Carbon metabolism–mediated myogenic differentiation (2010)
Abigail L Bracha, Arvind Ramanathan, Sui Huang, Donald E Ingber, Stuart L Schreiber
A Model of Sequential Branching in Hierarchical Cell Fate Determination (2009)
Foster, David V., Foster, Jacob G., Huang, Sui, Kauffman, Stuart A.
Multipotent stem or progenitor cells undergo a sequential series of binary fate decisions, which ultimately generate the diversity of differentiated cells. Efforts to understand cell fate control...
Harvard Medical School, (2008)
research focuses on complexity in multicellularity and cancer.
Danyang Chen, Miroslav Dundr, Chen Wang, Anthony Leung, Angus Lamond, Tom Misteli, ...
Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins 1 2
Transcriptome-wide noise controls lineage choice in mammalian progenitor cells (2008)
Hannah H. Chang, Martin Hemberg, Mauricio Barahona, Donald E. Ingber, Sui Huang
Title: Colourful Simplicial Depth Authors: (2008)
Antoine Deza, Sui Huang, Tamon Stephen, Tamás Terlaky, Antoine Deza, Sui Huang, ...
Abstract. Inspired by Bárány’s colourful Carathéodory theorem [Bár82], we introduce a colourful generalization of Liu’s simplicial depth [Liu90]. We prove a parity property and conjecture...
THE COLOURFUL FEASIBILITY PROBLEM (2008)
Antoine Deza, Sui Huang, Tamon Stephen, Tamás Terlaky
Abstract. We study a colourful generalization of the linear programming feasibility problem, comparing the algorithms introduced by Bárány and Onn with new methods. This is a challenging problem on...
Geometry © 2006 Springer Science+Business Media, Inc. (2008)
Colourful Simplicial Depth, Antoine Deza, Sui Huang, Tamon Stephen, Tamás Terlaky
Abstract. Inspired by Bárány’s Colourful Carathéodory Theorem [4], we introduce a colourful generalization of Liu’s simplicial depth [13]. We prove a parity property and conjecture that the...
THE COLOURFUL FEASIBILITY PROBLEM (2008)
Antoine Deza, Sui Huang, Tamon Stephen, Tamás Terlaky, Dedicated To Leonid Khachiyan
Abstract. We study a colourful generalization of the linear programming feasibility problem, comparing the algorithms introduced by Bárány and Onn with new methods. We perform benchmarking on...
Empirical Multiscale Networks of Cellular Regulation (2007)
Benjamin De Bivort, Sui Huang, Yaneer Bar-Yam
Grouping genes by similarity of expression across multiple cellular conditions enables the identification of cellular modules. The known functions of genes enable the characterization of the...
Multistable and multistep dynamics in neutrophil differentiation (2006)
Chang, Hannah H, Oh, Philmo Y, Ingber, Donald E, Huang, Sui
Abstract Background Cell differentiation has long been theorized to represent a switch in a bistable system, and recent experimental work in micro-organisms has revealed bistable dynamics in small...
Colourful Simplicial Depth (2006)
Antoine Deza, Sui Huang, Tamon Stephen, Tamás Terlaky, Carathéodory Theorem
s14
Yuchun Guo, Gabriel S. Eichler, Ying Feng, Donald E. Ingber, Sui Huang
Genome-wide gene expression profile studies encompass increasingly large number of samples, posing a challenge to their presentation and interpretation without losing the notion that each...
The Colourful Feasibility Problem (2005)
Deza, Antoine, Huang, Sui, Stephen, Tamon, Terlaky, Tamás
We study a colourful generalization of the linear programming feasibility problem, comparing the algorithms introduced by Barany and Onn with new methods. We perform benchmarking on generic and...
Colourful Simplicial Depth (2005)
Deza, Antoine, Huang, Sui, Stephen, Tamon, Terlaky, Tamás
Inspired by Barany's colourful Caratheodory theorem, we introduce a colourful generalization of Liu's simplicial depth. We prove a parity property and conjecture that the minimum colourful simplicial...
High-Betweenness Proteins in the Yeast Protein Interaction Network (2005)
Maliackal Poulo Joy, Amy Brock, Donald E. Ingber, Sui Huang
Structural features found in biomolecular networks that are absent in random networks produced by simple algorithms can provide insight into the function and evolution of cell regulatory networks....
Hall, Megan P, Huang, Sui, Black, Douglas L
We have examined the subcellular localization of the KH-type splicing regulatory protein (KSRP). KSRP is a multidomain RNA-binding protein implicated in a variety of cellular processes, including...
Back to the biology in systems biology: What can we learn from biomolecular networks? (2004)
Genome-scale molecular networks, including protein interaction and gene regulatory networks, have taken centre stage in the investigation of the burgeoning disciplines of systems biology and...
