Publications 1992 2016

  • 29 h-Index
  • 110 Article
  • 22 Conference contribution
  • 5 Chapter
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Article
2016
1 Citations

An approach to enhance alignment and myelination of dorsal root ganglion neurons

Liu, C. & Chan, C. Aug 24 2016 In : Journal of Visualized Experiments. 2016, 114, e54085

Research output: Research - peer-reviewArticle

Spinal Ganglia
Axons
Neurons
Direction compound
Schwann Cells

Characterization of transcription factor response kinetics in parallel

Bilgin, B., Nath, A., Chan, C. & Walton, S. P. 2016 In : BMC Biotechnology. 16, 1, 62

Research output: Research - peer-reviewArticle

Transcription Factors
Palmitic Acid
Tumor Necrosis Factor-alpha
Glucocorticoid Receptors
TATA-Box Binding Protein
13 Citations
Fatty Acids
Genes
Neoplasms
Lipogenesis
Transcriptome
2 Citations

Haplotype-phased synthetic long reads from short-read sequencing

Stapleton, J. A., Kim, J., Hamilton, J. P., Wu, M., Irber, L. C., Maddamsetti, R., Briney, B., Newton, L., Burton, D. R., Brown, C. T., Chan, C., Buell, C. R. & Whitehead, T. A. Jan 1 2016 In : PLoS One. 11, 1, e0147229

Research output: Research - peer-reviewArticle

Haplotypes
haplotypes
Genes
DNA
sampling

Schwann Cells Migration on Patterned Polydimethylsiloxane Microgrooved Surface

Liu, C., Kray, J., Toomajian, V. & Chan, C. Jul 1 2016 In : Tissue Engineering - Part C: Methods. 22, 7, p. 644-651 8 p.

Research output: Research - peer-reviewArticle

Schwann Cells
Cell Movement
baysilon
Polydimethylsiloxane
Cells
2015
3 Citations

Brain derived neurotrophic factor release from layer-by-layer coated agarose nerve guidance scaffolds

Lynam, D. A., Shahriari, D., Wolf, K. J., Angart, P. A., Koffler, J., Tuszynski, M. H., Chan, C., Walton, P. & Sakamoto, J. May 1 2015 In : Acta Biomaterialia. 18, p. 128-131 4 p.

Research output: Research - peer-reviewArticle

Scaffolds
Brain
Nerve Growth Factors
Brain-Derived Neurotrophic Factor
Sepharose
19 Citations

Elevated free fatty acid uptake via CD36 promotes epithelial-mesenchymal transition in hepatocellular carcinoma

Nath, A., Li, I., Roberts, L. R. & Chan, C. Oct 1 2015 In : Scientific Reports. 5, 14752

Research output: Research - peer-reviewArticle

Epithelial-Mesenchymal Transition
Nonesterified Fatty Acids
Hepatocellular Carcinoma
Therapeutics
Liver Neoplasms
1 Citations

How can novel microscopic approaches shed light on the function of nucleic acid-based drugs?

Vocelle, D., Chan, C. & Walton, S. P. Sep 1 2015 In : Future Medicinal Chemistry. 7, 13, p. 1623-1625 3 p.

Research output: Research - peer-reviewArticle

2 Citations

Improving drug sensitivity prediction using different types of data

Hejase, H. A. & Chan, C. Feb 1 2015 In : CPT: Pharmacometrics and Systems Pharmacology. 4, 2, p. 98-105 8 p.

Research output: Research - peer-reviewArticle

Drugs
Prediction
Cell Line
Pharmaceutical Preparations
Cells
11 Citations

Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing

Kowalsky, C. A., Faber, M. S., Nath, A., Dann, H. E., Kelly, V. W., Liu, L., Shanker, P., Wagner, E. K., Maynard, J. A., Chan, C. & Whitehead, T. A. Oct 30 2015 In : Journal of Biological Chemistry. 290, 44, p. 26457-26470 14 p.

