Student Publications
Updated: June 7, 2010

Name Publications
I. Bomash

Pandarinath C, Bomash I, Victor J, Prusky G, Tschetter W, and Nirenberg S. A novel mechanism for switching a neural system fron one state to another. Frontiers in Computational Neuroscience, 4 March 2010.

Nirenberg S, Bomash I, Pillow J, and Victor J. Heterogeneous response dynamics in retinal ganglion cells: the interplay of predictive coding and adaptation. Journal of Neurophysiology, 2010.

E. Cerami

 

 

Cerami E, Demir E, Schultz N, Taylor BS, Sander C., Automated network analysis identifies core pathways in glioblastoma. PLoS One. 2010 Feb 12; 5 (2): e8918.

Cancer Genome Atlas Research Network (...Cerami E,...). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4. PubMed PMID: 18772890; PubMed Central PMCID: PMC2671642.

MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007;2(10):2366-82.

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 9;5:44.

 
SW Chi Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes miRNA-mRNA interaction maps. Nature, Jul 23; 460 (7254): 479-86, 2009

Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature, Nov 27; 456 (7221): 464-9, 2008.

Cho, S, G., Kim, J. W., Lee, Y. H., Hwang, H. S., Kim, M. S., Ryoo, K., Kim, M. J., Noh, K. T., Kim, E. K., Cho, J. H.,Yoon, K. W., Cho, E. G., Park, H. S., Chi, S. W., Lee, M. J., Kang, S. S., Ichijo, H., and Choi, E. J. Identification of a novel anti-apoptotic protein that antagonizes ASK1 and CAD activities. Journal of Cell Biology, vol. 163, pp.71-81, 2003.

Zhang, B. T, Yang, J. and Chi, S. W. Self-Organizing Latent Lattice Models for Temporal Gene Expression Profiling, Machine Learning, vol. 52, no. 1/2, pp. 67-89, 2003.

Chang, J. H., Chi, S. W., and Zhang, B. T. Gene Expression Pattern Analysis via Latent Variable Models Coupled with Topographic Clustering. Genomics & Informatics, vol. 1, no. 1, pp. 32-39, 2003.
H. Ingólfsson

Ingolfsson H.I., R.E. Koeppe II and O.S. Andersen. Modification of Lipid Bilayer Material Properties as a Common Mode of Action for a Wide Range of Phenolic Phytochemicals. Biointerfaces Symposium, Columbia University, New York, NY. (abstract and poster). (2009).

Ingolfsson H.I., V.V. Vostrikov, H. Gu, R.E. Koeppe II, J.F. Hinton, B. Roux, T.W. Allen and O.S. Andersen. Evaluating Gramicidin A Channel Backbone Dynamics by Molecular Dynamics and Nuclear Magnetic Resonance. Biophys. J. Supplement, Abstract, 787-Pos.(2009).

Ingolfsson H.I., R. Kapoor, S.A. Collingwood and O.S. Andersen. Single Molecule Methods for Monitoring Changes in Bilayer Elastic Properties. Journal of Visualized Experiments. (2008).

Kapoor R., J.H. Kim, H.I. Ingolfsson and O.S. Andersen. Preparation of Artificial Bilayers for Electrophysiology Experiments. Journal of Visualized Experiments. (2008).

Olaf S. Andersen, Helgi I. Ingolfsson and Jens A. Lundbaek. Ion Channels. In Wiley Encyclopedia of Chemical Biology. John Wiley & Sons, Inc. (book chapter). (2008).

Ingolfsson, H. and Yona, G. Protein domain prediction. In Structural Proteomics - High-throughput Methods, edited by Guss, M., Huber, T., and Kobe, B. Humana Press (book chapter). (2008).

Ingolfsson H.I., S. Mukherjee, R.E. Koeppe II, F.R. Maxfield and O.S. Andersen. Green tea catechins modify bilayer mechanical properties. Biophys. J. Supplement, Abstract, L80-Pos. (2008).

Lundbaek J.A., H.I. Ingolfsson, M.J. Bruno, A.M. Maer and O.S. Andersen. 2008. Membrane Protein Function and Lipid Intrinsic Curvature - Why Many Water-Soluble Amphiphiles Do Not Follow The Rules. Biophys. J. Supplement, Abstract, 404-Pos. (2008).

Ingolfsson H.I., Koeppe R.E. II and Andersen O.S. Curcumin is a modulator of bilayer material properties. Biochemistry, 46, 10384-10391, (2007).

Adachi, S., Nagao, T., Ingolfsson, H.I., Maxfield, F.R., Andersen, O.S., Kopelovich, L., and Weinstein, I.B. The Inhibitory Effect of (-)-Epigallocatechin Gallate (EGCG) on Activation of the Epidermal Growth Factor Receptor is Associated With Altered Lipid Order in HT29 Colon Cancer Cells. Cancer Research, 67, 6493-501, (2007).

Ingolfsson H.I., Koeppe II, R.E., and Andersen, O.S. (-)-epigallocatechin-3-gallate (EGCG) is a potent modifier of gramicidin function. Biophys. J. Supplement, 578a, Abstract, 2760-Pos. (2007).

Ingolfsson, H.I., and Andersen, O.S. Curcumin is a modulator of bilayer mechanical properties. Biophys. J. Supplement, 364a, Abstract, 1768-Pos. (2006).

Ingolfsson H.I., and Andersen, O.S. Curcumin is a modulator of bilayer mechanical properties. EMBO, Cell membrane organization and dynamics, Bilbao, Spain (poster). (2006).

