Richard Bonneau
#23,125
Most Influential Person Now
American biochemist and academic
Richard Bonneau's AcademicInfluence.com Rankings
Richard Bonneaubiology Degrees
Biology
#2741
World Rank
#4315
Historical Rank
#1194
USA Rank
Biochemistry
#1714
World Rank
#1849
Historical Rank
#286
USA Rank
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Biology
Richard Bonneau's Degrees
- PhD Biochemistry University of Washington
- Bachelors Biochemistry University of Washington
Why Is Richard Bonneau Influential?
(Suggest an Edit or Addition)According to Wikipedia, Richard Bonneau is an American computational biologist and data scientist whose primary research is in the following areas: learning networks from functional genomics data, predicting and designing protein and peptiodomimetic structure and applying data science to social networks. A professor at New York University, he holds appointments in the department of biology, the Center for Data Science and the Courant Institute of Mathematical Sciences.
Richard Bonneau's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. (2012) (1049)
- A Validated Regulatory Network for Th17 Cell Specification (2012) (991)
- Sparse and Compositionally Robust Inference of Microbial Ecological Networks (2014) (861)
- The Rosetta all-atom energy function for macromolecular modeling and design (2017) (788)
- Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome (2010) (749)
- Tweeting From Left to Right (2015) (729)
- Ab initio protein structure prediction of CASP III targets using ROSETTA (1999) (574)
- The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo (2006) (533)
- High-definition spatial transcriptomics for in situ tissue profiling (2019) (496)
- Ab initio protein structure prediction: progress and prospects. (2001) (340)
- Macromolecular modeling and design in Rosetta: recent methods and frameworks (2020) (339)
- c-Maf-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont (2018) (316)
- An expanded evaluation of protein function prediction methods shows an improvement in accuracy (2016) (316)
- Helminth infection promotes colonization resistance via type 2 immunity (2016) (313)
- Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. (2004) (310)
- Rosetta in CASP4: Progress in ab initio protein structure prediction (2001) (306)
- An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses (2015) (306)
- Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE) (2013) (302)
- A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell (2007) (300)
- Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota (2014) (298)
- CX3CR1+ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22 (2014) (298)
- Automated prediction of CASP‐5 structures using the Robetta server (2003) (290)
- ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells. (2014) (272)
- De novo prediction of three-dimensional structures for major protein families. (2002) (269)
- Accurate de novo design of hyperstable constrained peptides (2016) (264)
- Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks (2006) (260)
- The Critical Periphery in the Growth of Social Protests (2015) (248)
- Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis (2018) (232)
- DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models (2010) (228)
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019) (219)
- Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR. (2007) (202)
- The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations (2019) (199)
- How Social Media Facilitates Political Protest: Information, Motivation, and Social Networks (2018) (199)
- A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis (2008) (199)
- A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin (2007) (198)
- Why are there hotspot mutations in the TP53 gene in human cancers? (2017) (196)
- Political Expression and Action on Social Media: Exploring the Relationship Between Lower- and Higher-Threshold Political Activities Among Twitter Users in Italy (2015) (185)
- An improved protein decoy set for testing energy functions for protein structure prediction (2003) (174)
- The Gaggle: An open-source software system for integrating bioinformatics software and data sources (2006) (171)
- An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses (2016) (167)
- Structure-based protein function prediction using graph convolutional networks (2021) (165)
- Oligo(N-aryl glycines): a new twist on structured peptoids. (2008) (160)
- A physical sciences network characterization of non-tumorigenic and metastatic cells (2013) (157)
- Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer (2018) (157)
- An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network (2015) (156)
- deepNF: deep network fusion for protein function prediction (2017) (149)
- DDX5 and its associated lncRNA Rmrp modulate Th17 cell effector functions (2015) (147)
- Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. (2004) (145)
- Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks (2013) (143)
- Who Leads? Who Follows? Measuring Issue Attention and Agenda Setting by Legislators and the Mass Public Using Social Media Data (2019) (141)
- Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms (2015) (134)
- Learning biological networks: from modules to dynamics. (2008) (132)
- Fungi stabilize connectivity in the lung and skin microbial ecosystems (2018) (122)