Research output: Research - peer-reviewArticle

Epitope Mapping
High-Throughput Nucleotide Sequencing
Mutagenesis
Epitopes
Antibodies
2014
49 Citations

A community computational challenge to predict the activity of pairs of compounds

Bansal, M. , Yang, J. , Karan, C. , Menden, M. P. , Costello, J. C. , Tang, H. , Xiao, G. , Li, Y. , Allen, J. , Zhong, R. , Chen, B. , Kim, M. , Wang, T. , Heiser, L. M. , Realubit, R. , Mattioli, M. , Alvarez, M. J. , Shen, Y. , Gallahan, D. , Singer, D. & 80 others Saez-Rodriguez, J., Xie, Y., Stolovitzky, G., Califano, A., Abbuehl, J. P., Altman, R. B., Balcome, S., Bell, A., Bender, A., Berger, B., Bernard, J., Bieberich, A. A., Borboudakis, G., Chan, C., Chen, T. H., Choi, J., Coelho, L. P., Creighton, C. J., Dampier, W., Davisson, V. J., Deshpande, R., Diao, L., Di Camillo, B., Dundar, M., Ertel, A., Goswami, C. P., Gottlieb, A., Gould, M. N., Goya, J., Grau, M., Gray, J. W., Hejase, H. A., Hoffmann, M. F., Homicsko, K., Homilius, M., Hwang, W., Ijzerman, A. P., Kallioniemi, O., Karacali, B., Kaski, S., Kim, J., Krishnan, A., Lee, J., Lee, Y. S., Lenselink, E. B., Lenz, P., Li, L., Li, J., Liang, H., Mpindi, J. P., Myers, C. L., Newton, M. A., Overington, J. P., Parkkinen, J., Prill, R. J., Peng, J., Pestell, R., Qiu, P., Rajwa, B., Sadanandam, A., Sambo, F., Sridhar, A., Sun, W., Toffolo, G. M., Tozeren, A., Troyanskaya, O. G., Tsamardinos, I., Van Vlijmen, H. W. T., Wang, W., Wegner, J. K., Wennerberg, K., Van Westen, G. J. P., Xia, T., Yang, Y., Yao, V., Yuan, Y., Zeng, H., Zhang, S., Zhao, J. & Zhou, J. Dec 1 2014 In : Nature Biotechnology. 32, 12, p. 1213-1222 10 p.

Research output: Research - peer-reviewArticle

Computer Simulation
Drug Combinations
Transcriptome
B-Lymphocytes
Therapeutics
120 Citations

A community effort to assess and improve drug sensitivity prediction algorithms

Costello, J. C. , Heiser, L. M. , Georgii, E. , Gönen, M. , Menden, M. P. , Wang, N. J. , Bansal, M. , Ammad-Ud-Din, M. , Hintsanen, P. , Khan, S. A. , Mpindi, J. P. , Kallioniemi, O. , Honkela, A. , Aittokallio, T. , Wennerberg, K. , Collins, J. J. , Gallahan, D. , Singer, D. , Saez-Rodriguez, J. , Kaski, S. & 113 others Gray, J. W., Stolovitzky, G., Abbuehl, J. P., Allen, J., Altman, R. B., Balcome, S., Battle, A., Bender, A., Berger, B., Bernard, J., Bhattacharjee, M., Bhuvaneshwar, K., Bieberich, A. A., Boehm, F., Califano, A., Chan, C., Chen, B., Chen, T. H., Choi, J., Coelho, L. P., Cokelaer, T., Collins, J. C., Creighton, C. J., Cui, J., Dampier, W., Davisson, V. J., De Baets, B., Deshpande, R., DiCamillo, B., Dundar, M., Duren, Z., Ertel, A., Fan, H., Fang, H., Gauba, R., Gottlieb, A., Grau, M., Gusev, Y., Ha, M. J., Han, L., Harris, M., Henderson, N., Hejase, H. A., Homicsko, K., Hou, J. P., Hwang, W., IJzerman, A. P., Karacali, B., Keles, S., Kendziorski, C., Kim, J., Kim, M., Kim, Y., Knowles, D. A., Koller, D., Lee, J., Lee, J. K., Lenselink, E. B., Li, B., Li, B., Li, J., Liang, H., Ma, J., Madhavan, S., Mooney, S., Myers, C. L., Newton, M. A., Overington, J. P., Pal, R., Peng, J., Pestell, R., Prill, R. J., Qiu, P., Rajwa, B., Sadanandam, A., Sambo, F., Shin, H., Song, J., Song, L., Sridhar, A., Stock, M., Sun, W., Ta, T., Tadesse, M., Tan, M., Tang, H., Theodorescu, D., Toffolo, G. M., Tozeren, A., Trepicchio, W., Varoquaux, N., Vert, J. P., Waegeman, W., Walter, T., Wan, Q., Wang, D., Wang, W., Wang, Y., Wang, Z., Wegner, J. K., Wu, T., Xia, T., Xiao, G., Xie, Y., Xu, Y., Yang, J., Yuan, Y., Zhang, S., Zhang, X. S., Zhao, J., Zuo, C., Van Vlijmen, H. W. T. & Van Westen, G. J. P. Dec 1 2014 In : Nature Biotechnology. 32, 12, p. 1202-1212 11 p.

