Miller, George, Socci, Nicholas D, Dhall, Deepti, D'Angelica, Michael, DeMatteo, Ronald P, Allen, Peter J, ...
Abstract Background The pathogenesis of biliary cancers is ill-defined. This study investigates changes in gene expression and copy number in biliary cancers and correlates these changes with...
Estilo, Cherry L, O-charoenrat, Pornchai, Talbot, Simon, Socci, Nicholas D, Carlson, Diane L, Ghossein, Ronald, ...
Abstract Background The present study is aimed at identifying potential candidate genes as prognostic markers in human oral tongue squamous cell carcinoma (SCC) by large scale gene expression...
Elkabetz, Yechiel, Panagiotakos, Georgia, Al Shamy, George, Socci, Nicholas D., Tabar, Viviane, Studer, Lorenz
Neural stem cells (NSCs) yield both neuronal and glial progeny, but their differentiation potential toward multiple region-specific neuron types remains remarkably poor. In contrast, embryonic stem...
Non-equilibrium raft-like membrane domains under continuous recycling (2006)
Turner, Matthew S., Sens, Pierre, Socci, Nicholas D.
We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domains have a broad...
MicroRNA profiling of the murine hematopoietic system (2005)
Monticelli, Silvia, Ansel, K Mark, Xiao, Changchun, Socci, Nicholas D, Krichevsky, Anna M, Thai, To-Ha, ...
Abstract Background MicroRNAs (miRNAs) are a class of recently discovered noncoding RNA genes that post-transcriptionally regulate gene expression. It is becoming clear that miRNAs play an important...
Derivation of Multipotent Mesenchymal Precursors from Human Embryonic Stem Cells (2005)
Tiziano Barberi, Lucy M. Willis, Nicholas D. Socci, Lorenz Studer
Lorenz Studer and colleagues describe the use of embryonic stem cells to derive mesenchymal precursors and then fat, cartilage, bone, and skeletal muscle cells.
Derivation of Multipotent Mesenchymal Precursors from Human Embryonic Stem Cells (2005)
Tiziano Barberi, Lucy M. Willis, Nicholas D. Socci, Lorenz Studer
Background Human embryonic stem cells provide access to the earliest stages of human development and may serve as a source of specialized cells for regenerative medicine. Thus, it becomes crucial to...
Non-equilibrium raft-like membrane domains under continuous recycling (2005)
Turner, Matthew S., Sens, Pierre, Socci, Nicholas D.
We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domains have a broad...
Lewis, Brian C., Klimstra, David S., Socci, Nicholas D., Xu, Su, Koutcher, Jason A., Varmus, Harold E.
We have generated a mouse model for hepatocellular carcinoma using somatic delivery of oncogene-bearing avian retroviral vectors to the liver cells of mice expressing the viral receptor TVA under the...
Non-equilibrium raft-like membrane domains under continuous recycling (2005)
Turner, Matthew S., Sens, Pierre, Socci, Nicholas D.
We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domains have a broad...
Computational identification of microRNA targets (2004)
Rajewsky, Nikolaus, Socci, Nicholas D
Abstract Recent experiments have shown that the genomes of organisms such as worm, fly, human and mouse encode hundreds of microRNA genes. Many of these microRNAs are thought to regulate the...
Naef, Felix, Socci, Nicholas D., Magnasco, Marcelo
Motivation: Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been...
The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons (2003)
Rajewsky, Nikolaus, Socci, Nicholas D., Zapotocky, Martin, Siggia, Eric D.
Naef, Felix, Socci, Nicholas D., Magnasco, Marcelo
Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been limited. The...
The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons (2002)
Rajewsky, Nikolaus, Socci, Nicholas D., Zapotocky, Martin, Siggia, Eric D.
Bruno, William J., Socci, Nicholas D., Halpern, Aaron L.
We introduce a distance-based phylogeny reconstruction method called “weighted neighbor joining,” or “Weighbor” for short. As in neighbor joining, two taxa are joined in each iteration;...
Leptin-specific patterns of gene expression in white adipose tissue (2000)
Soukas, Alexander, Cohen, Paul, Socci, Nicholas D., Friedman, Jeffrey M.
Socci, Nicholas D., Onuchic, José Nelson
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are...
Folding Kinetics of Protein Like Heteropolymers (1994)
Socci, Nicholas D., Onuchic, Jose' Nelson
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of...
Properties and Origins of Protein Secondary Structure (1994)
Socci, Nicholas D., Bialek, William S., Onuchic, Jose' Nelson
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local...
