Institution · La Jolla Bioengineering Institute
Most cited papers from La Jolla Bioengineering Institute
What are the most cited papers from La Jolla Bioengineering Institute?
The most cited paper from La Jolla Bioengineering Institute is "PHENIX : a comprehensive Python-based system for macromolecular structure solution" (Paul D. Adams, Pavel V. Afonine, G. Bunkóczi et al., 2010), with 24,924 citations. Next come "A component based noise correction method (CompCor) for BOLD and perfusion based fMRI" (4,975) and "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking" (4,812).
Showing 50 of 58 papers. Every paper with more than 810 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | PHENIX : a comprehensive Python-based system for macromolecular structure solution Paul D. Adams, Pavel V. Afonine, G. Bunkóczi et al. · Acta Crystallographica Section D Biological Crystallography | 21 Jan 2010 | 24,924 |
| 2 | A component based noise correction method (CompCor) for BOLD and perfusion based fMRI Yashar Behzadi, Khaled Restom, Joy Liau et al. · NeuroImage | 4 May 2007 | 4,975 |
| 3 | Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Mingxun Wang et al. · Nature Biotechnology | Aug 2016 | 4,812 |
| 4 | Integration of biological networks and gene expression data using Cytoscape Melissa Cline et al. · Nature Protocols | 27 Sep 2007 | 2,601 |
| 5 | Effects of Disturbed Flow on Vascular Endothelium: Pathophysiological Basis and Clinical Perspectives Jeng‐Jiann Chiu, Shu Chien · Physiological Reviews | 2011 | 2,273 |
| 6 | Macrophage Polarization: Different Gene Signatures in M1(LPS+) vs. Classically and M2(LPS–) vs. Alternatively Activated Macrophages Marco Orecchioni, Yanal Ghosheh, Akula Bala Pramod et al. · Frontiers in Immunology | 24 May 2019 | 2,138 |
| 7 | Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 Jan Schellenberger, Richard A. Que, Ronan M. T. Fleming et al. · Nature Protocols | 4 Aug 2011 | 1,925 |
| 8 | A protocol for generating a high-quality genome-scale metabolic reconstruction Ines Thiele, Bernhard Ørn Palsson · Nature Protocols | 2010 | 1,918 |
| 9 | Neuromorphic Silicon Neuron Circuits Giacomo Indiveri, B. Linares-Barranco, Tara Julia Hamilton et al. · Frontiers in Neuroscience | 2011 | 1,844 |
| 10 | Immunity and Inflammation in Atherosclerosis Dennis Wolf, Klaus Ley · Circulation Research | 17 Jan 2019 | 1,768 |
| 11 | ClassyFire: automated chemical classification with a comprehensive, computable taxonomy Yannick Djoumbou-Feunang, Roman Eisner, Craig Knox et al. · Journal of Cheminformatics | 4 Nov 2016 | 1,655 |
| 12 | COBRApy: COnstraints-Based Reconstruction and Analysis for Python Ali Ebrahim, Joshua A. Lerman, Bernhard Ørn Palsson et al. · BMC Systems Biology | 8 Aug 2013 | 1,565 |
| 13 | Network‐based classification of breast cancer metastasis Han‐Yu Chuang, Eunjung Lee, Yu‐Tsueng Liu et al. · Molecular Systems Biology | 16 Oct 2007 | 1,458 |
| 14 | electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation Nigel W. Moriarty, Ralf W. Grosse‐Kunstleve, Paul D. Adams · Acta Crystallographica Section D Biological Crystallography | 15 Sep 2009 | 1,456 |
| 15 | A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information Adam M. Feist, Christopher S. Henry, Jennifer L. Reed et al. · Molecular Systems Biology | 26 Jun 2007 | 1,438 |
| 16 | LMSD: LIPID MAPS structure database Manish Sud, Eoin Fahy, David Cotter et al. · Nucleic Acids Research | 13 Nov 2006 | 1,421 |
| 17 | Genome-wide analysis of mammalian promoter architecture and evolution Piero Carninci et al. · Nature Genetics | 27 Apr 2006 | 1,421 |
| 18 | Technology Roadmap for Flexible Sensors Yifei Luo et al. · ACS Nano | 9 Mar 2023 | 1,368 |
| 19 | Deciphering cell–cell interactions and communication from gene expression Erick Armingol, Adam Officer, Olivier Harismendy et al. · Nature Reviews Genetics | 9 Nov 2020 | 1,367 |
| 20 | Somatic coding mutations in human induced pluripotent stem cells Athurva Gore et al. · Nature | Mar 2011 | 1,274 |
| 21 | In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration Keiichiro Suzuki et al. · Nature | 15 Nov 2016 | 1,216 |
| 22 | Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice Gil Sharon et al. · Cell | May 2019 | 1,214 |
| 23 | Tensile properties of the human femur-anterior cruciate ligament-tibia complex Savio L‐Y. Woo, J. Marcus Hollis, Douglas J. Adams et al. · The American Journal of Sports Medicine | May 1991 | 1,203 |
| 24 | Turning a surface superrepellent even to completely wetting liquids Tingyi “Leo” Liu, Chang‐Jin Kim · Science | 28 Nov 2014 | 1,154 |