Research output: Research - peer-reviewArticle

Pharmaceutical Preparations
Datasets
Reverse engineering
Microarrays
Gene expression
7 Citations

Augmenting protein release from layer-by-layer functionalized agarose hydrogels

Lynam, D., Peterson, C., Maloney, R., Shahriari, D., Garrison, A., Saleh, S., Mehrotra, S., Chan, C. & Sakamoto, J. Mar 15 2014 In : Carbohydrate Polymers. 103, 1, p. 377-384 8 p.

Research output: Research - peer-reviewArticle

Hydrogels
Sepharose
Proteins
Gels
Hydrogel
1 Citations
Palmitates
Phosphotransferases
Fatty Acids
Binding Sites
Ligands
2 Citations

CREB modulates calcium signaling in cAMP-induced bone marrow stromal cells (BMSCs)

Zhang, L., Liu, L., Thompson, R. & Chan, C. Oct 1 2014 In : Cell Calcium. 56, 4, p. 257-268 12 p.

Research output: Research - peer-reviewArticle

Cyclic AMP Response Element-Binding Protein
Calcium Signaling
Mesenchymal Stromal Cells
Cyclic AMP
Calcium
7 Citations

Distinguishing patients with Parkinson's disease subtypes from normal controls based on functional network regional efficiencies

Zhang, D., Liu, X., Chen, J., Liu, B. & Chan, C. Dec 22 2014 In : PLoS One. 9, 12, e115131

Research output: Research - peer-reviewArticle

Parkinson Disease
Parkinson disease
Cerebellum
cerebellum
Tremor
7 Citations

Effect of static pre-stretch induced surface anisotropy on orientation of mesenchymal stem cells

Liu, C., Baek, S., Kim, J., Vasko, E., Pyne, R. & Chan, C. 2014 In : Cellular and Molecular Bioengineering. 7, 1, p. 106-121 16 p.

Research output: Research - peer-reviewArticle

Stem Cells
Stretch
Anisotropy
Cell
Stem cells
4 Citations

Improved asymmetry prediction for short interfering RNAs

Malefyt, A. P., Wu, M., Vocelle, D. B., Kappes, S. J., Lindeman, S. D., Chan, C. & Walton, S. P. Jan 2014 In : FEBS Journal. 281, 1, p. 320-330 11 p.

Research output: Research - peer-reviewArticle

Small Interfering RNA
Thermodynamics
Thermodynamic stability
Nucleotides
Protein Kinases

Improving drug sensitivity prediction using different types of data

Hejase, H. A. & Chan, C. 2014 In : CPT: Pharmacometrics and Systems Pharmacology. 3, 5, 666

Research output: Research - peer-reviewArticle

Drugs
Prediction
Cell Line
Pharmaceutical Preparations
Cells
21 Citations
Inflammasomes
Palmitates
Ice
Interleukin-1beta
Astrocytes
6 Citations

Prediction of therapeutic microRNA based on the human metabolic network

Wu, M. & Chan, C. 2014 In : Bioinformatics. 30, 8, p. 1163-1171 9 p.