- Detecting Bots on Russian Political Twitter (2017) (120)
- Why are there hotspot mutations in the TP53 gene in human cancers? (2018) (117)
- EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments[OPEN] (2016) (116)
- DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator (2010) (115)
- General transcription factor specified global gene regulation in archaea (2007) (114)
- CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer. (2019) (109)
- A preliminary survey of the peptoid folding landscape. (2009) (108)
- Contact order and ab initio protein structure prediction (2002) (107)
- Learning accurate representations of microbe-metabolite interactions (2019) (105)
- SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases (2020) (105)
- UniPep - a database for human N-linked glycosites: a resource for biomarker discovery (2006) (100)
- GABA-receptive microglia selectively sculpt developing inhibitory circuits (2020) (95)
- A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity (2017) (95)
- FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells (2014) (94)
- Social media and political communication: A survey of Twitter users during the 2013 Italian general election (2013) (89)
- Rational Design of Topographical Helix Mimics as Potent Inhibitors of Protein–Protein Interactions (2014) (88)
- Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation (2017) (87)
- Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors. (2014) (86)
- BioNetBuilder: automatic integration of biological networks (2006) (86)
- 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments (2016) (85)
- Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments (2019) (84)
- Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation (2001) (84)
- Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design (2012) (84)
- Dynamic MicroRNA Gene Transcription and Processing during T Cell Development (2012) (82)
- Distributions of beta sheets in proteins with application to structure prediction (2002) (82)
- Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates. (2019) (80)
- SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases (2021) (78)
- Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet (2016) (77)
- De novo structure prediction and experimental characterization of folded peptoid oligomers (2012) (77)
- Lower airway dysbiosis affects lung cancer progression. (2020) (74)
- Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2. (2017) (72)
- Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells (2018) (72)
- The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis (2009) (67)
- Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity (2018) (64)
- Diurnally Entrained Anticipatory Behavior in Archaea (2009) (63)
- Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet (2016) (63)
- Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology (2007) (59)
- Multi-study inference of regulatory networks for more accurate models of gene regulation (2018) (57)
- Robust classification of protein variation using structural modelling and large-scale data integration (2016) (56)
- Elites Tweet to Get Feet Off the Streets: Measuring Regime Social Media Strategies During Protest (2018) (51)
- Engineered coiled-coil protein microfibers. (2014) (51)
- Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells. (2019) (50)
- Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer (2018) (50)
- Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1 (2004) (49)
- Zinc status modulates bronchopulmonary eosinophil infiltration in a murine model of allergic inflammation. (2003) (49)
- SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σD in Bacillus subtilis (2012) (48)
- NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains (2019) (47)
- Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design (2013) (47)
- Structure-Based Function Prediction using Graph Convolutional Networks (2019) (46)
- Breaking TADs: insights into hierarchical genome organization. (2015) (46)
- Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions (2016) (44)
- Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing (2016) (44)
- The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models (2009) (43)
- A Miniature Protein Stabilized by a Cation-π Interaction Network. (2016) (43)
- Ab initio methods. (2003) (42)
- Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models (2017) (42)
- An Assembly Model of Rift Valley Fever Virus (2012) (41)
- Quantitative proteomic analysis of the budding yeast cell cycle using acid‐cleavable isotope‐coded affinity tag reagents (2006) (41)
- The Proteome Folding Project: proteome-scale prediction of structure and function. (2011) (41)
- BioNetBuilder2.0: bringing systems biology to chicken and other model organisms (2009) (39)
- N-Naphthyl peptoid foldamers exhibiting atropisomerism. (2012) (39)
- Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability (2016) (39)
- Interleukin‐17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin‐25–Driven Intestinal Inflammation (2019) (38)
- Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination (2016) (37)
- Multi-species integrative biclustering (2010) (37)
- Negative Example Selection for Protein Function Prediction: The NoGO Database (2014) (37)
- A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells (2013) (37)
- Masked graph modeling for molecule generation (2020) (36)
