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• Protease degradomics: A new challenge for proteomics
  openalex Carlos López-Otı́n, Christopher M. Overall 2002-07-01 置信度 0.72 ProteasesProteaseComputational biologyProteomicsOrganism
• Proteome and proteomics: New technologies, new concepts, and new words
  The goal of proteomics is a comprehensive, quantitative description of protein expression and its changes under the influence of biological perturbations such as disease or drug treatment. Quantitative analysis of protein expression data obtained by high-throu…
  openalex N. Leigh Anderson, Norman G. Anderson, Norman G. Anderson, Norman G. Anderson 1998-08-01 置信度 0.72 ProteomicsProteomeComputational biologyGenomicsMechanism (biology)
• Quantitative Proteomics of the Cancer Cell Line Encyclopedia
  openalex David P. Nusinow, John Szpyt, Mahmoud Ghandi, Christopher M. Rose 等 2020-01-01 置信度 0.72 BiologyProteomicsEncyclopediaComputational biologyCancer
• Proteomic Analysis of Dendritic Cell-Derived Exosomes: A Secreted Subcellular Compartment Distinct from Apoptotic Vesicles
  Dendritic cells constitutively secrete a population of small (50-90 nm diameter) Ag-presenting vesicles called exosomes. When sensitized with tumor antigenic peptides, dendritic cells produce exosomes, which stimulate anti-tumor immune responses and the reject…
  openalex Clotilde Théry, Muriel Boussac, P. Véron, Paola Ricciardi‐Castagnoli 等 2001-06-01 置信度 0.72 MicrovesiclesCell biologyExosomeBiologyPopulation
• The minimum information about a proteomics experiment (MIAPE)
  openalex Chris Taylor, Norman W. Paton, Kathryn S. Lilley, Pierre‐Alain Binz 等 2007-08-01 置信度 0.72 ProteomicsData scienceProteomeComputer scienceUnderpinning
• Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
  openalex J. Robert Newman, Sina Ghaemmaghami, Jan Ihmels, David K. Breslow 等 2006-05-14 置信度 0.72 Computational biologyBiologyProteomicsNoise (video)Messenger RNA
• Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy
  openalex Cigall Kadoch, Diana C. Hargreaves, H. Courtney Hodges, Laura Elias 等 2013-05-05 置信度 0.72 BiologySWI/SNFProtein subunitGeneticsMutation
• Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics
  Measurements of mass spectral peak intensities and spectral counts are promising methods for quantifying protein abundance changes in shotgun proteomic analyses. We describe Serac, software developed to evaluate the ability of each method to quantify relative …
  openalex William M. Old, Karen Meyer-Arendt, Lauren D. Aveline-Wolf, Kevin G. Pierce 等 2005-06-24 置信度 0.72 Shotgun proteomicsShotgunComputational biologyProteomicsLabel-free quantification
• PRIDE: The proteomics identifications database
  The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO…
  openalex Lennart Martens, Henning Hermjakob, Philip Jones, Marcin Adamski 等 2005-07-22 置信度 0.72 Computer scienceUploadInterface (matter)World Wide WebDatabase
• Serum Proteomic Patterns for Detection of Prostate Cancer
  Pathologic states within the prostate may be reflected by changes in serum proteomic patterns. To test this hypothesis, we analyzed serum proteomic mass spectra with a bioinformatics tool to reveal the most fit pattern that discriminated the training set of se…
  openalex Emanuel F. Petricoin 2002-10-15 置信度 0.72 Prostate cancerMedicineProstateCancerConfidence interval
• Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma
  openalex Ying Jiang, Aihua Sun, Yang Zhao, Wantao Ying 等 2019-02-27 置信度 0.72 Hepatocellular carcinomaLiver cancerOncologyMedicineCancer research
• Comprehensive proteomic analysis of the human spliceosome
  openalex Zhaolan Zhou, Lawrence J. Licklider, Steven P. Gygi, Robin Reed 2002-09-01 置信度 0.72 SpliceosomeRNA splicingIntronBiologyPolypyrimidine tract
• Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
  Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) …
  openalex Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon 等 2018-08-01 置信度 0.72 Library scienceSystems biologyBiologyComputational biologyComputer science
• An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome
  openalex Tilmann Bürckstümmer, Christoph Baumann, Stephan Blüml, Evelyn Dixit 等 2009-01-21 置信度 0.72 AIM2InflammasomeDNAInnate immune systemBiology
• Protein analysis on a proteomic scale