Brock, Amy, Huang, Sui, Ingber, Donald E
Abstract Background Interactions between mRNA and the cytoskeleton are critical for the localization of a number of transcripts in eukaryotic somatic cells. To characterize additional transcripts...
using microarray technology (2003)
Amy Brock, Sui Huang, Donald E Ingber
Research article Identification of a distinct class of cytoskeleton-associated mRNAs
Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles (2003)
Eichler, Gabriel S., Huang, Sui, Ingber, Donald E.
Summary: Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that...
Dan Braha, Helen Harte, Ali Minai, Larry Rudolph, Sui Huang, Michael Jacobson, ...
I would like to welcome you on behalf of the New England Complex Systems Institute and the executive committee to this conference on the unity of the study of complex systems. A dramatic change has...
SYMMETRY BREAKING IN CULTURED MAMMALIAN CELLS (2000)
CLIFFORD BRANGWYNNE, SUI HUANG, KEVIN KIT PARKER, DONALD E. INGBER
Chiu, Daniel T., Jeon, Noo Li, Huang, Sui, Kane, Ravi S., Wargo, Christopher J., Choi, Insung S., ...
Three-dimensional microfluidic systems were fabricated and used to pattern proteins and mammalian cells on a planar substrate. The three-dimensional topology of the microfluidic network in the stamp...
Identification and Characterization of Perinucleolar Compartment-Associated Protein (1998)
During transformation, ribosome biogenesis increases concurrently with the size and number of nucleoli. The U3 snoRNP is involved in the cleavage of pre-rRNA and 4OS preribosomal particle assembly...
Identification and Characterization of a Perinucleolar Compartment-Associated Protein (1998)
During transformation, ribosome synthesis increases concurrently with the size and number of nucleoli. U3 snoRNA-associated complexes are involved in the cleavage of pre-rRNA and 4OS preribosome...
Despite accumulating data about the topology ("wiring diagram") of genome-wide gene regulatory networks little is known about the system behavior of such complex networks which produce the...
Initiation of Nucleolar Assembly Is Independent of RNA Polymerase I Transcription
Dousset, Thibaut, Wang, Chen, Verheggen, Céline, Chen, Danyang, Hernandez-Verdun, Danièle, Huang, Sui
This report examines the distribution of an RNA polymerase I transcription factor (upstream binding factor; UBF), pre-rRNA processing factors (nucleolin and fibrillarin), and pre-rRNAs throughout...
Chiu, Daniel T., Jeon, Noo Li, Huang, Sui, Kane, Ravi S., Wargo, Christopher J., Choi, Insung S., ...
Three-dimensional microfluidic systems were fabricated and used to pattern proteins and mammalian cells on a planar substrate. The three-dimensional topology of the microfluidic network in the stamp...
Huang, Sui, Chen, Christopher S., Ingber, Donald E.
The extracellular matrix (ECM) plays an essential role in the regulation of cell proliferation during angiogenesis. Cell adhesion to ECM is mediated by binding of cell surface integrin receptors,...
Nucleocytoplasmic Shuttling of Polypyrimidine Tract-binding Protein Is Uncoupled from RNA Export
Kamath, Rajesh V., Leary, Daniel J., Huang, Sui
Polypyrimidine tract binding protein, PTB/hnRNP I, is involved in pre-mRNA processing in the nucleus and RNA localization and translation in the cytoplasm. In this report, we demonstrate that PTB...
TBP Dynamics in Living Human Cells: Constitutive Association of TBP with Mitotic Chromosomes
Chen, Danyang, Hinkley, Craig S., Henry, R. William, Huang, Sui
The recruitment of TATA binding protein (TBP) to gene promoters is a critical rate-limiting step in transcriptional regulation for all three eukaryotic RNA polymerases. However, little is known...
Pendergrast, P. Shannon, Wang, Chen, Hernandez, Nouria, Huang, Sui
FBI-1 is a cellular POZ-domain–containing protein that binds to the HIV-1 LTR and associates with the HIV-1 transactivator protein Tat. Here we show that elevated levels of FBI-1 specifically...
Wang, Chen, Politz, Joan C., Pederson, Thoru, Huang, Sui
The perinucleolar compartment (PNC) is a nuclear substructure present in transformed cells. The PNC is defined by high concentrations of certain RNA binding proteins and a subset of small RNAs...
Leary, Daniel J., Terns, Michael P., Huang, Sui
U3 small nucleolar RNA (snoRNA) and associated proteins are required for the processing of preribosomal RNA (pre-rRNA) and assembly of preribosomes. There are two major U3 snoRNA-containing...
Hall, Megan P., Huang, Sui, Black, Douglas L.