- Political psycholinguistics: A comprehensive analysis of the language habits of liberal and conservative social media users. (2020) (36)
- Fused Regression for Multi-source Gene Regulatory Network Inference (2016) (35)
- Longman, R.S. et al. CX(3)CR1(+) mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22. J. Exp. Med. 211, 1571-1583 (2014) (35)
- Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot (2016) (35)
- Semisynthesis of peptoid-protein hybrids by chemical ligation at serine. (2014) (35)
- Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection (2020) (34)
- Functional inferences from blind ab initio protein structure predictions. (2001) (34)
- Genetic and epigenetic coordination of cortical interneuron development (2021) (34)
- Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions (2015) (34)
- Parametric Bayesian priors and better choice of negative examples improve protein function prediction (2013) (34)
- A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers (2014) (34)
- A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination (2016) (33)
- Designing Peptides on a Quantum Computer (2019) (32)
- Liberal and Conservative Values: What We Can Learn From Congressional Tweets (2018) (31)
- Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate (2018) (31)
- Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. (2016) (31)
- Thermoresponsive Protein-Engineered Coiled-coil Hydrogel for Sustained Small Molecule Release. (2019) (31)
- Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling (2017) (29)
- Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ (2017) (28)
- Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility (2016) (28)
- Biophysically motivated regulatory network inference: progress and prospects (2016) (27)
- For Whom the Bot Tolls: A Neural Networks Approach to Measuring Political Orientation of Twitter Bots in Russia (2019) (27)
- YouTube Recommendations and Effects on Sharing Across Online Social Platforms (2020) (27)
- Side-Chain Conformational Preferences Govern Protein-Protein Interactions. (2016) (26)
- Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27 (2013) (24)
- Oligo(N-alkoxy glycines): trans substantiating peptoid conformations. (2011) (24)
- Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells (2017) (24)
- High-density spatial transcriptomics arrays for in situ tissue profiling (2019) (24)
- OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization (2022) (24)
- Big Data, Social Media, and Protest: Foundations for a Research Agenda (2016) (23)
- Shrinkage improves estimation of microbial associations under different normalization methods (2018) (23)
- Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints (2019) (22)
- Translating microbiome futures (2018) (22)
- Tweeting identity? Ukrainian, Russian, and #Euromaidan (2016) (22)
- Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction (2011) (21)
- One third of dynamic protein expression profiles can be predicted by a simple rate equation. (2014) (21)
- Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1 (2021) (21)
- Androgen receptor antagonism by divalent ethisterone conjugates in castrate-resistant prostate cancer cells. (2012) (21)
- High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0 (2021) (20)
- Peptoid atropisomers. (2011) (20)
- Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice. (2021) (20)
- Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2016) (20)
- Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems (2004) (20)
- Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. (2013) (19)
- Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine. (2014) (19)
- Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets (2017) (19)
- Initial Mapping of the New York City Wastewater Virome (2020) (19)
- The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations (2019) (19)
- Normalization methods for microbial abundance data strongly affect correlation estimates (2018) (18)
- Integrated inference and analysis of regulatory networks from multi-level measurements. (2012) (18)
- Trumping Hate on Twitter? Online Hate Speech in the 2016 U.S. Election Campaign and its Aftermath (2021) (18)
- Bacillus subtilis Systems Biology: Applications of -Omics Techniques to the Study of Endospore Formation. (2014) (17)
- Better together: Elements of successful scientific software development in a distributed collaborative community (2020) (17)
- Generalized Stability Approach for Regularized Graphical Models (2016) (17)
- Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data (2020) (16)
- Twitter flagged Donald Trump’s tweets with election misinformation: They continued to spread both on and off the platform (2021) (16)
- Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa (2019) (16)
- Testing the effects of Facebook usage in an ethnically polarized setting (2021) (16)
- Cracking Open the News Feed: Exploring What U.S. Facebook Users See and Share with Large-Scale Platform Data (2021) (15)
- Moderating with the Mob: Evaluating the Efficacy of Real-Time Crowdsourced Fact-Checking (2021) (15)
- A Comparison of Methods in Political Science Text Classification: Transfer Learning Language Models for Politics (2020) (15)
- Function-guided protein design by deep manifold sampling (2021) (14)
- Disentangling microbial associations from hidden environmental and technical factors via latent graphical models (2019) (14)