  openalex Eric M. Phizicky, Philippe I. H. Bastiaens, Heng Zhu, M Snyder 等 2003-03-01 置信度 0.72 ProteomeComputational biologyProteomicsIdentification (biology)Biology
• New views of old proteins: clarifying the enigmatic proteome
  All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to meet the challenges tha…
  arxiv Participants in a NIH Workshop on Functional, Integrative Proteomics, :, Kristin E. Burnum Johnson 等 2021-08-17T14:43:04Z 置信度 0.78 q-bio.BM
• An Optimized Data Structure for High Throughput 3D Proteomics Data: mzRTree
  As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. …
  arxiv Sara Nasso, Francesco Silvestri, Francesco Tisiot, Barbara Di Camillo 等 2010-02-19T17:17:02Z 置信度 0.78 cs.CEcs.DSq-bio.QM
• Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution
  Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chron…
  arxiv Gustavo Caetano-Anollés, M. Fayez Aziz, Fizza Mughal, Derek Caetano-Anollés 2026-02-17T04:33:42Z 置信度 0.78 q-bio.QM
• Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence
  Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportu…
  arxiv Yingying Sun, Jun A, Zhiwei Liu, Rui Sun 等 2025-02-21T13:20:33Z 置信度 0.78 q-bio.OTcs.AI
• Is a gene-centric human proteome project the best way for proteomics to serve biology?
  With the recent developments in proteomic technologies, a complete human proteome project (HPP) appears feasible for the first time. However, there is still debate as to how it should be designed and what it should encompass. In "proteomics speak", the debate …
  arxiv Thierry Rabilloud, Denis Hochstrasser, Richard J Simpson 2010-07-30T06:45:41Z 置信度 0.78 q-bio.GN
• Two-dimensional gel electrophoresis in proteomics: past, present and future
  Two-dimensional gel electrophoresis has been instrumental in the birth and developments of proteomics, although it is no longer the exclusive separation tool used in the field of proteomics. In this review, a historical perspective is made, starting from the d…
  arxiv Thierry Rabilloud, Mireille Chevallet, Sylvie Luche, Cécile Lelong 2010-08-16T08:16:47Z 置信度 0.78 q-bio.GN
• Guidelines for the next 10 years of proteomics
  In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of stringency required in proteo…
  arxiv Marc R Wilkins, Ron D Appel, Jennifer E Van Eyk, Maxey C M Chung 等 2009-04-05T15:58:06Z 置信度 0.78 q-bio.GN
• Two-dimensional gel electrophoresis in proteomics: A tutorial
  Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose of this tutorial pap…
  arxiv Thierry Rabilloud, Cécile Lelong 2011-09-14T19:39:19Z 置信度 0.78 q-bio.GN
• The proteomic to biology inference, a frequently overlooked concern in the interpretation of proteomic data: A plea for functional validation
  Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase in the speed and sens…
  arxiv Thierry Rabilloud, Pierre Lescuyer 2014-03-21T10:29:41Z 置信度 0.78 q-bio.GN
• Oxidative stress response: a proteomic view
  The oxidative stress response is characterized by various effects on a range of biologic molecules. When examined at the protein level, both expression levels and protein modifications are altered by oxidative stress. While these effects have been studied in t…
  arxiv Thierry Rabilloud, Mireille Chevallet, Sylvie Luche, Emmanuelle Leize-Wagner 2008-07-07T15:30:32Z 置信度 0.78 q-bio.GN
• Paleoproteomics explained to youngsters: how did the wedding of two-dimensional electrophoresis and protein sequencing spark proteomics on: Let there be light
  Taking the opportunity of the 20th anniversary of the word "proteomics", this young adult age is a good time to remember how proteomics came from enormous progress in protein separation and protein microanalysis techniques, and from the conjugation of these ad…
  arxiv Thierry Rabilloud 2014-08-06T15:42:50Z 置信度 0.78 q-bio.GN
• Progress in the definition of a reference human mitochondrial proteome
  Owing to the complexity of higher eukaryotic cells, a complete proteome is likely to be very difficult to achieve. However, advantage can be taken of the cell compartmentalization to build organelle proteomes, which can moreover be viewed as specialized tools …
  arxiv Pierre Lescuyer, Jean-Marc Strub, Sylvie Luche, Hélène Diemer 等 2006-11-24T13:01:05Z 置信度 0.78 q-bio.GN
• Zinc adaptation and resistance to cadmium toxicity in mammalian cells. Molecular insight by proteomic analysis
