D. Standley

发表

Improvements in Performance and Usability

K. Katoh, D. Standley, Sudhir Kumar, 2013 .

Tertiary structure prediction of mixed α/β proteins via energy minimization

R. Friesner, D. Standley, J. Gunn, 1998 .

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

Alexis Vandenbon, Daron M Standley, Shizuo Akira, 2012, BMC Genomics.

Docking of protein molecular surfaces with evolutionary trace analysis

Kengo Kinoshita, Haruki Nakamura, Yuko Tsuchiya, 2007, Proteins.

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

K. Katoh, D. Standley, 2013, Molecular biology and evolution.

Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions

Julie C. Mitchell, Jeffrey J. Gray, Z. Weng, 2013, Proteins.

Modeling of stimuli-responsive nanoreactors: rational rate control towards the design of colloidal enzymes

Dimitri Schritt, Daron M. Standley, Kazutaka Katoh, 2019, Molecular Systems Design & Engineering.

Structural Modeling of Lymphocyte Receptors and Their Antigens.

K. Katoh, D. Standley, Floris J Van Eerden, 2019, Methods in molecular biology.

Methods for sequence and structural analysis of B and T cell receptor repertoires

Daron M. Standley, Diego Diez, John Rozewicki, 2020, Computational and Structural Biotechnology Journal.

MAFFT-DASH: integrated protein sequence and structural alignment

Daron M. Standley, Kazutaka Katoh, Karlou Mar Amada, 2019, Nucleic Acids Res..

Functional clustering of B cell receptors using sequence and structural features

D. Standley, T. Kurosaki, Takeshi Inoue, 2019, Molecular Systems Design & Engineering.

Blind prediction of interfacial water positions in CAPRI

Kengo Kinoshita, Haruki Nakamura, Xiaoqin Zou, 2014, Proteins.

Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis.

S. Akira, D. Standley, T. Satoh, 2020, Immunity.

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.

Ryuzo Azuma, Damien Hall, Kazuo Yamashita, 2014, Biophysical chemistry.

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

V A Eyrich, D M Standley, R A Friesner, 1999, Journal of molecular biology.

Coadministered Antigen Follicular Helper Cell Responses to the Inflammation That Induces Th 2 Cell and T-Cyclodextrin Spikes Local β Hydroxypropyl

H. Yamada, C. Coban, K. Ishii, 2015 .

Hydroxypropyl-β-Cyclodextrin Spikes Local Inflammation That Induces Th2 Cell and T Follicular Helper Cell Responses to the Coadministered Antigen

H. Yamada, C. Coban, K. Ishii, 2015, The Journal of Immunology.

Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus

J. Takagi, D. Standley, Toshio Tanaka, 2017, Scientific Reports.

Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells

Yong Gu Lee, Nathan H. Roy, S. Grupp, 2021, Nature Medicine.

Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense

S. Akira, A. Iwasaki, D. Standley, 2017, Nature Immunology.

Various miRNAs are involved in efficient HCV replication

N. Dokholyan, D. Standley, Y. Matsuura, 2020, bioRxiv.

Various miRNAs compensate the role of miR-122 on HCV replication

N. Dokholyan, D. Standley, Y. Matsuura, 2020, PLoS pathogens.

Control of enantioselectivity in the enzymatic reduction of halogenated acetophenone analogs by substituent positions and sizes

D. Standley, T. Matsuda, M. Tamura, 2020 .

Access to both enantiomers of substituted 2-tetralol analogs by a highly enantioselective reductase

D. Standley, T. Matsuda, M. Tamura, 2020 .

Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain

D. Standley, T. Matsuda, Zichang Xu, 2019, Applied Microbiology and Biotechnology.

Structural basis for the assembly of the Ragulator-Rag GTPase complex

K. Nakayama, E. Yamashita, D. Standley, 2017, Nature Communications.

A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans.

D. Standley, Keiji Tanaka, Hitoshi Takahashi, 2011, The Journal of clinical investigation.

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Piero Carninci, Y. Hayashizaki, T. Lassmann, 2014, Proceedings of the National Academy of Sciences.

Outcome of a workshop on archiving structural models of biological macromolecules.