- Interpreting 4C-Seq data: how far can we go? (2014) (14)
- Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks (2018) (14)
- Chemoselective fragment condensation between peptide and peptidomimetic oligomers. (2013) (14)
- Protest in the age of social media (2015) (14)
- Improved Stability and Half‐Life of Fluorinated Phosphotriesterase Using Rosetta (2014) (14)
- Splotch: Robust estimation of aligned spatial temporal gene expression data (2019) (13)
- The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families (2012) (13)
- Tweeting Beyond Tahrir: Ideological Diversity and Political Intolerance in Egyptian Twitter Networks (2021) (13)
- Rotamer libraries for the high-resolution design of β-amino acid foldamers (2016) (13)
- Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks (2019) (13)
- Measuring the prevalence of online hate speech , with an application to the 2016 U . S . election (2018) (12)
- Protein Structural Alignments From Sequence (2020) (12)
- Learning global models of transcriptional regulatory networks from data. (2009) (12)
- Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks (2014) (12)
- Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes. (2017) (12)
- Digital Dissent: An Analysis of the Motivational Contents of Tweets From an Occupy Wall Street Demonstration (2018) (12)
- Inference of bacterial small RNA regulatory networks and integration with transcription factor driven regulatory networks (2019) (12)
- Conformational preferences of peptide–peptoid hybrid oligomers (2014) (11)
- GABA-receptive microglia selectively sculpt developing inhibitory circuits (2021) (11)
- Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions (2018) (11)
- A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV (2020) (11)
- A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures. (2017) (10)
- Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins (2018) (10)
- Positive-Unlabeled Learning in the Face of Labeling Bias (2015) (10)
- Is There Anybody Out There? The Eects of Legislators' Communication with their Constituents. (2013) (10)
- Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter. (2020) (9)
- EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation (2023) (9)
- PPII Helical Peptidomimetics Templated by Cation–π Interactions (2016) (9)
- News credibility labels have limited average effects on news diet quality and fail to reduce misperceptions (2022) (8)
- Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling (2020) (8)
- Why Botter: How Pro-Government Bots Fight Opposition in Russia (2022) (8)
- Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters (2011) (7)
- Towards region-specific propagation of protein functions (2018) (7)
- A convolutional neural network for common coordinate registration of high-resolution histology images (2020) (7)
- Inter-species pathway perturbation prediction via data-driven detection of functional homology (2015) (7)
- Elites Tweet to get Feet o the Streets: Measuring Elite Reaction to Protest Using Social Media (2015) (6)
- The 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing (2011) (6)
- Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs (2020) (6)
- Protest in the Age of Social Media: Technology and Ukraine’s #Euromaidan (2015) (6)
- What’s Not to Like? Facebook Page Likes Reveal Limited Polarization in Lifestyle Preferences (2021) (5)
- c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont (2018) (5)
- Author Correction: c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont (2019) (5)
- c-Maf-dependent regulatory T cells mediate immunological tolerance to intestinal microbiota (2017) (5)
- NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity (2020) (5)
- Echo Chambers, Rabbit Holes, and Algorithmic Bias: How YouTube Recommends Content to Real Users (2022) (5)
- Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions. (2017) (5)
- OutPredict: multiple datasets can improve prediction of expression and inference of causality (2020) (5)
- Cracking Open the News Feed (2021) (5)
- News Sharing on Social Media: Mapping the Ideology of News Media Content, Citizens, and Politicians (2020) (5)
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks (2021) (5)
- Macromolecular modeling and design in Rosetta: recent methods and frameworks (2020) (5)
- TM-Vec: template modeling vectors for fast homology detection and alignment (2022) (4)
- sbv IMPROVER Diagnostic Signature Challenge (2013) (4)
- Twitter activity about treatments during the COVID-19 pandemic: case studies of remdesivir, hydroxychloroquine, and convalescent plasma. (2020) (4)
- A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis (2012) (4)
- Erratum: Genome sequence of Haloarcula marismortui: A halophilic archaeon from the dead sea (Genome Research (2004) vol. 14 (2221-2234)) (2004) (4)
- Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions (2016) (4)
- Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function. (2017) (4)
- Short of Suspension: How Suspension Warnings Can Reduce Hate Speech on Twitter (2021) (3)
- Viewing the US presidential electoral map through the lens of public health (2020) (3)
- Exposure to the Russian Internet Research Agency foreign influence campaign on Twitter in the 2016 US election and its relationship to attitudes and voting behavior (2023) (3)
- Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks (2020) (3)
- Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates (2019) (3)
- Reply to: Examining microbe–metabolite correlations by linear methods (2021) (3)
- Evaluating the Conformations and Dynamics of Peptoid Macrocycles. (2022) (3)
- A Summary Statistic for Political Ideology of Web Domains Using Differentially Private Engagement Data with Applications to Social Science One (2021) (3)
- Racemization barriers of atropisomeric 3,3′-bipyrroles: an experimental study with theoretical verification (2016) (2)
- NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. (2022) (2)
- Robust Classification of Protein Variation Using Structural Modeling and Large-Scale Data Integration (2015) (2)
- Revisiting microbe-metabolite interactions: doing better than random (2019) (2)
- Social Media Data Reveal Patterns of Policy Engagement in State Legislatures (2020) (2)
- Election Fraud, YouTube, and Public Perception of the Legitimacy of President Biden (2022) (2)
- Coordinated control of neuronal differentiation and wiring by a sustained code of transcription factors (2022) (2)
- Explicit Modeling of RNA Stability Improves Large-Scale Inference of Transcription Regulation (2017) (2)
- Dissecting the Quorum-Sensing Receptor LuxN (2008) (2)
- Coordinated control of neuronal differentiation and wiring by sustained transcription factors (2022) (2)
- NSD2 overexpression drives clustered chromatin and transcriptional changes in insulated domains (2019) (2)
- Multi-segment preserving sampling for deep manifold sampler (2022) (2)
- Multi-omic analysis along the gut-brain axis points to a functional architecture of autism (2022) (2)
- NetTIME: Improving Multitask Transcription Factor Binding Site Prediction with Base-pair Resolution (2021) (1)
- Transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells (2018) (1)
- Author response: Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity (2018) (1)
- Tweeting Beyond Tahrir (2021) (1)
- Redirection of TH17 cells with a chimeric antigen receptor containing the ICOS costimulatory domain enhances function, antitumor activity and persistence of TH17 cells (P4350) (2013) (1)
- De Novo Structure Prediction: Methods and Applications (2008) (1)
- Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops (2021) (1)
- Characterizing the epigenetic landscape of cellular populations from bulk and single-cell ATAC-seq information (2019) (1)
- The Effects of Legislators ’ Communication with their Constituents (2013) (1)
- NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction (2022) (1)
- Scalable estimation of microbial co-occurrence networks with Variational Autoencoders (2021) (1)
- Prokaryotic Systems Biology (2009) (1)
- Generative Models for Quantification of DNA Modifications. (2018) (1)
- Sequence-structure-function relationships in the microbial protein universe (2022) (1)
- Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin (2022) (1)
- Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". (2022) (1)
- Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer (2018) (1)
- Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method (2022) (1)
- Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate (2018) (1)
- Correction: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota (2021) (1)
- An Automatic Framework to Continuously Monitor Multi-Platform Information Spread (2021) (1)
- Modeling gene regulation and spatial organization of sequence based motifs (2008) (1)
- Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments (2016) (1)
- Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers. (2022) (1)
- Fungi stabilize connectivity in the lung and skin microbial ecosystems (2018) (1)
- A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity (2017) (0)
- Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality (2020) (0)
- The impact of endogenous retroviruses on nuclear organization and gene expression (2018) (0)
- A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets inIGH-CRLF2patients (2019) (0)
- Digital Dissent: Informational and Motivational Pathways to Political Protests Through Social Media (2017) (0)
- Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection (2020) (0)
- Lung Cancer Survival and Prognosis Is Affected by Lower Airway Oral Commensal Enrichment (2020) (0)
- Critical role of the transcription factors IRF 1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation (2018) (0)
- QS437. Integrated Biological and Computational Analysis of Important But Largely Under-Studied Organisms (2008) (0)
- The interdependent nature of multi-loci associations can be revealed by 4C-Seq (2015) (0)
- Acknowledgment of Plant Physiology Reviewers (2015) (0)
- High-definition spatial transcriptomics for in situ tissue profiling (2019) (0)
- A comprehensive map of the human dendritic cell HIV-response transcriptional network (2019) (0)
- Identification of new therapeutic targets in CRLF2-overexpressing B-ALL through discovery of TF-gene regulatory interactions (2020) (0)
- A comprehensive map of the dendritic cell transcriptional network engaged upon innate sensing of HIV (2019) (0)
- How antibiotic resistance is shaped by host-microbiome interactions in influenza (2020) (0)
- The Times They Are Rarely A-Changin' (2021) (0)
- Session introduction (2011) (0)
- Processing during T Cell Development Dynamic MicroRNA Gene Transcription and (2012) (0)
