Literature DB >> 22954137

Measurement and modeling of signaling at the single-cell level.

Sarah E Kolitz1, Douglas A Lauffenburger.   

Abstract

It has long been recognized that a deeper understanding of cell function, with respect to execution of phenotypic behaviors and their regulation by the extracellular environment, is likely to be achieved by analyzing the underlying molecular processes for individual cells selected from across a population, rather than averages of many cells comprising that population. In recent years, experimental and computational methods for undertaking these analyses have advanced rapidly. In this review, we provide a perspective on both measurement and modeling facets of biochemistry at a single-cell level. Our central focus is on receptor-mediated signaling networks that regulate cell phenotypic functions.

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Year:  2012        PMID: 22954137      PMCID: PMC5621923          DOI: 10.1021/bi300846p

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  92 in total

1.  Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells.

Authors:  Qihui Shi; Lidong Qin; Wei Wei; Feng Geng; Rong Fan; Young Shik Shin; Deliang Guo; Leroy Hood; Paul S Mischel; James R Heath
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-27       Impact factor: 11.205

2.  Class assignment of sequence-unrelated members of enzyme superfamilies by activity-based protein profiling.

Authors:  Nadim Jessani; Jason A Young; Sandra L Diaz; Matthew P Patricelli; Ajit Varki; Benjamin F Cravatt
Journal:  Angew Chem Int Ed Engl       Date:  2005-04-15       Impact factor: 15.336

3.  A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates.

Authors:  Melissa D Shults; Kevin A Janes; Douglas A Lauffenburger; Barbara Imperiali
Journal:  Nat Methods       Date:  2005-03-23       Impact factor: 28.547

4.  Parallel picoliter rt-PCR assays using microfluidics.

Authors:  Joshua S Marcus; W French Anderson; Stephen R Quake
Journal:  Anal Chem       Date:  2006-02-01       Impact factor: 6.986

5.  High-content single-cell drug screening with phosphospecific flow cytometry.

Authors:  Peter O Krutzik; Janelle M Crane; Matthew R Clutter; Garry P Nolan
Journal:  Nat Chem Biol       Date:  2007-12-23       Impact factor: 15.040

Review 6.  Origins of regulated cell-to-cell variability.

Authors:  Berend Snijder; Lucas Pelkmans
Journal:  Nat Rev Mol Cell Biol       Date:  2011-01-12       Impact factor: 94.444

7.  Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae.

Authors:  Jacob Stewart-Ornstein; Jonathan S Weissman; Hana El-Samad
Journal:  Mol Cell       Date:  2012-02-24       Impact factor: 17.970

8.  A microfluidic platform for systems pathology: multiparameter single-cell signaling measurements of clinical brain tumor specimens.

Authors:  Jing Sun; Michael D Masterman-Smith; Nicholas A Graham; Jing Jiao; Jack Mottahedeh; Dan R Laks; Minori Ohashi; Jason DeJesus; Ken-ichiro Kamei; Ki-Bum Lee; Hao Wang; Zeta T F Yu; Yi-Tsung Lu; Shuang Hou; Keyu Li; Max Liu; Nangang Zhang; Shutao Wang; Brigitte Angenieux; Eduard Panosyan; Eric R Samuels; Jun Park; Dirk Williams; Vera Konkankit; David Nathanson; R Michael van Dam; Michael E Phelps; Hong Wu; Linda M Liau; Paul S Mischel; Jorge A Lazareff; Harley I Kornblum; William H Yong; Thomas G Graeber; Hsian-Rong Tseng
Journal:  Cancer Res       Date:  2010-07-14       Impact factor: 12.701

9.  Identification and testing of a gene expression signature of invasive carcinoma cells within primary mammary tumors.

Authors:  Weigang Wang; Sumanta Goswami; Kyle Lapidus; Amber L Wells; Jeffrey B Wyckoff; Erik Sahai; Robert H Singer; Jeffrey E Segall; John S Condeelis
Journal:  Cancer Res       Date:  2004-12-01       Impact factor: 12.701

10.  Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.

Authors:  Fuchou Tang; Catalin Barbacioru; Siqin Bao; Caroline Lee; Ellen Nordman; Xiaohui Wang; Kaiqin Lao; M Azim Surani
Journal:  Cell Stem Cell       Date:  2010-05-07       Impact factor: 24.633

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  14 in total

1.  Single Cell Profiling Using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation.

Authors:  Thanh D Do; Troy J Comi; Sage J B Dunham; Stanislav S Rubakhin; Jonathan V Sweedler
Journal:  Anal Chem       Date:  2017-02-10       Impact factor: 6.986

Review 2.  Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

Authors:  Lily A Chylek; Leonard A Harris; Chang-Shung Tung; James R Faeder; Carlos F Lopez; William S Hlavacek
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-09-30

3.  Quantitative analysis of receptor tyrosine kinase-effector coupling at functionally relevant stimulus levels.

Authors:  Simin Li; Devayani Bhave; Jennifer M Chow; Thomas V Riera; Sandra Schlee; Simone Rauch; Mariya Atanasova; Richard L Cate; Adrian Whitty
Journal:  J Biol Chem       Date:  2015-01-29       Impact factor: 5.157

Review 4.  Influence of the microenvironment on cell fate determination and migration.

Authors:  Alexander B Bloom; Muhammad H Zaman
Journal:  Physiol Genomics       Date:  2014-03-11       Impact factor: 3.107

5.  Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods.

Authors:  Mustafa Ozen; Tomasz Lipniacki; Andre Levchenko; Effat S Emamian; Ali Abdi
Journal:  Integr Biol (Camb)       Date:  2020-05-21       Impact factor: 2.192

Review 6.  Diversity training for signal transduction: leveraging cell-to-cell variability to dissect cellular signaling, differentiation and death.

Authors:  Jesse W Cotari; Guillaume Voisinne; Grégoire Altan-Bonnet
Journal:  Curr Opin Biotechnol       Date:  2013-06-07       Impact factor: 9.740

7.  Morphological single cell profiling of the epithelial-mesenchymal transition.

Authors:  Susan E Leggett; Jea Yun Sim; Jonathan E Rubins; Zachary J Neronha; Evelyn Kendall Williams; Ian Y Wong
Journal:  Integr Biol (Camb)       Date:  2016-11-07       Impact factor: 2.192

8.  A model for aryl hydrocarbon receptor-activated gene expression shows potency and efficacy changes and predicts squelching due to competition for transcription co-activators.

Authors:  Ted W Simon; Robert A Budinsky; J Craig Rowlands
Journal:  PLoS One       Date:  2015-06-03       Impact factor: 3.240

9.  Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.

Authors:  Carito Guziolowski; Santiago Videla; Federica Eduati; Sven Thiele; Thomas Cokelaer; Anne Siegel; Julio Saez-Rodriguez
Journal:  Bioinformatics       Date:  2013-07-12       Impact factor: 6.937

10.  Deciphering the mechanism behind Fibroblast Growth Factor (FGF) induced biphasic signal-response profiles.

Authors:  Jitendra Kanodia; Diana Chai; Jannik Vollmer; Jaeyeon Kim; Andreas Raue; Greg Finn; Birgit Schoeberl
Journal:  Cell Commun Signal       Date:  2014-05-15       Impact factor: 5.712

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