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https://www.preventivemedicine.northwestern.edu/divisions/biostatistics/

Core where division members engage in statistical methods development and application, research design and statistical computing for health science research. Faculty interests encompass Bayesian methods, bioinformatics, causal inference, computational biology, clinical trials, diagnostic testing, longitudinal modeling, missing data modeling, observational data methods, semi-parametric models, spatial modeling, statistical genetics and survival analysis.

Proper citation: Northwestern University Biostatistics Collaborative Center (RRID:SCR_017943) Copy   

•   Source: SciCrunch Registry

http://proteomics.northwestern.edu/collaborate

Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS.

Proper citation: Northwestern University Proteomics Core Facility (RRID:SCR_017945) Copy   

•   Source: SciCrunch Registry

https://education.musc.edu/colleges/medicine/departments/pharmacology/redox-center/cores/bioenergetics-profiling-core

Core provides several technologies that enable researchers to quantify fluxes of these metabolic reactions in cells, tissues, organoids and small animal models such as zebrafish embryos and nematodes.Technologies include high resolution respirometry using XF technology from Seahorse Biosciences/Agilent. Instrumentation utilizes 96-well microplates to provide sufficient sample numbers to provide flux profiles of glycolysis, mitochondrial respiration, fatty acid oxidation, glutamine utilization and other related metabolic processes. Rapid, high-throughput imaging optimized to XF plate architecture provides normalization of cell/tissue numbers, health, and other.Provides training, data analyses support and aid in experimental design.

Proper citation: South Carolina Medical University Bioenergetics Profiling Core Facility (RRID:SCR_017953) Copy   

•   Source: SciCrunch Registry

https://www.biotech.cornell.edu/core-facilities-brc/facilities/bioinformatics-facility

Facility provides access to high performance computing environment, BioHPC, which includes both hosted hardware and shared machines. Provides consulting and collaborations for Bioinformatics analysis and workflows.

Proper citation: Cornell University BRC Bioinformatics Core Facility (RRID:SCR_021757) Copy   

•   Source: SciCrunch Registry

http://www.primervfx.com/#welcome

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

Proper citation: PrimerStudio (RRID:SCR_008232) Copy   

•   Source: SciCrunch Registry

http://locustdb.genomics.org.cn/

The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.

Proper citation: Migratory Locust EST Database (RRID:SCR_008201) Copy   

•   Source: SciCrunch Registry

http://www.schematikon.org/Nh3D.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. It is a dataset of structurally dissimilar proteins. This dataset has been compiled by selecting well resolved representatives from the Topology level of the CATH database which hierarchically classifies all protein structures. These have been been pruned to remove: i) domains that may contain homologous elements (by pairwise sequence comparison and structural superposition of aligned residues) ii) internal duplications (by repeat detection) iii) regions with high B-Factor The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfill minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here a reference dataset of non-homologous protein domains is provided, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. Even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB.

Proper citation: Nh3D: A Reference Dataset of Structures of Non-homologous Proteins (RRID:SCR_008212) Copy   

•   Source: SciCrunch Registry

http://www.cs.tau.ac.il/~spike/

Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways

Proper citation: SPIKE (RRID:SCR_010466) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/phenotypes.shtml

Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.

Proper citation: Phenotypes and Mutant Alleles (RRID:SCR_017523) Copy   

•   Source: SciCrunch Registry

https://www.sourcebioscience.com/products/life-sciences-research/clones/rnai-resources/c-elegans-rnai-collection-ahringer/

C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies.

Proper citation: C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) Copy   

•   Source: SciCrunch Registry

https://ualr.edu/bioinformatics/midsouth-bioinformatics-center/

Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice.

Proper citation: University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) Copy   

•   Source: SciCrunch Registry

https://git.io/vAeKZ

It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.

Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy   

•   Source: SciCrunch Registry

https://epilepsy.uni-freiburg.de/freiburg-seizure-prediction-project

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM).