  To identify proteins involved in cellular adaptive responses to zinc, a comparative proteome analysis between a previously developed high zinc- and cadmium- resistant human epithelial cell line (HZR) and the parental HeLa cells has been carried out. Differenti…
  arxiv Estelle Rousselet, Alain Martelli, Mireille Chevallet, Hélène Diemer 等 2008-03-06T12:40:10Z 置信度 0.78 q-bio.GN
• Improved proteomic analysis of nuclear proteins, as exemplified by the comparison of two myeloïd cell lines nuclear proteomes
  One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear acids. Several experimen…
  arxiv Cécile Lelong, Mireille Chevallet, Hélène Diemer, Sylvie Luche 等 2012-10-17T20:02:51Z 置信度 0.78 q-bio.GN
• Spatial proteomics guided by H&E-based AI reveals recurrence-risk niches in triple-negative breast cancer
  Deep learning models can predict cancer recurrence from H&E stained slides, but the localized molecular states underlying these predictions remain largely obscured. Here, we developed an outcome informed spatial pathology framework in TNBC that integrates …
  arxiv Yesung Cho, Ji Hwan Park, Chanil Kim, Hyewon Kim 等 2026-08-04T05:19:35Z 置信度 0.78 cs.AIq-bio.QM
• Molecular responses of mouse macrophages to copper and copper oxide nanoparticles inferred from proteomic analyses
  The molecular responses of macrophages to copper-based nanoparticles have been investigated via a combination of proteomic and biochemical approaches, using the RAW264.7 cell line as a model. Both metallic copper and copper oxide nanoparticles have been tested…
  arxiv Sarah Triboulet, Catherine Aude-Garcia, Marie Carrière, Hélène Diemer 等 2013-11-04T18:23:47Z 置信度 0.78 q-bio.GN
• Organelle proteomics
  This unit describes strategies for studying the proteomes of organelles, which is one example of targeted proteomics. It relies heavily on previously published units dealing with organelle preparation, protein solubilization, and proteomics techniques. A speci…
  arxiv Pierre Lescuyer, Mireille Chevallet, Sylvie Luche, Thierry Rabilloud 2009-04-03T18:53:00Z 置信度 0.78 q-bio.GN
• Quantum Proteomics
  We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic structure of the prot…
  arxiv Fabio Pichierri 2011-07-29T01:25:47Z 置信度 0.78 q-bio.BMq-bio.GN
• How to use 2D gel electrophoresis in plant proteomics
  Two-dimensional electrophoresis has nurtured the birth of proteomics. It is however no longer the exclusive setup used in proteomics, with the development of shotgun proteomics techniques that appear more fancy and fashionable nowadays.Nevertheless, 2D gel-bas…
  arxiv Thierry Rabilloud 2013-12-04T08:53:08Z 置信度 0.78 q-bio.GN
• Neural Proteomics Fields for Super-resolved Spatial Proteomics Prediction
  Spatial proteomics maps protein distributions in tissues, providing transformative insights for life sciences. However, current sequencing-based technologies suffer from low spatial resolution, and substantial inter-tissue variability in protein expression fur…
  arxiv Bokai Zhao, Weiyang Shi, Hanqing Chao, Zijiang Yang 等 2025-08-24T14:53:12Z 置信度 0.78 q-bio.QMcs.AIcs.CV
• Keynotes on membrane proteomics
  This review article deals with the specificities of the proteomics analysis of membrane proteins.
  arxiv Thierry Rabilloud 2008-07-07T15:27:20Z 置信度 0.78 q-bio.GN
• The Whereabouts of 2D Gels in Quantitative Proteomics
  Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative compa…
  arxiv Thierry Rabilloud 2012-06-14T04:57:18Z 置信度 0.78 q-bio.GN
• Guidelines for reporting the use of gel electrophoresis in proteomics
  the MIAPE Gel Electrophoresis (MIAPE-GE) guidelines specify the minimum information that should be provided when reporting the use of n-dimensional gel electrophoresis in a proteomics experiment. Developed through a joint effort between the gel-based analysis …
  arxiv Frank Gibson, Leigh Anderson, Gyorgy Babnigg, Mark Baker 等 2009-04-04T07:21:20Z 置信度 0.78 q-bio.GN
• Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry
  Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into pe…
  arxiv Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A. Neely 等 2023-11-13T22:58:30Z 置信度 0.78 q-bio.QM
• Fecal microbiome transplant in food allergy in humans and mice identifies a role for bile acid metabolites in oral tolerance.