Nymeyer, Hugh, Socci, Nicholas D., Onuchic, José Nelson
We present a method for determining structural properties of the ensemble of folding transition states from protein simulations. This method relies on thermodynamic quantities (free energies as a...
Stretching lattice models of protein folding
Socci, Nicholas D., Onuchic, José Nelson, Wolynes, Peter G.
A new class of experiments that probe folding of individual protein domains uses mechanical stretching to cause the transition. We show how stretching forces can be incorporated in lattice models of...
Leptin-specific patterns of gene expression in white adipose tissue
Soukas, Alexander, Cohen, Paul, Socci, Nicholas D., Friedman, Jeffrey M.
Leptin is a hormone that regulates body weight by decreasing food intake and increasing energy expenditure. ob/ob mice carry leptin mutations and are obese and hyperphagic. Leptin administration to...
Site and mechanism of leptin action in a rodent form of congenital lipodystrophy
Asilmaz, Esra, Cohen, Paul, Miyazaki, Makoto, Dobrzyn, Pawel, Ueki, Kohjiro, Fayzikhodjaeva, Gulnorakhon, ...
Lipodystrophy is characterized by the complete or partial absence of adipose tissue, insulin resistance, hepatic steatosis, and leptin deficiency. Here, we show that low-dose central leptin corrects...
The Absence of p53 Promotes Metastasis in a Novel Somatic Mouse Model for Hepatocellular Carcinoma†
Lewis, Brian C., Klimstra, David S., Socci, Nicholas D., Xu, Su, Koutcher, Jason A., Varmus, Harold E.
We have generated a mouse model for hepatocellular carcinoma using somatic delivery of oncogene-bearing avian retroviral vectors to the liver cells of mice expressing the viral receptor TVA under the...
Derivation of Multipotent Mesenchymal Precursors from Human Embryonic Stem Cells
Barberi, Tiziano, Willis, Lucy M, Socci, Nicholas D, Studer, Lorenz
Lorenz Studer and colleagues describe the use of embryonic stem cells to derive mesenchymal precursors and then fat, cartilage, bone, and skeletal muscle cells.
MicroRNA profiling of the murine hematopoietic system
Monticelli, Silvia, Ansel, K Mark, Xiao, Changchun, Socci, Nicholas D, Krichevsky, Anna M, Thai, To-Ha, ...
The first report of systematic miRNA profiling in cells of the hematopoietic system suggests that, in addition to regulating commitment to particular cellular lineages, miRNAs might have a general...
The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons
Rajewsky, Nikolaus, Socci, Nicholas D., Zapotocky, Martin, Siggia, Eric D.
The comparison of homologous noncoding DNA for organisms a suitable evolutionary distance apart is a powerful tool for the identification of cis regulatory elements for transcription and translation...
Nymeyer, Hugh, Socci, Nicholas D., Onuchic, José Nelson
We present a method for determining structural properties of the ensemble of folding transition states from protein simulations. This method relies on thermodynamic quantities (free energies as a...
Stretching lattice models of protein folding
Socci, Nicholas D., Onuchic, José Nelson, Wolynes, Peter G.
A new class of experiments that probe folding of individual protein domains uses mechanical stretching to cause the transition. We show how stretching forces can be incorporated in lattice models of...
The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons
Rajewsky, Nikolaus, Socci, Nicholas D., Zapotocky, Martin, Siggia, Eric D.
The comparison of homologous noncoding DNA for organisms a suitable evolutionary distance apart is a powerful tool for the identification of cis regulatory elements for transcription and translation...
Leptin-specific patterns of gene expression in white adipose tissue
Soukas, Alexander, Cohen, Paul, Socci, Nicholas D., Friedman, Jeffrey M.
Leptin is a hormone that regulates body weight by decreasing food intake and increasing energy expenditure. ob/ob mice carry leptin mutations and are obese and hyperphagic. Leptin administration to...
Site and mechanism of leptin action in a rodent form of congenital lipodystrophy
Asilmaz, Esra, Cohen, Paul, Miyazaki, Makoto, Dobrzyn, Pawel, Ueki, Kohjiro, Fayzikhodjaeva, Gulnorakhon, ...
Lipodystrophy is characterized by the complete or partial absence of adipose tissue, insulin resistance, hepatic steatosis, and leptin deficiency. Here, we show that low-dose central leptin corrects...