We have examined the subcellular localization of the KH-type splicing regulatory protein (KSRP). KSRP is a multidomain RNA-binding protein implicated in a variety of cellular processes, including...
Upstream binding factor association induces large-scale chromatin decondensation
Chen, Danyang, Belmont, Andrew S., Huang, Sui
The function of upstream binding factor (UBF), an essential component of the RNA polymerase (pol) I preinitiation complex, is unclear. Recently, UBF was found distributed throughout ribosomal gene...
Dynamics of cellular level function and regulation derived from murine expression array data
De Bivort, Benjamin, Huang, Sui, Bar-Yam, Yaneer
A major open question of systems biology is how genetic and molecular components interact to create phenotypes at the cellular level. Although much recent effort has been dedicated to inferring...
High-Betweenness Proteins in the Yeast Protein Interaction Network
Joy, Maliackal Poulo, Brock, Amy, Ingber, Donald E., Huang, Sui
Structural features found in biomolecular networks that are absent in random networks produced by simple algorithms can provide insight into the function and evolution of cell regulatory networks....
Evidence by molecular profiling for a placental origin of infantile hemangioma
Barnés, Carmen M., Huang, Sui, Kaipainen, Arja, Sanoudou, Despina, Chen, Emy J., Eichler, Gabriel S., ...
The origin of the pathogenic endothelial cells in common infantile hemangioma is unknown. We show here that the transcriptomes of human placenta and infantile hemangioma are sufficiently similar to...
Initiation of Nucleolar Assembly Is Independent of RNA Polymerase I Transcription
Dousset, Thibaut, Wang, Chen, Verheggen, Céline, Chen, Danyang, Hernandez-Verdun, Danièle, Huang, Sui
This report examines the distribution of an RNA polymerase I transcription factor (upstream binding factor; UBF), pre-rRNA processing factors (nucleolin and fibrillarin), and pre-rRNAs throughout...
Chiu, Daniel T., Jeon, Noo Li, Huang, Sui, Kane, Ravi S., Wargo, Christopher J., Choi, Insung S., ...
Three-dimensional microfluidic systems were fabricated and used to pattern proteins and mammalian cells on a planar substrate. The three-dimensional topology of the microfluidic network in the stamp...
Huang, Sui, Chen, Christopher S., Ingber, Donald E.
The extracellular matrix (ECM) plays an essential role in the regulation of cell proliferation during angiogenesis. Cell adhesion to ECM is mediated by binding of cell surface integrin receptors,...
Nucleocytoplasmic Shuttling of Polypyrimidine Tract-binding Protein Is Uncoupled from RNA Export
Kamath, Rajesh V., Leary, Daniel J., Huang, Sui
Polypyrimidine tract binding protein, PTB/hnRNP I, is involved in pre-mRNA processing in the nucleus and RNA localization and translation in the cytoplasm. In this report, we demonstrate that PTB...
TBP Dynamics in Living Human Cells: Constitutive Association of TBP with Mitotic Chromosomes
Chen, Danyang, Hinkley, Craig S., Henry, R. William, Huang, Sui
The recruitment of TATA binding protein (TBP) to gene promoters is a critical rate-limiting step in transcriptional regulation for all three eukaryotic RNA polymerases. However, little is known...
Pendergrast, P. Shannon, Wang, Chen, Hernandez, Nouria, Huang, Sui
FBI-1 is a cellular POZ-domain–containing protein that binds to the HIV-1 LTR and associates with the HIV-1 transactivator protein Tat. Here we show that elevated levels of FBI-1 specifically...
Wang, Chen, Politz, Joan C., Pederson, Thoru, Huang, Sui
The perinucleolar compartment (PNC) is a nuclear substructure present in transformed cells. The PNC is defined by high concentrations of certain RNA binding proteins and a subset of small RNAs...
Leary, Daniel J., Terns, Michael P., Huang, Sui
U3 small nucleolar RNA (snoRNA) and associated proteins are required for the processing of preribosomal RNA (pre-rRNA) and assembly of preribosomes. There are two major U3 snoRNA-containing...
Hall, Megan P., Huang, Sui, Black, Douglas L.
We have examined the subcellular localization of the KH-type splicing regulatory protein (KSRP). KSRP is a multidomain RNA-binding protein implicated in a variety of cellular processes, including...
Upstream binding factor association induces large-scale chromatin decondensation
Chen, Danyang, Belmont, Andrew S., Huang, Sui
The function of upstream binding factor (UBF), an essential component of the RNA polymerase (pol) I preinitiation complex, is unclear. Recently, UBF was found distributed throughout ribosomal gene...
Dynamics of cellular level function and regulation derived from murine expression array data
De Bivort, Benjamin, Huang, Sui, Bar-Yam, Yaneer
A major open question of systems biology is how genetic and molecular components interact to create phenotypes at the cellular level. Although much recent effort has been dedicated to inferring...