| 25 | Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis Teruaki Nakatsuji et al. · Science Translational Medicine | 22 Feb 2017 | 1,120 |
| 26 | Preparation of Hydrogel Substrates with Tunable Mechanical Properties Justin R. Tse, Adam Jeffrey Engler · Current Protocols in Cell Biology | Jun 2010 | 1,110 |
| 27 | A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011 Jeffrey D. Orth, Tom M Conrad, Jessica Na et al. · Molecular Systems Biology | 11 Oct 2011 | 1,086 |
| 28 | Fractal design concepts for stretchable electronics Jonathan A. Fan, Woon‐Hong Yeo, Yewang Su et al. · Nature Communications | 7 Feb 2014 | 1,085 |
| 29 | Genome-scale models of microbial cells: evaluating the consequences of constraints Nathan D. Price, Jennifer L. Reed, Bernhard Ørn Palsson · Nature Reviews Microbiology | 20 Oct 2004 | 1,052 |
| 30 | An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Jennifer L. Reed, Thuy D. Vo, Christophe H. Schilling et al. · Genome biology | 28 Aug 2003 | 1,032 |
| 31 | In situ sprayed bioresponsive immunotherapeutic gel for post-surgical cancer treatment Qian Chen, Chao Wang, Xudong Zhang et al. · Nature Nanotechnology | 4 Dec 2018 | 1,028 |
| 32 | Matrix stiffness drives epithelial–mesenchymal transition and tumour metastasis through a TWIST1–G3BP2 mechanotransduction pathway Spencer C. Wei, Laurent Fattet, Jeff H. Tsai et al. · Nature Cell Biology | 20 Apr 2015 | 1,004 |
| 33 | The Phenix software for automated determination of macromolecular structures Paul D. Adams, Pavel V. Afonine, G. Bunkóczi et al. · Methods | 2 Aug 2011 | 994 |
| 34 | Conformable amplified lead zirconate titanate sensors with enhanced piezoelectric response for cutaneous pressure monitoring Canan Dağdeviren, Yewang Su, Pauline Joe et al. · Nature Communications | 5 Aug 2014 | 986 |
| 35 | Skin microbiota: a source of disease or defence? Anna L. Cogen, Victor Nizet, Richard L. Gallo · British Journal of Dermatology | 11 Feb 2008 | 985 |
| 36 | Materials as stem cell regulators William L. Murphy, Todd C. McDevitt, Adam Jeffrey Engler · Nature Materials | 21 May 2014 | 967 |
| 37 | In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Jeremy S. Edwards, Rafael U. Ibarra, Bernhard Ørn Palsson · Nature Biotechnology | Feb 2001 | 961 |
| 38 | Interplay of matrix stiffness and protein tethering in stem cell differentiation Jessica H. Wen, Ludovic G. Vincent, Alexander Fuhrmann et al. · Nature Materials | 8 Aug 2014 | 959 |
| 39 | Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini et al. · Nature Communications | 19 May 2020 | 944 |
| 40 | Chronic Venous Disease John J. Bergan, Geert W. Schmid‐Schönbein, Philip D Coleridge Smith et al. · New England Journal of Medicine | 2 Aug 2006 | 937 |
| 41 | Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures Gerhard Liebisch, Eoin Fahy, Junken Aoki et al. · Journal of Lipid Research | 19 Oct 2020 | 922 |
| 42 | High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell Song Chen, Blue B. Lake, Kun Zhang · Nature Biotechnology | 14 Oct 2019 | 918 |
| 43 | Mechanotransduction and endothelial cell homeostasis: the wisdom of the cell Shu Chien · American Journal of Physiology-Heart and Circulatory Physiology | 13 Nov 2006 | 915 |
| 44 | Monitoring of the central blood pressure waveform via a conformal ultrasonic device Chonghe Wang et al. · Nature Biomedical Engineering | 4 Sep 2018 | 902 |
| 45 | Constraint-based models predict metabolic and associated cellular functions Aarash Bordbar, Jonathan M. Monk, Zachary A. King et al. · Nature Reviews Genetics | 16 Jan 2014 | 890 |
| 46 | Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Rafael U. Ibarra, Jeremy S. Edwards, Bernhard Ørn Palsson · Nature | Nov 2002 | 885 |
| 47 | Deterministically patterned biomimetic human iPSC-derived hepatic model via rapid 3D bioprinting Xuanyi Ma, Xin Qu, Wei Zhong Zhu et al. · Proceedings of the National Academy of Sciences | 8 Feb 2016 | 884 |
| 48 | Applications of genome‐scale metabolic reconstructions Matthew Oberhardt, Bernhard Ørn Palsson, Jason A. Papin · Molecular Systems Biology | 3 Nov 2009 | 871 |
| 49 | Differential network biology Trey Ideker, Nevan J. Krogan · Molecular Systems Biology | 17 Jan 2012 | 853 |
| 50 | Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models Nathan E. Lewis, Kim K. Hixson, Tom M Conrad et al. · Molecular Systems Biology | 27 Jul 2010 | 846 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for an institution when any of its authors gave it as an affiliation; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.