Roland L Dunbrack, Roland L. Dunbrack, Wah Chiu, 2006, Structure.

A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3

D. Standley, K. Takeda, Masahiro Yamamoto, 2009, The Journal of experimental medicine.

Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production

D. Standley, Toshio Tanaka, T. Kishimoto, 2020, Science Signaling.

Systems biology approaches to toll-like receptor signaling

S. Akira, D. Standley, K. Takeda, 2012, Wiley interdisciplinary reviews. Systems biology and medicine.

Acquisition of resistance to wild-type spike-immune sera by emerging SARS-CoV-2 variants

J. Takagi, D. Standley, M. Okada, 2021 .

The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation.

S. Akira, D. Standley, O. Takeuchi, 2012, Immunity.

Title Translation-dependent unwinding of stem ‒ loops by UPF 1 licenses Regnase-1 to degrade inflammatory mRNAs

Yutaka Suzuki, Kentaro Inoue, D. Standley, 2019 .

Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02351c

D. Standley, Y. Hori, K. Kikuchi, 2015, Chemical science.

Flexible docking of an amyloid‐forming peptide from β2‐microglobulin

Haruki Nakamura, D. Standley, Y. Yonezawa, 2006 .

TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a

D. Standley, T. Kishimoto, Mitsuru Higa, 2017, Nucleic acids research.

Structural Determinants of the APOBEC3G N-Terminal Domain for HIV-1 RNA Association

L. Sardo, D. Standley, Jessica L Smith, 2019, Front. Cell. Infect. Microbiol..

Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem‐loop structure in its 3′UTR

D. Standley, T. Kishimoto, Mitsuru Higa, 2018, European journal of immunology.

TLR 4-induced NF-B and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid 5 a

D. Standley, T. Kishimoto, Mitsuru Higa, 2017 .

Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense

D. Standley, Masahiro Yamamoto, E. Takashima, 2019, Life Science Alliance.

An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo

K. Katoh, D. Standley, D. Motooka, 2022, Science Translational Medicine.

Hepatitis C virus modulates signal peptide peptidase to alter host protein processing

D. Standley, Masahiro Yamamoto, K. Koike, 2021, Proceedings of the National Academy of Sciences.

The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions.

D. Standley, M. Housaindokht, T. Matsuda, 2022, Physical chemistry chemical physics : PCCP.

TCR binding to peptide-MHC complex acts as a drawbridge for CD3 cross-membrane signaling

D. Standley, M. Llamas-Covarrubias, Floris J. van Eerden, 2022 .

CiDRE+ M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity

Jay W. Shin, S. Akira, D. Standley, 2022, bioRxiv.

Three-dimensional motions of GroEL during substrate protein recognition

D. Standley, N. Miyazaki, E. Mizohata, 2022, bioRxiv.

Engineering ACE2 decoy receptors to combat viral escapability

D. Standley, T. Okamoto, A. Hoshino, 2022, Trends in Pharmacological Sciences.

RabGDIα is a negative regulator of interferon-γ–inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii

D. Standley, K. Takeda, Masahiro Yamamoto, 2015, Proceedings of the National Academy of Sciences.

Landscape of infection enhancing antibodies in COVID-19 and healthy donors

D. Standley, M. Okada, Y. Horiguchi, 2022, bioRxiv.

Advances in antibody discovery from human BCR repertoires

D. Standley, Zichang Xu, Dianita S. Saputri, 2022, Frontiers in Bioinformatics.

Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine

D. Standley, Diego Diez, S. Imazato, 2022, bioRxiv.

Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications

D. Standley, T. Matsuda, T. Senda, 2020, Applied Microbiology and Biotechnology.

TCR binding to peptide-MHC complex acts as a drawbridge for CD3 cross-membrane signaling

D. Standley, M. Llamas-Covarrubias, Floris J. van Eerden, 2022, bioRxiv.

Emerging SARS-CoV-2 variants follow a historical pattern recorded in outgroups infecting non-human hosts

K. Katoh, D. Standley, 2021, Communications biology.

Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep

Dimitri Perrin, H. Ueda, R. Yamada, 2022, bioRxiv.

