| # | Title | Journal | Year | Citations |
|---|
| 1 | A component based noise correction method (CompCor) for BOLD and perfusion based fMRI | NeuroImage | 2007 | 3,466 |
| 2 | Probing the Cytotoxicity of Semiconductor Quantum Dots | Nano Letters | 2004 | 3,159 |
| 3 | Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking | Nature Biotechnology | 2016 | 2,802 |
| 4 | The potential and challenges of nanopore sequencing | Nature Biotechnology | 2008 | 2,201 |
| 5 | Luminescent quantum dots for multiplexed biological detection and imaging | Current Opinion in Biotechnology | 2002 | 1,975 |
| 6 | Network‐based classification of breast cancer metastasis | Molecular Systems Biology | 2007 | 1,320 |
| 7 | A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information | Molecular Systems Biology | 2007 | 1,234 |
| 8 | Somatic coding mutations in human induced pluripotent stem cells | Nature | 2011 | 1,147 |
| 9 | A fast, robust and tunable synthetic gene oscillator | Nature | 2008 | 1,079 |
| 10 | Neuromorphic Silicon Neuron Circuits | Frontiers in Neuroscience | 2011 | 1,004 |
| 11 | Immunity and Inflammation in Atherosclerosis | Circulation Research | 2019 | 972 |
| 12 | Increased methylation variation in epigenetic domains across cancer types | Nature Genetics | 2011 | 968 |
| 13 | Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain | Science | 2016 | 822 |
| 14 | Interplay of matrix stiffness and protein tethering in stem cell differentiation | Nature Materials | 2014 | 812 |
| 15 | Reconstruction of biochemical networks in microorganisms | Nature Reviews Microbiology | 2009 | 797 |
| 16 | Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain | Nature Biotechnology | 2018 | 762 |
| 17 | Applications of genome‐scale metabolic reconstructions | Molecular Systems Biology | 2009 | 759 |
| 18 | Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox | Nature Protocols | 2007 | 757 |
| 19 | Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods | Nature Reviews Microbiology | 2012 | 721 |
| 20 | Constraint-based models predict metabolic and associated cellular functions | Nature Reviews Genetics | 2014 | 714 |
| 21 | The Cardiac Mechanical Stretch Sensor Machinery Involves a Z Disc Complex that Is Defective in a Subset of Human Dilated Cardiomyopathy | Cell | 2002 | 712 |
| 22 | Protein networks in disease | Genome Research | 2008 | 712 |
| 23 | Microbiome analyses of blood and tissues suggest cancer diagnostic approach | Nature | 2020 | 691 |
| 24 | Engineered gene circuits | Nature | 2002 | 660 |
| 25 | Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective | Journal of Theoretical Biology | 2000 | 649 |
| 26 | Rapid self-healing hydrogels | Proceedings of the National Academy of Sciences of the United States of America | 2012 | 633 |
| 27 | Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models | Molecular Systems Biology | 2010 | 615 |
| 28 | Neuronal activity modifies the DNA methylation landscape in the adult brain | Nature Neuroscience | 2011 | 601 |
| 29 | The 4D nucleome project | Nature | 2017 | 579 |
| 30 | Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model | Genome Research | 2004 | 557 |
| 31 | High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell | Nature Biotechnology | 2019 | 550 |
| 32 | Real-time neuroimaging and cognitive monitoring using wearable dry EEG | IEEE Transactions on Biomedical Engineering | 2015 | 536 |
| 33 | Intracellular Delivery of Quantum Dots for Live Cell Labeling and Organelle Tracking | Advanced Materials | 2004 | 524 |
| 34 | Probing the role of multicellular organization in three-dimensional microenvironments | Nature Methods | 2006 | 523 |
| 35 | Recapitulation of premature ageing with iPSCs from Hutchinson–Gilford progeria syndrome | Nature | 2011 | 510 |
| 36 | Context-Specific Metabolic Networks Are Consistent with Experiments | PLoS Computational Biology | 2008 | 509 |
| 37 | COVID-19 vaccine development and a potential nanomaterial path forward | Nature Nanotechnology | 2020 | 501 |
| 38 | Delay-induced stochastic oscillations in gene regulation | Proceedings of the National Academy of Sciences of the United States of America | 2005 | 498 |
| 39 | Modeling cellular machinery through biological network comparison | Nature Biotechnology | 2006 | 492 |
| 40 | The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli | Nature Biotechnology | 2008 | 491 |
| 41 | Inferring Pathway Activity toward Precise Disease Classification | PLoS Computational Biology | 2008 | 475 |
| 42 | Naturally derived myocardial matrix as an injectable scaffold for cardiac tissue engineering | Biomaterials | 2009 | 471 |
| 43 | The evolution of molecular biology into systems biology | Nature Biotechnology | 2004 | 460 |
| 44 | Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming | Nature Biotechnology | 2009 | 458 |
| 45 | The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming | Cell Research | 2012 | 452 |
| 46 | Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues | Nature Protocols | 2015 | 422 |
| 47 | Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction | Molecular Systems Biology | 2013 | 411 |
| 48 | Stiffness Gradients Mimicking In Vivo Tissue Variation Regulate Mesenchymal Stem Cell Fate | PLoS ONE | 2011 | 392 |
| 49 | Connecting extracellular metabolomic measurements to intracellular flux states in yeast | BMC Systems Biology | 2009 | 391 |
| 50 | Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data | Journal of Biological Chemistry | 2007 | 387 |