Research output: Research - peer-reviewArticle

MicroRNA
Metabolic Network
Prediction
Human
Metabolic Networks and Pathways
4 Citations

Systematic modeling for the insulin signaling network mediated by IRS1 and IRS2

Huang, C., Wu, M., Du, J., Liu, D. & Chan, C. Aug 21 2014 In : Journal of Theoretical Biology. 355, p. 40-52 13 p.

Research output: Research - peer-reviewArticle

Insulin
Modeling
insulin
kinetics
Model
66 Citations

The role of inflammasome in Alzheimer's disease

Liu, L. & Chan, C. 2014 In : Ageing Research Reviews. 15, 1, p. 6-15 10 p.

Research output: Research - peer-reviewArticle

Inflammasomes
Alzheimer Disease
Central Nervous System
Neurology
Inflammation
2013
12 Citations

A classification framework applied to cancer gene expression profiles

Hijazi, H. & Chan, C. Jun 2013 In : Journal of Healthcare Engineering. 4, 2, p. 255-283 29 p.

Research output: Research - peer-reviewArticle

Neoplasm Genes
Transcriptome
Neoplasms
Gene expression
Support vector machines
5 Citations

A multi-layer inference approach to reconstruct condition-specific genes and their regulation

Wu, M., Liu, L., Hijazi, H. & Chan, C. Jun 15 2013 In : Bioinformatics. 29, 12, p. 1541-1552 12 p.

Research output: Research - peer-reviewArticle

Multilayer
Gene
Genes
Breast Neoplasms
Breast Cancer
21 Citations

Curcumin-induced upregulation of the anti-tau cochaperone BAG2 in primary rat cortical neurons

Patil, S. P., Tran, N., Geekiyanage, H., Liu, L. & Chan, C. Oct 25 2013 In : Neuroscience Letters. 554, p. 121-125 5 p.

Research output: Research - peer-reviewArticle

Curcumin
Up-Regulation
Neurons
Polyphenols
Alzheimer Disease
13 Citations

Design of siRNA therapeutics from the molecular scale

Angart, P., Vocelle, D., Chan, C. & Patrick Walton, S. Mar 25 2013 In : Pharmaceuticals. 6, 4, p. 440-468 29 p.

Research output: Research - peer-reviewArticle

Small Interfering RNA
Therapeutics
Biological Phenomena
Drug Industry
RNA Interference
12 Citations

Early phosphoproteomic changes in the mouse spleen during deoxynivalenol-induced ribotoxic stress

Pan, X., Whitten, D. A., Wu, M., Chan, C., Wilkerson, C. G. & Pestka, J. J. Sep 2013 In : Toxicological Sciences. 135, 1, p. 129-143 15 p.

Research output: Research - peer-reviewArticle

Spleen
deoxynivalenol
Phosphorylation
Proteins
Mitogen-Activated Protein Kinases
16 Citations

Global protein phosphorylation dynamics during deoxynivalenol-induced ribotoxic stress response in the macrophage

Pan, X., Whitten, D. A., Wu, M., Chan, C., Wilkerson, C. G. & Pestka, J. J. Apr 5 2013 In : Toxicology and Applied Pharmacology. 268, 2, p. 201-211 11 p.

Research output: Research - peer-reviewArticle

Macrophages
Phosphorylation
Proteins
deoxynivalenol
Trichothecenes
23 Citations

Inhibition of serine palmitoyltransferase reduces Aβ and tau hyperphosphorylation in a murine model: a safe therapeutic strategy for Alzheimer's disease

Geekiyanage, H., Upadhye, A. & Chan, C. Aug 2013 In : Neurobiology of Aging. 34, 8, p. 2037-2051 15 p.

