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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Authority Synonyms Record Last Update Mentions Count
HALT-C Trial
 
Resource Report
Resource Website
HALT-C Trial (RRID:SCR_001534) HALT-C Trial, HALT-C bibliography, clinical trial, data or information resource, resource Multi-center, randomized controlled study designed to determine if continuing interferon long term over several years will suppress the Hepatitis C virus, prevent progression to cirrhosis, prevent liver cancer and reduce the need for liver transplantation. Patient enrollment began in 2000 and was completed in 2003 at 10 clinical centers, which were supported by a data coordinating center, virological testing center, and central sample repository. Patients with chronic hepatitis C and advanced fibrosis or cirrhosis on liver biopsy who failed to respond to a previous course of interferon alfa were enrolled in this study. Patients were initially treated with a 24-week course of peginterferon alfa-2a and ribavirin. Patients who remained hepatitis C virus RNA positive were then randomized to receive maintenance, low-dose peginterferon or to be followed on no treatment. Liver biopsies were done before enrollment and after 2 and 4 years of treatment or follow-up. The endpoints were development of cirrhosis, hepatic decompensation, hepatocellular carcinoma, death, or liver transplantation. 1050 patients were randomized and followed through the 4 year randomized phase of the trial and as long as 4 years off treatment. Serum samples collected at multiple time points, DNA and liver tissue are available for scientific investigation. interferon, progression, cirrhosis, prevention, liver cancer, liver transplantation, liver, pegylated interferon, clinical, outcome, adult human, dna, liver tissue, serum, blood, b lymphoblastoid cell-line, epstein-barr virus infection in peripheral blood mononuclear cell, peripheral blood mononuclear cell, biomaterial supply resource, formalin fixed, histology, frozen, stained liver slide, unstained liver slide, advanced fibrosis, liver biopsy, peginterferon alfa-2a, ribavirin is listed by: One Mind Biospecimen Bank Listing
is listed by: ClinicalTrials.gov
is listed by: NIDDK Central Repository
is listed by: NIDDK Research Resources
is listed by: NIDDK Information Network (dkNET)
Hepatitis C virus, Chronic hepatitis C NIDDK Free, Freely available nlx_152835 http://archives.niddk.nih.gov/haltctrial/displaypage.aspx?pagename=haltctrial/index.htm http://www.haltctrial.org/ SCR_001534 SciCrunch Registry Hepatitis C Antiviral Long-term Treatment against Cirrhosis, Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial, Hepatitis C Antiviral Long-term Treatment against Cirrhosis Trial 2026-09-26 02:13:00 0
Center for Biomedical OCT Research
 
Resource Report
Resource Website
1+ mentions
Center for Biomedical OCT Research (RRID:SCR_001418) CBORT training resource Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence has parent organization: Harvard Medical School; Massachusetts; USA NIBIB P41EB015903 Free, Freely Available nlx_152640 SCR_001418 SciCrunch Registry Center for Biomedical OCT Research and Translation 2026-09-26 02:12:59 2
BioMEMS Resource Center
 
Resource Report
Resource Website
1+ mentions
BioMEMS Resource Center (RRID:SCR_001417) BMRC training resource Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments. cell, tissue, microengineering, diagnostics, chip has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; NIBIB 5P41EB002503-12 Free, Freely Available nlx_152639 SCR_001417 SciCrunch Registry Bio MicroElectroMechanical Systems (BioMEMS) Resource Center, Biomicroelectromechanical Systems (BioMEMS) Resource Center, BioMEMS, Bio MicroElectroMechanical Systems Resource Center 2026-09-26 02:12:59 4
National Center for Integrative Biomedical Informatics
 
