Bioinformatics services

Explore our services for information on our capabilities and contact us if you have questions. Please get in touch with us at least three weeks before major deadlines.

 

Next-generation sequencing

We provide next-generation sequencing data analysis including RNA-Seq analysis, de novo transcriptome assembly, whole-genome sequencing, genome resequencing, single-cell sequencing, etc.

  • Single cell RNA sequencing data analysis

    We have built data analysis pipelines for both 10x Genomics and Drop Seq single cell RNA sequencing platforms, include barcode demultiplexing, read alignment, UMI-aware gene-level quantification, QC matrix, identification of cell types, etc.

  • RNA-seq gene level data analysis

    We have extensive experience in the analysis of RNA sequences (RNA-seq) and the identification of differentially expressed genes. Our typical RNA-seq workflow includes data quality control, cleaning of input sequence data, alignment to the reference genome and genes of the organism, quantification of transcript abundances, and statistical testing for genes with significant differences in expression between conditions.

  • RNA-seq de novo transcriptome assembly

    Next-generation sequencing, and the rapid production of large volumes of sequence data thereof, has extended the promise of whole-transcriptome reconstruction to investigators of non-model organisms, albeit with significant computational challenges. We aim to meet those challenges and offer de novo transcriptome assembly services which incorporate quality control, error correction, Trinity and additional cutting-edge assembly algorithms, assembly evaluation, filtration, and protein annotation.

  • Genome resequencing

    Core personnel have developed a resequencing toolkit to study whole genomic and/or targeted sequence-identification of variations in individuals and within populations, to identify novel mutations, single nucleotide polymorphisms (SNPs), indels, and structural variations for applications including Genotyping-by-sequencing and direct forward genetic mapping-by-sequencing. This toolkit includes dDocent, FreeBayes, vcftools, and R libraries for statistical analysis of population structure. Genotyping data are analyzed to provide robust, reproducible and meaningful identification of sequence variations.

 

Mass spectrometry proteomics

High-throughput mass spectrometry proteomic bioinformatics support includes downstream analysis of label-free, SILAC, and TMT data. We take the protein identification and quantification data from PD and process the downstream analysis that typically includes data quality control and preprocessing, data normalization and differential analysis, pathway and functional analysis.

 

Customized bioinformatics support

  • Other omics data analyses such as metabolomics, microbiome, metaomics, etc.
  • Data mining, modeling, and visualization
  • Computational tools hosting and training for researchers and students
  • Customized bioinformatics and statistical services including data quality control, power studies, hypothesis tests, regression, clustering, network analysis, function annotation, pathway analysis by IPA®, etc.
 

Project consultation & proposal support

We gladly provide investigators biostatistical, bioinformatic, and sequencing consultation services to guide researchers towards the effective design, execution, and analysis of their studies and research questions. We further offer support to researchers at the pre-proposal phase to help researchers win competitive grant funding and at the manuscript phase in method writing and data visualization.

Teaching & training

We perform workshops, seminars, and personal training sessions for our investigators, students, and our collaborative undergraduate institutions. Past workshops have covered topics such as: Python crash course, R programming, BLAST methodologies, sequence assembly, and sequence analysis with functional annotation.

Check our events calendar for upcoming workshops and training events.