Ingolfsson H.I., and Andersen, O.S. Curcumin is a modulator of bilayer mechanical properties. Vincent DuVigneaud Research Symposium, New York, NY (poster). (2006).

E. Kenny

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Min Kang H, Newton-Cheh C, Daly M, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL and Pe'er I. Increased power of mixed-models facilitates association mapping of 10 loci for metabolic traits in an isolated population. HMG, in press, 2010.

Kenny EE, Gusev A, Riegel K, Lutjohann D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman JM, Breslow JL, Pe'er I and Sehayek E. Systematic haplotype analysis resoves a complex locus affecting plasma plant sterol levels in a Micronesian Island population. Proc Natl Acad Sci USA. Aug 18; 106 (33): 13886-91 (2009)

Kenny EE, Kim M, Kany HM, Lowe JL, Salit J, Eskin E and Pe’er I. “A comprehensive comparison of methods for association mapping in a highly related founder population” (manuscript in preparation – 2009)

Kenny EE, Gusav A, Riegel K, Lütjohann D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman JM, Breslow JL, Pe’er I and Sehayek E “Systematic haplotype analysis resolves a complex locus affecting plasma plant sterol levels in a Micronesian Island population” (submitted -- PNAS) (2009)

Lowe JK, Maller JB, Pe’er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, Ji W, Noel M, Nee Foo J, Blundell ML, Garcia L, Sullivan ML, Lee HE, Utterman A, Ferdowsian H, Lifton RP, Breslow JL, Stoffel M, Daly MJ, Altshuler DM, Friedman JM “Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae” PLoS Genet 5(2):e1000365 (2009)

Burkhardt R, Kenny EE and Breslow JL “Genome-wide associations and lipid risk factors” Current Cardiovascular Lipid Reports 3(1):12-17 (2009) Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe’er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM and Breslow JL “Common SNPs in HMGCR in Micronesians and Caucasians assciated with LDL-cholesterol levels affect alternative splicing of exon 13” Atherosclerosis, Thrombosis and Vascular Biology 28:11:2078-84 (2008)

Ralph Burkhardt , Eimear Kenny , Jennifer Lowe , Andrew Birkeland , Rebecca Josowitz , Martha Noel , Jacqueline Salit , Julian Maller , Itsik Pe'er , Mark Daly , David Altshuler , Markus Stoffel , Jeffrey Friedman, Jan Breslow Common SNPs in HMGCR in Micronesians and Caucasians associated with LDL-cholesterol levels affect alternative splicing of exon13 under submission, 2008. (paper)

 
A. Maoz Maoz, A., Krogh-Madsen, T., and Christini, D. Instability in action potential morphology underlies phase-2 reentry-a mathematical modeling study. Heart Rhythm Journal, 2009 (in press).

Maoz, A., Krogh-Madsen, T., and Christini, D. Unmasking the Substrate for Phase-2 Reentry Using Mathematical Modeling. Biophysical Annual Meeting (poster). (2008).

Zaider, M., Meli, J., Maoz, A., Cohen, G., Rosenfeld, A.B., Cutajar, D.L., Lerch, M.L.F., and Bucci, J. Operational aspects of a new in-vivo uerthral solid-state spectrometer-dosimeter. Presented in the “27th American Brachytherapy Society Annual Meeting” (abstract). (2006).
E. Molinelli Wang Q, Navarro MVAS, Peng G, Molinelli E, Goh SL, Judson BL, Rajashankar KR, Sodermann H. Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin. Proc Natl Acad Sci USA. 2009 vol. 106 (31) pp. 12700-5.
M. Phillips

Katsutomo Okamura, Michael D Phillips, David M Tyler, Hong Duan, Yu-Ting Chou, Eric C Lai (2008). The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol 15, 354-363.

Na Liu, Katsutomo Okamura, David M Tyler, Michael D Phillips, Wei-Jen Chung, Eric C Lai (2008). The evolution and functional diversification of animal microRNA genes. Cell Research, in press.

P. Ng

Ng P and Keich U. GIMSAN: A Gibbs motif finder with significance analysis. Bioinformatics, 24 (19): 2256-2267, 2008.

Ng, P., Nagarajan, N., Jones, N., and Keich, U. Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone Bioinformatics. Bioinformatics, 22(14):e393-e401. (2006).

D. Terry Zhao, Y, Terry, D.S., Shi, L, Weinstein, H, Blanchard, S.C. and Javitch, J.A. Single-molecule dynamics of gating in a neurotransmitter transporter homolog. Nature (in press).

Feldman, M.B., Terry, D.S., Altman, R.B., and Blanchard, S.C. Aminoglycoside activity observed on single pre-translocation ribosome complexes. Nature Chemical Biology 6: 54-62 (2010).

Dave, R., Terry, D. S., Munro, J. B., and Blanchard, S. C. (2009). Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J 96, 2371-2381.
O. Weitz Blankenship, J.T., Backovic, S.T., Sanny, J.S.P, Weitz,O., Zallen, J.A. Multicellular Rosette Formation Links Planar Cell Polarity to Tissue Morphogenesis. Dev. Cell, Vol 11, 459-470, (2006).
C. Wellock Wellock, C. D., and Coop, A. D. Role of the Golgi cell in a cerebellar cortical circuit. Presented at the annual meeting of the Society for Neuroscience ("Neuroscience 2006") in Atlanta, GA. (poster). (2006).