High-Betweenness Proteins in the Yeast Protein Interaction Network
Joy, Maliackal Poulo, Brock, Amy, Ingber, Donald E., Huang, Sui
Structural features found in biomolecular networks that are absent in random networks produced by simple algorithms can provide insight into the function and evolution of cell regulatory networks....
Evidence by molecular profiling for a placental origin of infantile hemangioma
Barnés, Carmen M., Huang, Sui, Kaipainen, Arja, Sanoudou, Despina, Chen, Emy J., Eichler, Gabriel S., ...
The origin of the pathogenic endothelial cells in common infantile hemangioma is unknown. We show here that the transcriptomes of human placenta and infantile hemangioma are sufficiently similar to...
Guo, Yuchun, Eichler, Gabriel S., Feng, Ying, Ingber, Donald E., Huang, Sui
Genome-wide gene expression profile studies encompass increasingly large number of samples, posing a challenge to their presentation and interpretation without losing the notion that each...
Diaz-Perez, Silvia V., Ferguson, David O., Wang, Chen, Csankovszki, Gyorgyi, Wang, Chengming, Tsai, Shih-Chang, ...
The inactive X chromosome of female mammals displays several properties of heterochromatin including late replication, histone H4 hypoacetylation, histone H3 hypomethylation at lysine-4, and...
PPARα Deficiency in Inflammatory Cells Suppresses Tumor Growth
Kaipainen, Arja, Kieran, Mark W., Huang, Sui, Butterfield, Catherine, Bielenberg, Diane, Mostoslavsky, Gustavo, ...
Inflammation in the tumor bed can either promote or inhibit tumor growth. Peroxisome proliferator-activated receptor (PPAR)α is a central transcriptional suppressor of inflammation, and may...
Empirical Multiscale Networks of Cellular Regulation
De Bivort, Benjamin, Huang, Sui, Bar-Yam, Yaneer
Grouping genes by similarity of expression across multiple cellular conditions enables the identification of cellular modules. The known functions of genes enable the characterization of the...
Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins
Chen, Danyang, Dundr, Miroslav, Wang, Chen, Leung, Anthony, Lamond, Angus, Misteli, Tom, ...
During mitosis, chromosomes are highly condensed and transcription is silenced globally. One explanation for transcriptional repression is the reduced accessibility of transcription factors. To...
The Perinucleolar Compartment and Transcription
Huang, Sui, Deerinck, Thomas J., Ellisman, Mark H., Spector, David L.
The perinucleolar compartment (PNC) is a unique nuclear structure localized at the periphery of the nucleolus. Several small RNAs transcribed by RNA polymerase III and two hnRNP proteins have been...
The Dynamic Organization of the Perinucleolar Compartment in the Cell Nucleus
Huang, Sui, Deerinck, Thomas J., Ellisman, Mark H., Spector, David L.
The perinucleolar compartment (PNC) is a unique nuclear structure preferentially localized at the periphery of the nucleolus. Several small RNAs transcribed by RNA polymerase III (e.g., the Y RNAs,...
Building an efficient factory: where is pre-rRNA synthesized in the nucleolus?
The subnucleolar structure that is involved in rDNA transcription has been controversial. A report by Koberna et al. (2002)(this issue, page 743) adds significant weight toward the idea that dense...
Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription
Spann, Timothy P., Goldman, Anne E., Wang, Chen, Huang, Sui, Goldman, Robert D.
RTegulation of gene activity is mediated by alterations in chromatin organization. In addition, chromatin organization may be governed in part by interactions with structural components of the...
We examined the mobilities of nucleolar components that act at various steps of the ribosome biogenesis pathway. Fluorescence recovery after photobleaching (FRAP) and fluorescence loss in...
Panigrahy, Dipak, Kaipainen, Arja, Huang, Sui, Butterfield, Catherine E., Barnés, Carmen M., Fannon, Michael, ...
Angiogenesis and inflammation are central processes through which the tumor microenvironment influences tumor growth. We have demonstrated recently that peroxisome proliferator-activated receptor...
Noise-Driven Stem Cell and Progenitor Population Dynamics
Hoffmann, Martin, Chang, Hannah H., Huang, Sui, Ingber, Donald E., Loeffler, Markus, Galle, Joerg
PPARs: A Double-Edged Sword in Cancer Therapy?
Panigrahy, Dipak, Kaipainen, Arja, Kieran, Mark W., Huang, Sui
Wang, Chen, Norton, John T., Ghosh, Supurna, Kim, Julie, Fushimi, Kazuo, Wu, Jane Y., ...
RNA processing is altered during malignant transformation, and expression of the polypyrimidine tract-binding protein (PTB) is often increased in cancer cells. Although some data support that PTB...