  The gut microbiome has been implicated in the pathogenesis of food allergy (FA), prompting microbiome-focused interventions. We evaluated, in a phase 1 open-label trial (NCT02960074), the safety and efficacy of oral encapsulated fecal microbiome transplantatio…
  pubmed Rachid R, Martinez-Blanco M, Kuziel GA, Stephen-Victor E 等 2026 Aug 5 置信度 0.82
• SCHEPHERD: A modular, programmable, direct current platform to control cell behavior.
  Spanning frogs, fish, and humans, direct current (dc) bioelectric cues play critical roles beyond neuromuscular function, such as modulating morphogenesis, immune response, and healing through electrotaxis-electrically directed cell migration. Harnessing this …
  pubmed Lin Y, Yodh JS, Rodriguez C, Kreymborg P 等 2026 Aug 7 置信度 0.82
• Localized immunomodulation with cytokine-producing cells to mitigate foreign body responses in rodents and a nonhuman primate.
  The efficacy of cell-based therapeutics is often compromised by host immune recognition of implanted cells and biomaterials, resulting in fibrotic encapsulation and loss of function. Here, we address this challenge with an immunomodulatory cell-based therapy, …
  pubmed Kim B, Vohidova D, Nash A, Chan YS 等 2026 Aug 7 置信度 0.82
• Early fate diversification of radial glial progenitors during corticogenesis.
  Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. We combined Mosaic Analysis with Double Markers at embryonic stages (E)12.5 and E13.5 with early postnatal callosal tracing …
  pubmed Varela-Martínez I, Villalba A, García-Marqués J, Aguilera A 等 2026 Aug 7 置信度 0.82
• Development of a structurally distinct TopBP1 inhibitor that enhances PARP blockade and reverses osimertinib resistance.
  Therapeutic resistance remains a major challenge in cancer treatment, driven by compensatory signaling and stress response pathways that sustain tumor survival. Topoisomerase IIβ-binding protein 1 (TopBP1), a multifunctional scaffold protein with nine BR…
  pubmed Lin FT, Lin SJ, Liu K, Xiao Y 等 2026 Aug 7 置信度 0.82
• SARS-CoV-2 nucleocapsid induces hyperinflammation and vascular leakage through the Toll-like receptor signaling axis in macrophages.
  A substantial proportion of hospitalized COVID-19 patients require ICU admission, often associated with an imbalance between antiviral responses and inflammatory signaling leading to uncontrolled cytokine secretion. The SARS-CoV-2 nucleocapsid (N) protein is a…
  pubmed Yao Z, Alvarez PA, Chavez C, Delgado Y 等 2026 Aug 7 置信度 0.82
• Cohesin facilitates nucleosome invasion by transcription factors.
  Nucleosomes present a major barrier to transcription factor (TF) binding. However, a subgroup of TFs known as pioneer factors (PFs) can recognize motifs covered by nucleosomes and initiate chromatin opening. PFs also bind nucleosomal substrates with high affin…
  pubmed Stoeber S, Chen H, Chen RW, Smith C 等 2026 Aug 7 置信度 0.82
• A metabolite morphogen coordinates multicellular development in Bacillus subtilis.
  The transition from unicellular to multicellular growth requires diversification of cellular functions within genetically identical populations. In Bacillus subtilis , biofilm formation is historically viewed as a developmental precursor to sporulation along a…
  pubmed Updegrove TB, Pande V, She F, Gilmore MC 等 2026 Aug 7 置信度 0.82
• Intermediate stages in the origin of metabolism at a phosphorylating hydrothermal vent.
  The origin of life required the emergence of metabolism, an autocatalytic network of enzymatic reactions that synthesize amino acids, nucleotides, and cofactors. At the origin of metabolism, there were no enzymes-how did it start? Empirical studies addressing …
  pubmed Mrnjavac N, Hoffmann NK, Schlikker ML, Burmeister M 等 2026 Aug 7 置信度 0.82
• Health risks of arsenic and chromium in groundwater and surface water in India: A systematic review.