Research output: Research - peer-reviewArticle

Serine C-Palmitoyltransferase
Amyloid
Alzheimer Disease
Therapeutics
Inhibition (Psychology)
24 Citations

Palmitate-activated astrocytes via serine palmitoyltransferase increase BACE1 in primary neurons by sphingomyelinases

Liu, L., Martin, R. & Chan, C. Feb 2013 In : Neurobiology of Aging. 34, 2, p. 540-550 11 p.

Research output: Research - peer-reviewArticle

Serine C-Palmitoyltransferase
Sphingomyelin Phosphodiesterase
Palmitates
Astrocytes
Neurons
13 Citations

Palmitate induces transcriptional regulation of BACE1 and presenilin by STAT3 in neurons mediated by astrocytes

Liu, L., Martin, R., Kohler, G. & Chan, C. Oct 2013 In : Experimental Neurology. 248, p. 482-490 9 p.

Research output: Research - peer-reviewArticle

Presenilins
Palmitates
Astrocytes
Alzheimer Disease
Neurons
7 Citations

Quantitative, solution-phase profiling of multiple transcription factors in parallel

Bilgin, B., Liu, L., Chan, C. & Patrick Walton, S. Mar 2013 In : Analytical and Bioanalytical Chemistry. 405, 8, p. 2461-2468 8 p.

Research output: Research - peer-reviewArticle

Transcription Factors
Assays
Genes
Amplification
DNA
15 Citations

Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells

Cho, H., Wu, M., Zhang, L., Thompson, R., Nath, A. & Chan, C. Jan 22 2013 In : BMC Systems Biology. 7, 9

Research output: Research - peer-reviewArticle

Endoplasmic Reticulum
Transcription Factor
Cell
Activating Transcription Factor 4
Endoplasmic Reticulum Stress
2012
128 Citations

Blood serum miRNA: Non-invasive biomarkers for Alzheimer's disease

Geekiyanage, H., Jicha, G. A., Nelson, P. T. & Chan, C. Jun 2012 In : Experimental Neurology. 235, 2, p. 491-496 6 p.

Research output: Research - peer-reviewArticle

MicroRNAs
Alzheimer Disease
Biomarkers
Serum
Aptitude
2 Citations

Ensemble classification of cancer types and biomarker identification

Hijazi, H., Wu, M., Nath, A. & Chan, C. Nov 2012 In : Drug Development Research. 73, 7, p. 414-419 6 p.

Research output: Research - peer-reviewArticle

Tumor Biomarkers
Neoplasms
Biomarkers
Drug Design
Research
10 Citations

Latest developments in experimental and computational approaches to characterize protein-lipid interactions

Cho, H., Wu, M., Bilgin, B., Walton, S. P. & Chan, C. Nov 2012 In : Proteomics. 12, 22, p. 3273-3285 13 p.

Research output: Research - peer-reviewArticle

Lipids
Proteins
Technology
Molecules
DNA
8 Citations

Learning transcriptional regulation on a genome scale: A theoretical analysis based on gene expression data

Wu, M. & Chan, C. Mar 2012 In : Briefings in Bioinformatics. 13, 2, p. 150-161 12 p., bbr029

Research output: Research - peer-reviewArticle

Data Mining
Gene Regulatory Networks
Gene Expression Profiling
MicroRNAs
Computer Simulation
2 Citations

Oligomerization of the transmembrane domain of IRE1α in SDS micelles

Cho, H., LaMarca, R. & Chan, C. Nov 2 2012 In : Biochemical and Biophysical Research Communications. 427, 4, p. 764-767 4 p.

Research output: Research - peer-reviewArticle

Micelles
Proteins
Oligomerization
Enzymes
Unfolded Protein Response
14 Citations

Time controlled release of arabinofuranosylcytosine (Ara-C) from agarose hydrogels using layer-by-layer assembly: An in vitro study

Mehrotra, S., Lynam, D., Liu, C., Shahriari, D., Lee, I., Tuszynski, M., Sakamoto, J. & Chan, C. 2012 In : Journal of Biomaterials Science, Polymer Edition. 23, 1-4, p. 439-463 25 p.