Resource Report
Resource Website
1+ mentions
National Center for Integrative Biomedical Informatics (RRID:SCR_001538) data or information resource, organization portal, portal The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519. analysis tools, bipolar disorder, code, computational infrastructure, conceptual models, data, diabetes, knowledge repository, presentations, prostate cancer, query tools, seminar material, tool development, tutorials, videos, model is listed by: 3DVC
is related to: Biological Concept Diagram Editor
is related to: Gene Interaction Extraction from the Literature
is related to: National Centers for Biomedical Computing
has parent organization: University of Michigan; Ann Arbor; USA
is parent organization of: Substructure Index-based Approximate Graph Alignment
is parent organization of: miniTUBA
is parent organization of: Michigan Molecular Interactions
is parent organization of: Cell Line Knowledge Base
is parent organization of: HubMed
is parent organization of: MiMI Plugin for Cytoscape
Type 1 diabetes, Type 2 diabetes, Diabetes, Cancer, Bipolar disorder PMID:22101971 Free, Freely available nif-0000-09660 http://portal.ncibi.org/gateway/ SCR_001538 SciCrunch Registry NCIBI 2026-09-26 02:13:01 1
Enrichr
 
Resource Report
Resource Website
5000+ mentions
Enrichr (RRID:SCR_001575) Enrichr analysis service resource, data analysis service, production service resource, service resource, software application, software resource A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. bed, gene, software as a service, rna-seq, analyze, protein, function, gene list, visualization, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
PMID:23586463 Free, Freely available biotools:enrichr, SciRes_000171 https://bio.tools/enrichr SCR_001575 SciCrunch Registry 2026-09-26 02:13:01 5047
SCAN.UPC
 
Resource Report
Resource Website
10+ mentions
SCAN.UPC (RRID:SCR_001334) SCAN.UPC software resource A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A microarray, one channel, preprocessing, rna-seq, two channel is listed by: OMICtools
has parent organization: Bioconductor
Free, Available for download, Freely available OMICS_02006 SCR_001334 SciCrunch Registry Single-channel array normalization (SCAN) and Universal exPression Codes (UPC), Single-channel array normalization and Universal exPression Codes 2026-09-26 02:12:58 11
EEGbase
 
Resource Report
Resource Website
1+ mentions
EEGbase (RRID:SCR_001452) data or information resource, data repository, database, service resource, storage service resource EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework. eeg, erp, experiments, data storage and management, EEG/ERP data, EEG/ERP experiments, uses: NIX
uses: Open metadata mark up language
is used by: NIF Data Federation
has parent organization: University of West Bohemia; Pilsen; Czech Republic
Ministry of Education Czech Science Foundation Free, Freely Available nif-0000-08190 http://eegdatabase.kiv.zcu.cz/ SCR_001452 SciCrunch Registry 2026-09-26 02:13:00 7
betr
 
Resource Report
Resource Website
10+ mentions
betr (RRID:SCR_001332) betr software resource Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data. differentially expression, gene, microarray, time-course is listed by: OMICtools
has parent organization: Bioconductor
PMID:20003283 Free, Available for download, Freely available OMICS_01997 http://www.bioconductor.org/packages/release/bioc/html/betr.html SCR_001332 SciCrunch Registry Bayesian Estimation of Temporal Regulation 2026-09-26 02:12:58 17
Wake Forest University School of Medicine: Department of Neurology
 
Resource Report
Resource Website
Wake Forest University School of Medicine: Department of Neurology (RRID:SCR_001453) data or information resource, department portal, organization portal, portal, university Department at the Wake Forest University's School of Medicine that hosts physicians who specialize in neurological topics such as neuromuscular disease, epilepsy, pediatric neurology, strokes, neuropsychology, neurosonology, and neurorehabilitaiton. neurology, medicine, wake forest, stroke, neuropsychology, physicain Free, Freely Available nif-0000-10549 http://www1.wfubmc.edu/neurology/ SCR_001453 SciCrunch Registry WFUBMC Neurology 2026-09-26 02:13:00 0
Roche
 
Resource Report
Resource Website
500+ mentions
Roche (RRID:SCR_001326) commercial organization A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics. pharmaceutical, diagnostic, drug, medicine, commercial is affiliated with: European Federation of Pharmaceutical Industries and Associations
is related to: EU-AIMS
is related to: eTRIKS
is related to: OncoTrack
is related to: GetReal
is related to: IMIDIA
is related to: Kinetics for Drug Discovery
is related to: NEWMEDS
is related to: PharmaCog
is related to: PREDECT
is related to: EMIF
is parent organization of: EU-AIMS
is parent organization of: Genentech
is parent organization of: Roche Diagnostics
is parent organization of: Roche: cobas�� e 601
ISNI: 0000 0004 1759 0967, grid.486917.5, nlx_152451, Wikidata: Q41568432 https://ror.org/02hv5e369 SCR_001326 SciCrunch Registry Hoffmann-La Roche AG, Hoffmann-La Roche, Roche Holding AG, F. Hoffmann-La Roche, F. Hoffmann-La Roche Ltd 2026-09-26 02:12:58 544
GlyTorsion
 