- Ismb/eccb 2019 Proceedings Papers Committee (2019) (0)
- Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions (2018) (0)
- Tuning a coiled-coil hydrogel via computational design of supramolecular fiber assembly (2022) (0)
- UniPep: A database of human N-linked glycosylation sites and a resource for biomarker discovery (2006) (0)
- Mean external measures of bicluster "quality", as a function of iteration of bicluster optimization (2011) (0)
- NMR SOLUTION STRUCTURE OF ALPHA-CONOTOXIN GID MUTANT A10V (2017) (0)
- NMR SOLUTION STRUCTURE OF THE ALPHA-CONOTOXIN GID MUTANT V13Y (2017) (0)
- Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins (2018) (0)
- TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs (2022) (0)
- Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling (2020) (0)
- Modeling host-pathogen interactions: Computational biology and bioinformatics for infectious disease research (2011) (0)
- CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection (2022) (0)
- An adaptive geometric search algorithm for macromolecular scaffold selection (2017) (0)
- Alternative activation of macrophages is accompanied by chromatin remodeling and short-term dampening of macrophage secondary response (2018) (0)
- Details of Remaining Collective Challenges. (2020) (0)
- Dictionary-Assisted Supervised Contrastive Learning (2022) (0)
- A Damage-Independent Ro le for 53 BP 1 that Impacts Break Order and Igh Architecture during Class Switch Recombination Graphical (2016) (0)
- SAGES 2015. Symposium of Advances in Genomics, Epidemiology and Statistics 2015: Abstracts (2017) (0)
- Reply to: Examining microbe–metabolite correlations by linear methods (2021) (0)
- Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference (2023) (0)
- revealed by 4C-Seq (2015) (0)
- A Variational Inference Approach to Single-Cell Gene Regulatory Network Inference using Probabilistic Matrix Factorization (2023) (0)
- A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences (2022) (0)
- PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design (2022) (0)
- Automated Protein Function Description for Novel Class Discovery (2022) (0)
- Specific tests for Rosetta running on our automated testing framework. (2020) (0)
- PSR volume 116 issue 3 Cover and Front matter (2022) (0)
- the Halophilic Archaeon Systems Level Insights Into the Stress Response to UV Radiation in (2006) (0)
- Specificities of modeling membrane proteins using multi-template homology modeling (2020) (0)
- CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens (2020) (0)
- Predicting legislators’ votes on the government shutdown using Twitter (0)
- Using Social Media Data to Reveal Patterns of Policy Engagement in State Legislatures (2022) (0)
- Additional file 1: Figure S1. of Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet (2016) (0)
- Members of the RosettaCommons Consortium. (2020) (0)
- Managing and Analyzing Big-Data in Genomics (2012) (0)
- Author response: Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions (2015) (0)
- SCORCh.R: Clustering and visualization of sequencing derived multiple transcription factor loci (2005) (0)
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019) (0)
- Sequence-Dependent DNA Shape Features Regulate IL-4 Induced Chromatin Accessibility in Alternatively Activated Macrophages (2018) (0)
- Opinion Change and Learning in the 2016 U.S. Presidential Election: Evidence from a Panel Survey Combined with Direct Observation of Social Media Activity (2020) (0)
- Values Statement: Equality and Inclusion in the RosettaCommons. (2020) (0)
- Modeling RNA Stability in Network Inference (2017) (0)
- A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures (2017) (0)
- Descriptions of the Rosetta board positions. (2020) (0)
- Growth in Rosetta PIs and conference attendees. (2020) (0)
- Comparative genomics with cMonkey: Integrative biclustering of multiple species (0)
- Genome analysis Temporal probabilistic modeling of bacterial compositions derived from 16 S rRNA sequencing (2017) (0)
- Cecal Microbiota Transfer Rescues Antibiotic-Induced Acceleration of Type 1 Diabetes and Alteration of Intestinal Gene Expression (2021) (0)
- Commercial spin-off companies from the Rosetta community. (2020) (0)
- Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2017) (0)
- Computational-guided determination of the functional role of 447-52D long CDRH3. (2018) (0)
- Cage photolysis initiates protein folding under native conditions (1999) (0)
- The Times They Are Rarely A-Changin': Circadian Regularities in Social Media Use (2021) (0)
- Gene annotation using ab initio protein structure prediction: Method development and application to major protein families (2001) (0)
- Fluorescent azobenzene-confined coiled-coil mesofibers. (2022) (0)
- Typical development workflow in the Rosetta community. (2020) (0)
- The Mechanisms of Protest Recruitment through Social Media Networks∗ (2020) (0)
- Network Embedding Methods for Large Networks in Political Science (2021) (0)
- Genomic analysis of CD8 T cells during the early phases of the immune response (110.25) (2012) (0)
- Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality (2020) (0)
- Engineered multivalent self-assembled binder protein against SARS-CoV-2 RBD (2022) (0)
- Engineered Protein-Iron Oxide Hybrid Biomaterial for MRI-traceable Drug Encapsulation (2022) (0)
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