Improved Antibody‐Specific Epitope Prediction Using AlphaFold and AbAdapt

D. Standley, Shunsuke Teraguchi, Ana Davila, 2022, bioRxiv.

A simple method for predicting emerging SARS-CoV-2 variants using outgroups infecting non-human hosts

K. Katoh, D. Standley, 2021 .

Mapping of antibody epitopes based on docking and homology modeling

S. Vajda, D. Kozakov, D. Beglov, 2022, Proteins.

RNA-LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure.

D. Standley, R. Azuma, J. Carver, 2015, Analytical biochemistry.

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

Kazutaka Katoh, Daron M. Standley, K. Katoh, 2016, Bioinform..

The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines

D. Standley, A. Nakagawa, M. Okada, 2021, bioRxiv.

An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies

D. Standley, Masahiro Yamamoto, K. Ohmura, 2021, Cell.

Unbiased integration of single cell transcriptome replicates

D. Standley, Diego Diez, Shunsuke Teraguchi, 2021, bioRxiv.

Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction

D. Standley, T. Matsuda, Zichang Xu, 2019, Applied Microbiology and Biotechnology.

Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide

Haruki Nakamura, D. Standley, Y. Yonezawa, 2011 .

Deconstructing RNA: optical measurement of composition and structure.

Shandar Ahmad, D. Standley, A. Hobro, 2013, Physical chemistry chemical physics : PCCP.

Characterization of SPP inhibitors suppressing propagation of HCV and protozoa

T. Horii, D. Standley, Masahiro Yamamoto, 2017, Proceedings of the National Academy of Sciences.

Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase

Daron M Standley, D. Standley, A. Roger, 2008, Molecular microbiology.

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

K. Nakai, S. Akira, Yoshiaki Tanaka, 2010, Nature Immunology.

Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex

S. Akira, D. Standley, O. Takeuchi, 2014, The EMBO journal.

Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation

S. Akira, Yutaka Suzuki, D. Standley, 2013, Cell.

An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies

D. Standley, K. Ohmura, A. Nakagawa, 2020, bioRxiv.

Cyclin J–CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism

D. Standley, Y. Ishihama, O. Takeuchi, 2022, Science Signaling.

AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence

D. Kozakov, D. Standley, Songling Li, 2022, Bioinformatics advances.

The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1

Osamu Takeuchi, Daron M Standley, Shizuo Akira, 2011, Nature Immunology.

Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I

D. Standley, Masahiro Yamamoto, Y. Maniwa, 2022, bioRxiv.

Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6

Masahiro Yamamoto, D. Standley, Miwa Sasai, 2021, Life Science Alliance.

High cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD)

D. Standley, S. Tada, M. Kinoshita, 2022, Scientific Reports.

High cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD)

D. Standley, S. Tada, M. Kinoshita, 2022, Scientific reports.

MAFFT: iterative refinement and additional methods.

Kazutaka Katoh, Daron M Standley, K. Katoh, 2014, Methods in molecular biology.

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

S. Akira, D. Standley, A. Vandenbon, 2012, BMC Genomics.

Functional characterization of protein domains common to animal viruses and mouse

A. Kinjo, D. Standley, O. Takeuchi, 2011, BMC Genomics.

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

Haruki Nakamura, Osamu Takeuchi, Daron M. Standley, 2009, Nature.

Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome

K. Mizuguchi, K. Ishii, S. Akira, 2014, Nature Communications.

Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus

J. Takagi, D. Standley, Toshio Tanaka, 2017, Scientific Reports.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

The evolution of structural genomics

K. Katoh, D. Standley, Songling Li, 2022, Biophysical Reviews.

High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

Haruki Nakamura, Kenji Mizuguchi, Junichi Higo, 2014, Proteins.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

Akira R. Kinjo, Hirofumi Suzuki, Haruki Nakamura, 2011, Nucleic Acids Res..

Membrane attachment facilitates ligand access to the active site in monoamine oxidase A.

Haruki Nakamura, D. Standley, Y. Yonezawa, 2009, Biochemistry.