Resource Report
Resource Website
1+ mentions
GlyTorsion (RRID:SCR_001568) GlyTorsion analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource Service that performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank. Such as protein conformation can be described by the backbone torsion angles, a carbohydrate structure is mainly characterised by its linkage torsions. With the aid of pdb2linucs, a dataset of carbohydrate torsion angles was derived from from carbohydrate structures found in the PDB. This weekly updated dataset contains, besides linkage torsions, also ring torsions, omega torsions, N-acetyle group torsions and sidechain torsions of Asn residues involved in Glycan bonds. It can be queried by GlyTorsion. carbohydrate, torsion angle, torsion, angle, linkage torsion, ring torsion, omega torsion, n-acetyle group torsion, sidechain torsion, asn residue, glycan bond, statistical analysis is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: pdb2linucs
is related to: CARP
has parent organization: glycosciences.de
DFG PMID:15608187 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152881 SCR_001568 SciCrunch Registry GlyTorsion: Analysis of Carbohydrate Torsion Angles found in the Protein Data Bank (PDB) 2026-09-26 02:13:01 4
GlySeq
 
Resource Report
Resource Website
1+ mentions
GlySeq (RRID:SCR_001569) GlySeq analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource Service dedicated to statistically analyze the sequences around glycosylation sites. Glycosylation belongs to the most common and most important co- and postranslational modifications of proteins. Since it is often difficult to determine which potential glycosylation sites are in fact glycosylated, there is only few data available about glycoproteins. Sources from which such data can be retrieved are SwissProt and the Protein Data Bank (PDB). Data from the PDB is obtained using pdb2linucs and updated weekly. GlySeq is dedicated to statistically analyze these sequences, especially the areas around glycosylation sites. sequence, glycosylation site, glycoprotein sequence, glycoprotein, carbohydrate is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: pdb2linucs
has parent organization: glycosciences.de
DFG PMID:15608187 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152882 SCR_001569 SciCrunch Registry GlySeq - Statistical Analysis of Glycoprotein Sequences 2026-09-26 02:13:01 1
gprege
 
Resource Report
Resource Website
1+ mentions
gprege (RRID:SCR_001324) gprege software resource Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007). differential expression, microarray, preprocessing, time course, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
PMID:21599902 Free, Available for download, Freely available OMICS_02011, biotools:gprege http://www.bioconductor.org/packages/release/bioc/html/gprege.html SCR_001324 SciCrunch Registry Gaussian Process Ranking and Estimation of Gene Expression time-series 2026-09-26 02:12:58 1
waveTiling
 
Resource Report
Resource Website
waveTiling (RRID:SCR_001322) waveTiling software resource Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models. differential expression, microarray, gene expression, time course is listed by: OMICtools
has parent organization: Bioconductor
PMID:22974078 Free, Available for download, Freely available OMICS_02014 http://www.bioconductor.org/packages/release/bioc/html/waveTiling.html SCR_001322 SciCrunch Registry waveTiling - Wavelet-Based Models for Tiling Array Transcriptome Analysis 2026-09-26 02:12:58 0
The Biomedical Research Foundation - Current Research
 
Resource Report
Resource Website
The Biomedical Research Foundation - Current Research (RRID:SCR_001564) data or information resource, portal, topical portal THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This laboratory facilities contain core research space for monoclonal antibody production, oligonucleotide and peptide synthesis, gene cloning, DNA sequencing, high performance liquid chromatography, tissue culture, positron emission tomography, magnetic resonance spectroscopy and electron microscopy. drug, electron microscopy, - flow cytometry, gene, abuse, alcohol, automated cell imaging, cancer, cloning, confocal and digital microscopy, dna, dna gene chip analysis, immunology, inflammation, ischemic disorder, liquid chromatography, magnetic resonance spectroscopy, mass spectrometry, monoclonal antibody production, neuroscience, oligonucleotide, peptide, polymerase chain reaction (pcr), positron emission tomography, sequencing, signal transduction, synthesis, tissue culture THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10446 http://www.biomed.org/home http://www.biomed.org/bio_med_research.cfm SCR_001564 SciCrunch Registry BRI Research 2026-09-26 02:13:01 0
KAnalyze
 