Research output: Research - peer-reviewArticle

Hydrogels
Cytarabine
Sepharose
In Vitro Techniques
Cells
2011
23 Citations

CAMP initiates early phase neuron-like morphology changes and late phase neural differentiation in mesenchymal stem cells

Zhang, L., Seitz, L. C., Abramczyk, A. M., Liu, L. & Chan, C. Mar 2011 In : Cellular and Molecular Life Sciences. 68, 5, p. 863-876 14 p.

Research output: Research - peer-reviewArticle

Mesenchymal Stromal Cells
Neurons
Potassium Chloride
Second Messenger Systems
Cyclic AMP-Dependent Protein Kinases
14 Citations

Identification of novel targets for breast cancer by exploring gene switches on a genome scale

Wu, M., Liu, L. & Chan, C. Nov 3 2011 In : BMC Genomics. 12, 547

Research output: Research - peer-reviewArticle

Neoplasm Genes
Genome
Breast Neoplasms
Neoplasms
Switch Genes
111 Citations

Micro RNA-137/181c regulates serine palmitoyltransferase and in turn amyloid β novel targets in sporadic Alzheimer's disease

Geekiyanage, H. & Chan, C. Oct 12 2011 In : Journal of Neuroscience. 31, 41, p. 14820-14830 11 p.

Research output: Research - peer-reviewArticle

Serine C-Palmitoyltransferase
MicroRNAs
Amyloid
Alzheimer Disease
Ceramides
3 Citations

Molecular mechanism by which palmitate inhibits PKR autophosphorylation

Cho, H., Mukherjee, S., Palasuberniam, P., Pillow, L., Bilgin, B., Nezich, C., Walton, S. P., Feig, M. & Chan, C. Feb 15 2011 In : Biochemistry. 50, 6, p. 1110-1119 10 p.

Research output: Research - peer-reviewArticle

Palmitates
Phosphotransferases
Adenosine Triphosphate
Binding Sites
Proteins
6 Citations

Polyelectrolyte multilayer stamping in aqueous phase and non-contact mode

Mehrotra, S., Lee, I., Liu, C. & Chan, C. Aug 3 2011 In : Industrial and Engineering Chemistry Research. 50, 15, p. 8851-8858 8 p.

Research output: Research - peer-reviewArticle

Stamping
Polyelectrolytes
Multilayers
Substrates
Scaffolds
3 Citations

Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells

Wang, X., Nath, A., Yang, X., Portis, A., Walton, S. P. & Chan, C. Nov 23 2011 In : PLoS One. 6, 11, e28138

Research output: Research - peer-reviewArticle

palmitates
insulin
cells
Desmoplakins
Palmitates
2010
7 Citations

Cancer-drug associations: A complex system

Dalkic, E., Wang, X., Wright, N. & Chan, C. 2010 In : PLoS One. 5, 4, e10031

Research output: Research - peer-reviewArticle

Pharmaceutical Preparations
Neoplasms
drugs
neoplasms
Large scale systems
37 Citations

Cell adhesive behavior on thin polyelectrolyte multilayers: Cells attempt to achieve homeostasis of its adhesion energy

Mehrotra, S., Hunley, S. C., Pawelec, K. M., Zhang, L., Lee, I., Baek, S. & Chan, C. Aug 3 2010 In : Langmuir. 26, 15, p. 12794-12802 9 p.

Research output: Research - peer-reviewArticle

homeostasis
adhesives
adhesion
cells
energy
14 Citations

Confocal microscopy for the analysis of siRNA delivery by polymeric nanoparticles

Portis, A. M., Carballo, G., Baker, G. L., Chan, C. & Walton, S. P. Sep 2010 In : Microscopy Research and Technique. 73, 9, p. 878-885 8 p.

Research output: Research - peer-reviewArticle

Confocal Microscopy
Nanoparticles
Small Interfering RNA
delivery
microscopy