ASH structure alignment package: Sensitivity and selectivity in domain classification

Haruki Nakamura, Hiroyuki Toh, Daron M. Standley, 2007, BMC Bioinformatics.

Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis

S. Hamada, D. Standley, H. Inohara, 2019, The Journal of allergy and clinical immunology.

Quantifying sequence and structural features of protein–RNA interactions

Daron M. Standley, Kazuo Yamashita, Karlou Mar Amada, 2014, Nucleic acids research.

N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation

Osamu Takeuchi, Daron M Standley, Sho Miyamoto, 2019, Nature Microbiology.

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions

Osamu Takeuchi, Daron M. Standley, Kazuo Yamashita, 2016, Scientific Reports.

Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs

Osamu Takeuchi, Tomoko Emura, Mariko Okada-Hatakeyama, 2019, Nucleic acids research.

Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA

Standley, Higa, D. Standley, 2016, The Journal of experimental medicine.

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

Osamu Takeuchi, Uwe Ohler, Daron M. Standley, 2015, Cell.

Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins

Ashwini Patil, Shunsuke Teraguchi, Daron M. Standley, 2010, BMC Bioinformatics.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines

H. Yamada, C. Coban, K. Ishii, 2016, EBioMedicine.

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites

Shunsuke Teraguchi, Yutaro Kumagai, Daron M. Standley, 2013, BMC Bioinformatics.

Prediction of dinucleotide-specific RNA-binding sites in proteins

Shandar Ahmad, Kenji Mizuguchi, Akinori Sarai, 2011, BMC Bioinformatics.

Construction of a T cell receptor signaling range for spontaneous development of autoimmune disease

T. Nomura, D. Standley, R. Ueda, 2022, The Journal of experimental medicine.

The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling.

S. Akira, D. Standley, T. Kawai, 2013, Cell Host and Microbe.

Binding Energetics of Ferredoxin‐NADP+ Reductase with Ferredoxin and Its Relation to Function

T. Ikegami, D. Standley, T. Hase, 2011, Chembiochem : a European journal of chemical biology.

Protein tertiary structure prediction using a branch and bound algorithm

Anthony K. Felts, V A Eyrich, D M Standley, 1999, Proteins.

A branch and bound algorithm for protein structure refinement from sparse NMR data sets.

Anthony K. Felts, Volker A. Eyrich, V A Eyrich, 1999, Journal of molecular biology.

Protein Loop Modeling with Optimized Backbone Potential Functions.

Chi Zhang, Shide Liang, Jamica Sarmiento, 2012, Journal of chemical theory and computation.

Advances and Applications in Bioinformatics and Chemistry Dovepress Mapping Circulating Serum Mirnas to Their Immune-related Target Mrnas

K. Ishii, D. Standley, A. Vandenbon, 2022 .

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures

Haruki Nakamura, Hiroyuki Toh, Daron M. Standley, 2005, BMC Bioinformatics.

Detecting local structural similarity in proteins by maximizing number of equivalent residues

Haruki Nakamura, Daron M Standley, Haruki Nakamura, 2004, Proteins.

Protein structure prediction using a combination of sequence‐based alignment, constrained energy minimization, and structural alignment

V A Eyrich, D M Standley, Y An, 2001, Proteins.

Celastrol suppresses humoral immune responses and autoimmunity by targeting the COMMD3/8 complex

D. Standley, M. Ikawa, Kazuhiro Suzuki, 2023, Science Immunology.

Hepatocyte Factor JMJD5 Regulates Hepatitis B Virus Replication through Interaction with HBx

D. Standley, M. Sugiyama, M. Mizokami, 2016, Journal of Virology.

Functional annotation by sequence‐weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan

Haruki Nakamura, Daron M Standley, Haruki Nakamura, 2008, Proteins.

External stimulation induces the secretion of autophagosome-like vesicles by B cells

D. Standley, H. Kikutani, S. Sakakibara, 2023, Autophagy Reports.

Protein structure databases with new web services for structural biology and biomedical research

Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura, 2008, Briefings Bioinform..

Analysis of Protein Intermolecular Interactions with MAFFT-DASH.

Kazutaka Katoh, Daron M Standley, John Rozewicki, 2021, Methods in molecular biology.