Proper citation: Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) Copy   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/index

Core equipped for structural and functional studies of genomes, includes equipment for next generation sequencing applications (Illumina HiSeq 1500, GAIIx and MiSeq, Life Technologies Ion Torrent PGM), RNA and microRNA expression profiling, array-based DNA methylation analyses and SNP genotyping (Illumina HiScan and Agilent High Resolution microarray scanners), informatics and bioinformatics (a server farm for genomics data computation and a high capacity data storage unit), fluorescence and confocal microscopy, long-term sample storage, cell culture, including a facility for generation and handling of viral vectors for gene transfer and gene therapy, access to a small animal facility for ''in vivo'' experimentations. Trained biotechnologists, molecular biologists and bioinformaticians handle all aspects related to experimental design, technical implementation and data analysis and storage.

Proper citation: University of Salerno Laboratory of Molecular Medicine and Genomics (RRID:SCR_011047) Copy   

•   Source: SciCrunch Registry

https://dna.uga.edu/

Core laboratory for nucleic acid sequencing and bioinformatics. Used for research support, education, and training. Services include genomic techniques and applications, sequencing technologies, and bioinformatics analyses, writting letters of support for grant applications submitted to funding agencies. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon).

Proper citation: Georgia Genomics and Bioinformatics Core at the University of Georgia (RRID:SCR_010994) Copy   

•   Source: SciCrunch Registry

https://pharmacycorefacilities.usc.edu/translational-lab/

Core is equipped with a wide variety of technologically advanced instruments essential for cutting edge biomedical discovery and therapeutic development research. TRLab is composed of two major units. The Computational Bioinformatics Unit houses graphic workstations and modeling programs that enable in silico virtual screening and rational drug design applications. The Therapeutic Screening Unit houses a number of specialized instruments that enable a broad range of automated and multiplexed biological analyses in a throughput manner. The core mission of the TRLab has been to provide investigators with a state-of-the-art technological platform and technical expertise to advance translational research endeavors in the School of Pharmacy and at USC.

Proper citation: University of Southern California School of Pharmacy Translational Research Laboratory (RRID:SCR_012253) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/epigenome-center-data-production-facility-usc

Core conducts genome-scale epigenetic and genetic data production and analysis, technology development, and epigenomic and population-based genomic research.

Proper citation: University of Southern California Epigenome Center Data Production Facility (RRID:SCR_012476) Copy   

•   Source: SciCrunch Registry

http://pctriadd.com/genomic-analysis/overview

Core offers sequencing and microarray services, solutions for the profiling of FFPE tissues, and complete, project-tailored downstream bioinformatics analysis. The core's structure enables the management of research projects from experimental design to analysis and interpretation of data as well as support for grant applications and publications. The LAGA provides open fee-for-service access as a core facility (intra-institutional services to its researchers) and as regional, national and international facility (inter-institutional services).

Proper citation: Vancouver Prostate Centre Laboratory for Advanced Genome Analysis (RRID:SCR_012394) Copy   

•   Source: SciCrunch Registry

https://systemsbiology.columbia.edu/genome-center

Core sells sequencing data and bioinformatic analytics services to the scientific community. Core aims to permit the development of research on sequencing protocols and encourage collaboration with clinicians to develop the next generation genomic DNA testing.

Proper citation: JP Sulzberger Columbia Genome Center (RRID:SCR_012650) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_Cheminformatics.aspx

Core facility that supports assay development, high throughput (HTS), ultra-high throughput (uHTS), and high-content screening (HCS) activities performed at the Conrad Prebys Center for Chemical Genomics by providing databases and tools for compound registration and inventory, HTS plate formatting and tracking, HTS and HCS bioassay data processing as well as related data and information handling. Data mining and reporting are also facilitated with a user-friendly database interface. The Cheminformatics core also supports the design and obtaining of appropriate compound collections, as well as SAR follow-up of hits, hit-to-lead optimization and in silico screening through docking and other molecular modeling approaches.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Cheminformatics Core (RRID:SCR_014875) Copy   

•   Source: SciCrunch Registry