sutcliffe JG, Seyfried TN, Thomas EA.
Glycolipid and ganglioside metabolism imbalances in Huntington's disease.
Neurobiol Dis. 2007 May 22; [Epub ahead of print]
PMID: 17600724 [PubMed-as supplied by publisher]

 

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities, F. Ferre; Y. Ponty; W. A Lorenz; Peter Clote Nucleic Acids Research 2007; doi: 10.1093/nar/gkm344


Frickel, E.-M., V. Quesada, L. Muething, M.-J. Gubbels, E. Spooner, H. Ploegh and K. Artavanis-Tsakonas. 2007. UCHL3 retains dual specificity for ubiquitin and Nedd8 throughout evolution.  Cell Microbial. 6:1601-1610.

Gubbels, M.-J., J. Mazumdar, G. van Dooren, and B Striepen, 2007. Manipulating the Toxoplasma genome.  In "The biology of Toxoplasma gondii".D.Soldati and J. Ajioka (eds.). Horizon Scientific Pres, Norwich, UK. August.

Guo B, Blair D, Chiles TC, Lowell CA, Rothstein TL.  Cutting Edge: B cell receptor (BCR) cross-talk:  the IL-4-induced alternate pathway for BCR signaling operates in parallel with the classical pathway, is sensitive to Rottlerin, and depends on Lyn.  J Immunol. 2007 178:4726-4730.

Klucevsek, K., Wertz, M., Lucchi, J., Leszczynski, A. and Moroianu, J. (2007). Characterization of the Nuclear Localization Signal of High Risk HPV16 E2 Protein. Virology, 360(1):191-8.

Lee JP, Jeyakumar M, Gonzalez R, Takahashi H, Lee PJ, Baek RC, Clark D, Rose H, Fu G, Clarke J, McKercher S, Meerloo J, Muller FJ, Park KI, Butters TD, Dwek RA, Schwartz P, Tong G, Wenger D, Lipton SA, Seyfried TN, Platt FM, Snyder EY.
Stem cells act through multiple mechanisms to benefit mice with neurodegenerative metabolic disease.
NatMed. 2007 Apr;13(4):439-47. Epub 2007 Mar 11.
PMID: 17351625 [PubMed-in process]

Luo XY, Sharma D, Inouye H, Lee D, Avila RL, Salmona M, Kirschner DA. (2007) Cytoplasmic domain of human myelin P0 likely folded as beta structure in compact myelin. Biophys J 92:1585-1597.

Luo XY, Inouye H, Sharma D, Lee D, Avila RL, Salmona M, Kirschner DA (2007) Cytoplasmic domain of zebrafish myelin P0: Adhesive role depends on beta-conformation. Biophys J, in press.

McNally M, Baek R, Avila RL, Seyfried TN, Strichartz G, Kirschner DA (2007) Peripheral nervous system manifestations in a Sandhoff disease mouse model: Nerve conduction, myelin structure, lipid analysis. JNR BioMed 6:8  [open-access, on-line journal]

RNAbor: A web server for RNA structural neighbors. E. Freyhult, V. Mouton, P. Clote. Nucleic Acids Res.,Web Server issue (2007), doi: 10.1093/nar/gkm255

"Similarity of Synonymous Substitutions Rates Across Mammaliam Genomes."  Jeffrey H. Chuang and H. Li. Journal of Molecular Evolution, doi:10.1007/s 00239-007-9008-x (2007).

Xie B, Luo X, Zhao C, Priest CM, Chan S-Y, O’Connor PB, Kirschner DA, Costello CE (2007) Molecular characterization of myelin protein zero in Xenopus laevis peripheral nerve: Equilibrium between non-covalently associated dimer and monomer. International Journal of Mass Spectrometry, in press.

Zhou W, Mukherjee P, Kiebish MA, Markis WT, Mantis JG, Seyfried TN
The calorically restricted ketogenic diet, an effective alternative therapy for malignant brain cancer.
Nutr Metab (Lond). 2007 Feb 21;4:5.
PMID: 17313687 [PubMed]

Oocyte Maturation: new route MAP(K)
J Cell Sci 2007 120: e604 [Full Text] [PDF]
First published online on March 7, 2007