Resource Report
Resource Website
1+ mentions
KAnalyze (RRID:SCR_001323) software resource A Java toolkit designed to convert DNA and RNA sequences into k-mers. standalone software, java, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: SourceForge
PMID:24642064 Free, Available for download, Freely available biotools:kanalyze, OMICS_03565 https://bio.tools/kanalyze SCR_001323 SciCrunch Registry 2026-09-26 02:12:58 2
AffyExpress
 
Resource Report
Resource Website
1+ mentions
AffyExpress (RRID:SCR_001321) AffyExpress software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. differential expression, microarray, annotation, one channel, preprocessing, quality control, report writing, visualization, gene expression is listed by: OMICtools
has parent organization: Bioconductor
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02015 SCR_001321 SciCrunch Registry AffyExpress - Affymetrix Quality Assessment and Analysis Tool 2026-09-26 02:12:58 2
Macromolecular Crystallography Research Resource
 
Resource Report
Resource Website
1+ mentions
Macromolecular Crystallography Research Resource (RRID:SCR_001442) PXRR, PXRR at the NSLS access service resource, analysis service resource, biomedical technology research center, production service resource, service resource, training resource Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage. protein crystallography, macromolecule, structure, structure determination, synchrotron x-ray diffraction, crystallography, microspectrophotometry, structural biology technology center, beamline NCI 2P30CA023168-21 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152667 SCR_001442 SciCrunch Registry Macromolecular Crystallography Research Resource at the NSLS, Macromolecular Crystallography Research Resource at the National Synchrotron Light Source, Research Resource for Macromolecular Crystallography at the National Synchrotron Light Source 2026-09-26 02:13:00 2
Neural Maestro
 
Resource Report
Resource Website
Neural Maestro (RRID:SCR_001563) Neural Maestro data access protocol, software application, software library, software resource, software toolkit, web service THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. A C#.NET/C++.NET 4.0 API multi-threaded, parallel class library with CUDA kernels for EEG predictive analytics gleaned from the ModelMaker 2 application. This web service and component library offers functionality to do univariate and multivariate nonlinear time series and frequency based predictive analysis for EEG / Ecog / MEG signals for gaming applications. Neural Maestro works with both EEGLab / BCILab and eConnectome as well as other MATLAB and R packages. It enables one to build highly sophisticated neuroscience applications with little effort in Windows applications. univariate, multivariate, nonlinear time series, time series, frequency, predictive analysis, eeg, ecog, meg, gaming application, neuroscience, computer gaming, modeling, forecasting, matlab, r, artificial intelligence, analytics, neural assessment is related to: EEGLAB
is related to: Neural Cipher
is related to: BCILAB
is related to: ModelMaker
is related to: iBIOFind
has parent organization: The Cromwell Workshop
THIS RESOURCE IS NO LONGER IN SERVICE nlx_153440 SCR_001563 SciCrunch Registry 2026-09-26 02:13:01 0
YPED
 
Resource Report
Resource Website
1+ mentions
YPED (RRID:SCR_001436) YPED data or information resource, data repository, database, service resource, storage service resource Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards. proteomics, protein, database, mass spectrometry, neuroscience, data analysis service, small molecule, source code, peptide, protein expression, phosphoprotein, mudpit, dige, icat, itraq uses: PANTHER
is used by: Integrated Datasets
is related to: Integrated Manually Extracted Annotation
has parent organization: Yale School of Medicine; Connecticut; USA
NIDA P30 DA018343;
NHLBI N01-HV-28186
PMID:17867667 Free, Freely Available nlx_152660 http://medicine.yale.edu/keck/nida/yped.aspx SCR_001436 SciCrunch Registry Yale Protein Expression Database 2026-09-26 02:12:59 4

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