  Background and objectives India ranks third in global cancer incidence. Groundwater often carries undetectable contaminants such as arsenic, a highly toxic element, and chromium, a probable carcinogen. This systematic review aims to identify patterns of arseni…
  pubmed Sakalkar V, Singh S, Gupta E, Kumar A 等 2026 Aug 置信度 0.82
• A novel dimerization site in non-structural protein 5A of hepatitis C virus regulates viral replication fitness.
  We previously found that high genome replication fitness of the hepatitis C virus (HCV) was associated with severe disease in immunocompromised patients. Elevated replication fitness was mediated by accumulation of mutations in the replication enhancing domain…
  pubmed Rothhaar P, Tubiana T, Förster C, Vanegas Arias G 等 2026 Aug 5 置信度 0.82
• TREM2 plays a critical role in innate immune defense against acute Toxoplasma gondii infection by promoting macrophage antimicrobial activities.
  The TREM2 receptor is a well-known rheostat for inflammation and immunity, but its role in host defense against parasitic infection is only just emerging. We investigated the function of TREM2 during acute Toxoplasma gondii infection by comparing TREM2-deficie…
  pubmed Debray HZ, Cheng D, Ayala LA, Lam T 等 2026 Aug 置信度 0.82
• Molecular determinants of functional voltage-gated sodium (Nav) channel diversity in mammalian central neurons.
  Voltage-gated sodium (Nav) channels are key determinants of neuronal excitability, shaping action potential waveforms, repetitive firing patterns and responses to synaptic inputs, as well as controlling the output of neural circuits and influencing short- and …
  pubmed Ransdell JL, Nerbonne JM 2026 Aug 5 置信度 0.82
• Mean Field Analysis of Algorithms for Scale-free Networks in Molecular Biology
  The sampling of scale-free networks in Molecular Biology is usually achieved by growing networks from a seed using recursive algorithms with elementary moves which include the addition and deletion of nodes and bonds. These algorithms include the Barabasi-Albe…
  arxiv S Konini, EJ Janse van Rensburg 2017-02-01T13:15:01Z 置信度 0.78 physics.soc-phcond-mat.dis-nnq-bio.MN
• Reproducibility and scientific interpretation in the age of AI: consilience in biological systematics, ecology, and molecular biology
  Achieving complete reproducibility in science, particularly in research fields such as biodiversity, is challenging due to analytical choices, bias and interpretation. Here, we examine examples of reproducibility in biological systematics, ecology, and molecul…
  arxiv Charles Morphy D. Santos, Luciana Campos Paulino, Michaella P. Andrade, Gabriel Tognella-Poccia 等 2025-07-25T16:43:40Z 置信度 0.78 q-bio.OT
• Macro-trends in research on the central dogma of molecular biology
  The central dogma of molecular biology, formulated more than five decades ago, compartmentalized information exchange in the cell into the DNA, RNA and protein domains. This formalization has served as an implicit thematic distinguisher for cell biological res…
  arxiv Sepehr Ehsani 2013-01-11T07:00:57Z 置信度 0.78 q-bio.QMcs.DL
• Ten Simple Rules for Creating Biomolecular Graphics
  One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voet's "Biochemistry" in order to appreciate this field's profound communicative value in modern biological sciences -- ra…
  arxiv Cameron Mura 2014-07-15T17:48:16Z 置信度 0.78 q-bio.BMcs.HC
• Design of Geometric Molecular Bonds
  An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the affinity of the DNA base…
  arxiv David Doty, Andrew Winslow 2016-02-04T09:07:20Z 置信度 0.78 cs.ITcs.CGcs.ETq-bio.MN
• Strand displacement: a fundamental mechanism in RNA biology?
  DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures with predefined shap…
  arxiv Fan Hong, Petr Šulc 2019-03-28T18:05:29Z 置信度 0.78 q-bio.BMphysics.bio-phq-bio.MN
• Regulatory patterns in molecular interaction networks
  Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns that constrain network…
  arxiv David Murrugarra, Reinhard Laubenbacher 2011-02-18T02:42:32Z 置信度 0.78 q-bio.MN
• Quantum Computing for Molecular Biology
  Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these interactions are ver…
  arxiv Alberto Baiardi, Matthias Christandl, Markus Reiher 2022-12-23T09:23:04Z 置信度 0.78 quant-phcond-mat.str-elphysics.bio-phphysics.chem-phphysics.comp-ph
• Systems biology beyond degree, hubs and scale-free networks: the case for multiple metrics in complex networks
  Modeling and topological analysis of networks in biological and other complex systems, must venture beyond the limited consideration of very few network metrics like degree, betweenness or assortativity. A proper identification of informative and redundant ent…
  arxiv Soumen Roy 2012-05-10T17:26:02Z 置信度 0.78 q-bio.QMcond-mat.stat-mechcs.SIphysics.soc-ph
• Borges Dilemma, Fundamental Laws, and Systems Biology
  I reason here that the known folk law in biology that there is no general law in biology because of exceptions is false. The (quantitative) systems biology offers the potential to solve the Borges Dilemma, by transcending it. There have already a plenty of ind…
  arxiv P Ao 2007-09-01T00:16:45Z 置信度 0.78 q-bio.QMq-bio.OT
• Population-expression models of immune response
  The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenoty…
  arxiv Sean P Stromberg, Rustom Antia, Ilya Nemenman 2012-09-18T00:46:26Z 置信度 0.78 q-bio.PEq-bio.QM
• The two electron molecular bond revisited: from Bohr orbits to two-center orbitals
  In this review we first discuss extension of Bohr's 1913 molecular model and show that it corresponds to the large-D limit of a dimensional scaling (D-scaling) analysis, as developed by Herschbach and coworkers. In a separate but synergetic approach to the two…
  arxiv Goong Chen, Siu A. Chin, Yusheng Dou, Kishore T. Kapale 等 2005-08-24T01:49:39Z 置信度 0.78 physics.chem-ph
• Proofs of life: molecular-biology reasoning simulates cell behaviors from first principles
  We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The key is to note that…
  arxiv René Vestergaard, Emmanuel Pietriga 2018-10-30T11:29:45Z 置信度 0.78 q-bio.OTcs.LO
• The case for algebraic biology: from research to education
  Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play a central role -- a…
  arxiv Matthew Macauley, Nora Youngs 2020-02-29T18:06:29Z 置信度 0.78 q-bio.NCq-bio.OT
• Bayesian and Algebraic Strategies to Design in Synthetic Biology
  Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper and safer. But this re…
  arxiv Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf 2021-08-17T00:43:00Z 置信度 0.78 q-bio.MNq-bio.CB
• The role of CRKL in Breast Cancer Metastasis: Insights from Systems Biology
  MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally. They are involved in key biological processes and then may play a major role in the development of human diseases including cancer, in particular their involveme…
  arxiv Abderrahim Chafik 2016-08-09T10:29:39Z 置信度 0.78 q-bio.MN
• The CDMS view on molecular data needs of Herschel, SOFIA, and ALMA
  The catalog section of the Cologne Database for Molecular Spectroscopy, CDMS, contains mostly rotational transition frequencies, with auxiliary information, of molecules observable in space. The frequency lists are generated mostly from critically evaluated la…
  arxiv Holger S P Müller, C P Endres, J Stutzki, S Schlemmer 2013-04-06T14:19:15Z 置信度 0.78 astro-ph.GAastro-ph.COastro-ph.IMphysics.atm-clus
• Functional alignment of regulatory networks: A study of temperate phages
  The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the functions it directs. We…
  arxiv Ala Trusina, Kim Sneppen, Ian B. Dodd, Keith E. Shearwin 等 2005-11-28T20:06:27Z 置信度 0.78 q-bio.MNcond-mat.otherq-bio.GNq-bio.OT
• Efficiency, Robustness and Stochasticity of Gene Regulatory Networks in Systems Biology: lambda Switch as a Working Example
  Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics, proteomics, functions, …
  arxiv X. Zhu, L. Yin, L. Hood, D. Galas 等 2005-12-02T17:14:59Z 置信度 0.78 q-bio.SCcond-mat.othernlin.AOq-bio.MNq-bio.OT
• The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation
  Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here we analyzed genome-wide transcription profiling of an in-vitro transformation process. We focused on a cluster of genes whose expression le…
  arxiv Yuval Tabach, Michael Milyavsky, Igor Shats, Ran Brosh 等 2005-11-15T09:13:10Z 置信度 0.78 q-bio.MNq-bio.QM
• Computer algebra in systems biology
  Systems biology focuses on the study of entire biological systems rather than on their individual components. With the emergence of high-throughput data generation technologies for molecular biology and the development of advanced mathematical modeling techniq…
  arxiv Reinhard Laubenbacher, Bernd Sturmfels 2007-12-27T16:01:35Z 置信度 0.78 cs.SCq-bio.MNq-bio.QM
• Anharmonic Infrared Spectra of Thermally Excited Pyrene(C$_{16}$H$_{10}$): the combined view of DFT-based GVPT2 with AnharmonicCaOs and approximate DFT molecular dynamics with DemonNano
  The study of the Aromatic Infrared Bands (AIBs) in astronomical environments has opened interesting spectroscopic questions on the effect of anharmonicity on the infrared (IR) spectrum of hot polycyclic aromatic hydrocarbons (PAHs) and related species in isola…
  arxiv Shubhadip Chakraborty, Giacomo Mulas, Mathias Rapacioli, Christine Joblin 2021-02-12T15:44:13Z 置信度 0.78 astro-ph.GAphysics.atm-clusphysics.chem-phphysics.comp-ph
• Predicting synthetic rescues in metabolic networks
  An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with compensatory function. Here,…
  arxiv Adilson E. Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo Barabasi 2008-03-06T20:12:06Z 置信度 0.78 q-bio.MNcond-mat.dis-nnq-bio.CB
• Complex versus Complicated Systems Biology, Universality versus Detailed Modelling
  Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects of biological system…
  arxiv Kunihiko Kaneko 2026-03-18T01:43:42Z 置信度 0.78 physics.bio-ph
• Systems biology: From the cell to the brain
  With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to understanding the se…
  arxiv Sitabhra Sinha, T Jesan, Nivedita Chatterjee 2010-01-27T03:35:20Z 置信度 0.78 q-bio.MNphysics.bio-phq-bio.NC
• Molecular Recognition as an Information Channel: The Role of Conformational Changes
  Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar competing molecules. We c…
  arxiv Yonatan Savir, Tsvi Tlusty 2010-07-26T14:08:35Z 置信度 0.78 q-bio.BMcs.ITphysics.bio-ph
• Heterogeneous anomalous transport in cellular and molecular biology
  It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballist…
  arxiv Thomas A. Waigh, Nickolay Korabel 2023-10-15T21:00:19Z 置信度 0.78 physics.bio-phmath-ph
• Computing Pathways to Systems Biology: Key Contributions of Computational Methods in Pathway Identification
  Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a key role in systems …
  arxiv Sriganesh Srihari, Mark A. Ragan 2013-04-20T00:17:03Z 置信度 0.78 q-bio.MNcs.CE
• Continuum Electrostatics in Cell Biology
  Recent experiments revealing possible nanoscale electrostatic interactions in force generation at kinetochores for chromosome motions have prompted speculation regarding possible models for interactions between positively charged molecules in kinetochores and …
  arxiv L. John Gagliardi 2010-02-06T20:30:18Z 置信度 0.78 q-bio.CBq-bio.SC
• A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia
  A key aim of systems biology is the reconstruction of molecular networks, however we do not yet have networks that integrate information from all datasets available for a particular clinical condition. This is in part due to the limited scalability, in terms o…
  arxiv Edison Ong, Anthony Szedlak, Yunyi Kang, Peyton Smith 等 2014-07-25T16:27:38Z 置信度 0.78 q-bio.MNq-bio.QM
• Correlative-causative structures and the 'pericause': an analysis of causation and a model based on cellular biology
  The advent of molecular biology has led to the identification of definitive causative factors for a number of diseases, most of which are monogenic. Causes for most common diseases across the population, however, seem elusive and cannot be pinpointed to a limi…
  arxiv Sepehr Ehsani 2013-10-01T22:22:02Z 置信度 0.78 q-bio.QMq-bio.MN
• Paurush Praveen, Erfan Younesi and Martin Hofmann-Apitius
  The emergence of cross species interactions at protein level is a part of molecular mechanisms that lead to parasitic diseases. Comprehensive modelling can capture such interactions and could be useful to understand their pathophysiology and assist in identify…
  arxiv Modeling inter-species molecular cross-talks in three host- parasite systems by expansion of their sparse information space 2012-09-25T12:17:41Z 置信度 0.78 q-bio.MN
• Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences
  Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the object…
  arxiv Elizabeth Drellich, Andrew Gainer-Dewar, Heather A. Harrington, Qijun He 等 2015-09-14T13:40:44Z 置信度 0.78 q-bio.BM
• Biology-Derived Algorithms in Engineering Optimization
  Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural evolution and biological…
  arxiv Xin-She Yang 2010-03-09T14:53:12Z 置信度 0.78 math.OCcs.CEcs.NEq-bio.QM
• Quantum Information Biology: from information interpretation of quantum mechanics to applications in molecular biology and cognitive psychology
  We discuss foundational issues of quantum information biology (QIB) -- one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to co…
  arxiv Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya 等 2015-03-09T15:16:06Z 置信度 0.78 quant-phq-bio.CBq-bio.NC
• Molecular Distributions in Gene Regulatory Dynamics
  We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in degradation rates arising from…
  arxiv Michael C. Mackey, Marta Tyran-Kamińska, Romain Yvinec 2010-09-29T09:07:44Z 置信度 0.78 q-bio.MNmath.CAmath.PR
• Quantum Biology at the Cellular Level - elements of the research program
  Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level), a research…
  arxiv Michael Bordonaro, Vasily Ogryzko 2013-04-02T16:38:18Z 置信度 0.78 q-bio.OT
• Biophysics at the coffee shop: lessons learned working with George Oster
  Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this paradigm …
  arxiv Oleg Igoshin, Jing Chen, Jianhua Xing, Jian Liu 等 2019-02-20T21:45:23Z 置信度 0.78 q-bio.OT
• Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
  Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of graph neural networks (G…
  arxiv Ian Dunn, David Ryan Koes 2023-11-22T15:32:31Z 置信度 0.78 q-bio.BMcs.LG
• Foundations of biology
  It is often stated that there are no laws in biology, where everything is contingent and could have been otherwise, being solely the result of historical accidents. Furthermore, the customary introduction of fundamental biological entities such as individual o…
  arxiv Jean-Louis Sikorav, Alan Braslau, Arach Goldar 2014-01-13T14:12:10Z 置信度 0.78 q-bio.OT
• Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology
  Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been extensive standardization…
  arxiv Michael L. Blinov, John H. Gennari, Jonathan R. Karr, Ion I. Moraru 等 2021-04-09T21:09:27Z 置信度 0.78 q-bio.QMq-bio.CBq-bio.MN
• Topical Review: Extracting Molecular Frame Photoionization Dynamics from Experimental Data
  Methods for experimental reconstruction of molecular frame (MF) photoionization dynamics, and related properties - specifically MF photoelectron angular distributions (PADs) and continuum density matrices - are outlined and discussed. General concepts are intr…
  arxiv Paul Hockett, Varun Makhija 2022-09-09T13:49:27Z 置信度 0.78 physics.chem-phquant-ph
• TinkerCell: Modular CAD Tool for Synthetic Biology
  Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has b…
  arxiv Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro 2009-07-23T03:21:21Z 置信度 0.78 q-bio.MNq-bio.QM
• Perturbation Biology: inferring signaling networks in cellular systems
  We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of pertur…
  arxiv Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller 等 2013-08-23T18:08:05Z 置信度 0.78 q-bio.MN
• Stochastic approximations of higher-molecular by bi-molecular reactions
  Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical phenomena, such as mult…
  arxiv Tomislav Plesa 2018-11-07T05:34:59Z 置信度 0.78 q-bio.MNmath.DS
• SANTA: quantifying the functional content of molecular networks
  Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle,…
  arxiv Alex J. Cornish, Florian Markowetz 2014-07-17T12:59:42Z 置信度 0.78 q-bio.MNq-bio.QMstat.AP
• Discovery methods for systematic analysis of causal molecular networks in modern omics datasets
  With the increasing availability and size of multi-omics datasets, investigating the casual relationships between molecular phenotypes has become an important aspect of exploring underlying biology and genetics. This paper aims to introduce and review the avai…
  arxiv Jack Kelly, Carlo Berzuini, Bernard Keavney, Maciej Tomaszewski 等 2022-01-28T16:36:19Z 置信度 0.78 q-bio.MNq-bio.GN
• The contribution of statistical physics to evolutionary biology
  Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent develop…
  arxiv Harold P. de Vladar, Nick H. Barton 2011-04-14T18:14:50Z 置信度 0.78 q-bio.PEnlin.AOnlin.PSq-bio.QM