The Absence of p53 Promotes Metastasis in a Novel Somatic Mouse Model for Hepatocellular Carcinoma†
Lewis, Brian C., Klimstra, David S., Socci, Nicholas D., Xu, Su, Koutcher, Jason A., Varmus, Harold E.
We have generated a mouse model for hepatocellular carcinoma using somatic delivery of oncogene-bearing avian retroviral vectors to the liver cells of mice expressing the viral receptor TVA under the...
Derivation of Multipotent Mesenchymal Precursors from Human Embryonic Stem Cells
Barberi, Tiziano, Willis, Lucy M, Socci, Nicholas D, Studer, Lorenz
Lorenz Studer and colleagues describe the use of embryonic stem cells to derive mesenchymal precursors and then fat, cartilage, bone, and skeletal muscle cells.
MicroRNA profiling of the murine hematopoietic system
Monticelli, Silvia, Ansel, K Mark, Xiao, Changchun, Socci, Nicholas D, Krichevsky, Anna M, Thai, To-Ha, ...
The first report of systematic miRNA profiling in cells of the hematopoietic system suggests that, in addition to regulating commitment to particular cellular lineages, miRNAs might have a general...
Rossi, Ferdinand, Ehlers, Imke, Agosti, Valter, Socci, Nicholas D., Viale, Agnes, Sommer, Gunhild, ...
Kit receptor-activating mutations are critical in the pathogenesis of gastrointestinal stromal tumors (GIST). We investigated mechanisms of oncogenic Kit signaling and the consequences of therapeutic...
Profiling Bladder Cancer Using Targeted Antibody Arrays
Sanchez-Carbayo, Marta, Socci, Nicholas D., Lozano, Juan Jose, Haab, Brian B., Cordon-Cardo, Carlos
Bladder cancer is a common malignancy requiring a high degree of surveillance because of the frequent recurrences and the poor clinical outcome of invasive disease. To date, serum biomarkers for...
Gene Discovery in Bladder Cancer Progression using cDNA Microarrays
Sanchez-Carbayo, Marta, Socci, Nicholas D., Lozano, Juan Jose, Li, Wentian, Charytonowicz, Elizabeth, Belbin, Thomas J., ...
To identify gene expression changes along progression of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known...
Derivation of sarcomas from mesenchymal stem cells via inactivation of the Wnt pathway
Matushansky, Igor, Hernando, Eva, Socci, Nicholas D., Mills, Joslyn E., Matos, Tulio A., Edgar, Mark A., ...
Malignant fibrous histiocytoma (MFH), now termed high-grade undifferentiated pleomorphic sarcoma, is a commonly diagnosed mesenchymal tumor, yet both the underlying molecular mechanisms of...
Sanchez-Carbayo, Marta, Socci, Nicholas D., Richstone, Lee, Corton, Marta, Behrendt, Nille, Wulkfuhle, Julia, ...
Bladder cancer transformation and immortalization require the inactivation of key regulatory genes, including TP53. Genotyping of a large cohort of bladder cancer patients (n = 256) using the TP53...
Human ES cell-derived neural rosettes reveal a functionally distinct early neural stem cell stage
Elkabetz, Yechiel, Panagiotakos, Georgia, Al Shamy, George, Socci, Nicholas D., Tabar, Viviane, Studer, Lorenz
Neural stem cells (NSCs) yield both neuronal and glial progeny, but their differentiation potential toward multiple region-specific neuron types remains remarkably poor. In contrast, embryonic stem...
Functional Copy-Number Alterations in Cancer
Taylor, Barry S., Barretina, Jordi, Socci, Nicholas D., DeCarolis, Penelope, Ladanyi, Marc, Meyerson, Matthew, ...
Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples....
Matushansky, Igor, Hernando, Eva, Socci, Nicholas D., Matos, Tulio, Mills, Joslyn, Edgar, Mark A., ...
The importance of adult stem cells in the development of neoplastic diseases is becoming increasingly well appreciated. We hypothesized that sarcomas of soft tissue could be categorized by their...
Estilo, Cherry L, O-charoenrat, Pornchai, Talbot, Simon, Socci, Nicholas D, Carlson, Diane L, Ghossein, Ronald, ...
Cellular program controlling the recovery of adipose tissue mass: An in vivo imaging approach
Birsoy, Kıvanç, Soukas, Alexander, Torrens, Javier, Ceccarini, Giovanni, Montez, Jason, Maffei, Margherita, ...
The cellular program responsible for the restoration of adipose tissue mass after weight loss is largely uncharacterized. Leptin mRNA levels are highly correlated with adipose tissue mass, and leptin...