Fast and accurate prediction of protein side-chain conformations

Chi Zhang, Daron M. Standley, Dandan Zheng, 2011, Bioinform..

Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota

K. Katoh, D. Standley, E. Hara, 2023, Nature Cell Biology.

Structural basis for the assembly of the Ragulator-Rag GTPase complex

K. Nakayama, E. Yamashita, D. Standley, 2017, Nature Communications.

Intrinsic disorder mediates cooperative signal transduction in STIM1.

K. Namba, S. Akira, T. Ikegami, 2014, Journal of Molecular Biology.

N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation

T. Noda, F. Kirchhoff, D. Standley, 2019, Nature Microbiology.

Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep

Dimitri Perrin, H. Ueda, R. Yamada, 2023, bioRxiv.

Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling

D. Standley, M. Horiuchi, F. Inagaki, 2013, Proceedings of the National Academy of Sciences.

Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant

K. Katoh, J. Takagi, D. Standley, 2021, bioRxiv.

Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster

Haruki Nakamura, Junichi Higo, Jinzen Ikebe, 2011, Protein science : a publication of the Protein Society.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

Akira R. Kinjo, Kiyoko F. Aoki-Kinoshita, Kiyoshi Asai, 2010, J. Biomed. Semant..

TCR-pMHC complex formation triggers CD3 dynamics

D. Standley, S. Yamasaki, Arthur Millius, 2023, bioRxiv.

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation

Yutaka Suzuki, D. Standley, O. Takeuchi, 2014, BMC Genomics.

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

M. Zacharias, Chi Zhang, D. Standley, 2010, BMC Bioinformatics.

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies

Haruki Nakamura, Daron M. Standley, Shide Liang, 2014, Bioinform..

Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system

D. Standley, D. Motooka, Y. Kirita, 2023, bioRxiv.

InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires

D. Standley, S. Yamasaki, Songling Li, 2022, bioRxiv.

A novel function prediction approach using protein overlap networks

Chi Zhang, Daron M. Standley, Dandan Zheng, 2013, BMC Systems Biology.

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations.

Alexis Vandenbon, Daron M Standley, Shizuo Akira, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly

D. Standley, M. Giezen, 2012 .

Expression of the readthrough transcript CiDRE in alveolar macrophages boosts SARS-CoV-2 susceptibility and promotes COVID-19 severity.

Jay W. Shin, D. Standley, Y. Kochi, 2023, Immunity.

Flexible, Functional, and Familiar: Characteristics of SARS-CoV-2 Spike Protein Evolution

K. Katoh, D. Standley, Songling Li, 2020, Frontiers in Microbiology.

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

M. Zacharias, Chi Zhang, D. Standley, 2010, BMC Bioinformatics.

Chapter 19 – Modeling Biocatalysts

Kazutaka Katoh, Dimitri Schritt, Songling Li, 2017 .

A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3

D. Standley, K. Takeda, Masahiro Yamamoto, 2009, The Journal of experimental medicine.

A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans.

D. Standley, Keiji Tanaka, S. Murata, 2011, The Journal of clinical investigation.

Advances and Applications in Bioinformatics and Chemistry Dovepress Mapping Circulating Serum Mirnas to Their Immune-related Target Mrnas

K. Ishii, D. Standley, A. Vandenbon, 2022 .

The ClusPro AbEMap web server for the prediction of antibody epitopes

S. Vajda, D. Kozakov, D. Beglov, 2023, Nature Protocols.

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis

Katsumasa Fujita, Nicholas I Smith, Daron M Standley, 2010, Immunome research.

Blind prediction of interfacial water positions in CAPRI

Julie C. Mitchell, Jeffrey J. Gray, H. Wolfson, 2014, Proteins.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L. Dunbrack, David T. Jones, M. Levitt, 2009, Structure.

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

I. Amit, Amir Giladi, M. Landthaler, 2023, Blood.

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

M. Zacharias, Chi Zhang, D. Standley, 2010, BMC Bioinformatics.

Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep

Dimitri Perrin, H. Ueda, R. Yamada, 2023, bioRxiv.