Genetics Bioinformatics Service Center

Bioinformatics as a Service

Vision and mission

Our goal with bioinformatics-as-a-service (BaaS) is to help Stanford labs do cutting edge bioinformatics data analysis without a significant investment in laboratory personnel.The bioinformaticians supporting this service are embedded with ​Stanford Center for Genomics & Personalized Medicine (SCGPM) Bioinformatics Team​. Members of this team support various large-scale genomics projects at Stanford, including Stanford Sequencing Service Center, ​ENCODE​, ​Integrative Personal Omics Profiling​, Human Microbiome Project, ​Stanford Clinical Genomics Service​, ​CIRM Center of Excellence for Stem Cell Genomics​ and the ​Million Veteran Program​. You can be assured that you are getting the best practice that Stanford has to offer. And Stanford is indeed the best in bioinformatics​.

Services offered in pipeline development, secondary and tertiary analysis, data interpretation, and training. We support NGS data types like:

  1. RNA-Seq including single cell and with synthetic spike-ins
  2. ChIP-Seq
  3. DNA-Seq including Whole Genome Sequencing, Whole Exome Sequencing, Deep Sequencing (Gene panels) and Cancer Seq (Germline and somatic)
  4. Microbiome Seq
  5. Uncommon data types such as ATAC-seq, Hi-C, Methyl-Seq

Case Studies

The descriptions are minimized to preserve research confidentiality. Please follow links for publicly disclosed information.

Understanding birth defects by investigating meiosis with Hi-C

Villenueve lab investigates mechanisms underlying the faithful inheritance of eukaryotic chromosomes and focuses on elucidating the events required for orderly segregation of homologous chromosomes during meiosis, the crucial process by which diploid germ cells generate haploid gametes. Understanding these events is of central importance to sexually reproducing organisms, since errors in meiosis lead to chromosomal aneuploidy, one of the leading causes of miscarriages and birth defects in humans. Hi-C is a variant of the 3-C (Chromosome conformation capture) technology that uses crosslinking and ligation to detect proximity between DNA sequences within the cell nucleus on a genome-wide basis. BaaS services implemented a Hi-C data processessing pipeline that the laboratory can use to analyze DNA organization during meiosis in C. elegans. (more)


Effect of drug on huntington’s disease using RNA-Seq

Huntington’s disease is a progressive, fatal neurological disorder with no cure. It’s genetic, and a child of an affected parent has a 50 percent chance of also developing the condition. In an international collaboration, researchers at the National Yang-Ming University in Taiwan and Stanford’s School of Medicine discovered a protein that may one day be a viable therapeutic target for those afflicted with the condition. Our bioinformatics service provided analysis for an RNA-Seq study done to examine global gene expression patterns in healthy individuals and Huntington's disease patients with and without drug treatment is providing insights into a possible mode of action. (more)


Investigating skin cancer using whole exome sequencing

Immune suppressing drugs are taken during transplant, and for chronic autoimmune disorders, such as celiac disease, Crohn’s disease, Graves’ disease, lupus and rheumatoid arthritis. These drugs can increase risk of skin cancer. Stanford High-Risk Skin Cancer Clinic, serves as an early-warning system, a frontline defense and, if need be, an all-hands-on-board diagnosis and treatment center.  Our bioinformatics service has been supporting physicians at the Clinic do analysis of whole exome sequencing of squamous cell skin cancer in order to offer clues as to phenotype-driven variant signatures in terms of the implicated genes. (more


Genetic architecture of cardiomyopathy

Both familial hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are prevalent hereditary cardiac disorder linked to arrhythmia and sudden cardiac death. Joseph Wu's lab seeks to elucidate the mechanisms underlying HCM and DCM development for the purposes of modeling these 2 prevalent diseases using RNA-Seq, single-cell RNA-Seq studies and whole genome sequencing studies. BaaS servics are helping with data analysis and interpretation. (more)


Understanding drug induced developmental toxicity

One oral pharmaceutical drug is used for treatment of skin acne, and is also known to be a teratogen that causes heart malformations in newborns. In this study of Snyder Lab, molecular mechanisms underlying this drug induced developmental toxicity in cardiomyocyte differentiation were investigated using both human induced pluripotent stem cells and human embryonic stem cells. BaaS is helping the analyses of genome-wide transcriptomic profiling by RNA-seq and dynamics of open-chromatin profiling by ATAC-seq. The analysis revealed that multiple signaling pathways with respect to early-stage development are involved. Results from this study are expected to broaden our knowledge of the congenital diseases of newborns that arise as a result of maternal drug exposure during the pregnancy.

Vascular biology of atherosclerosis using single-cell RNA-Seq

Atherosclerosis is deposition of fatty substances along arterial walls form atherosclerotic plaques that become brittle and vulnerable to rupture, and ultimately cause heart attack and stroke. In collaboration with investigators at the David Geffen School of Medicine at UCLA and the Icahn School of Medicine in New York City, Stanford has discovered anti-tumor antibodies that could counter atherosclerosis. Our bioinformatics service, provided analysis of single-cell RNA-Seq study on the vascular biology of atherosclerosis disease to detect cell subpopulations and heterogeneity is providing fundamental insights into the field of vascular biology of this heart disease. (more


Probing aging using parabiosis and RNA-Seq

Wyss-Cory lab conducts research on neurodegeneration and age-related changes in the brain. RNA-Seq techniques are applied by the lab to study the transcriptional profile during normal aging and impact during parabiosis, a process in which mice are surgically connected to share blood circulation. The lab utilized our services to train its researchers to do best practice RNA-Seq analysis including individual sample quality assessment, read mapping, gene expression quantification, differently expressed genes detection, splice variant analysis, heat map generation, visualization of mapped reads using the integrative genomics viewer, and Gene Ontology term and pathway enrichment functional analysis. (more)


Understanding immune responses using single cell RNA-Seq

CD4+ T cells (TMPS) are known to be very important for most immune responses, but their precise role in the context of influenza vaccination and protection is not well understood. In collaboration with Howard Hughes Medical Institute, Mark Davis' lab is characterizing the time course with which specific TMPS appear in infants and children and also analyze whether their rise is continuous, or spikes with major vaccinations, acquisition of a microbiome or disease exposure.  BaaS services help Davis lab do single T cell RNA-sequencing of murine and human T cell receptors. (more)


Function of long non-coding RNA

Kirkegaard lab works on the function of a long non-coding RNA (Nettoie Salmonella pas Theiler’s, NeST) that affects pathogen susceptibility and is likely to function by recruiting activating chromatin modification complexes. Labs working hypothesis is that the lncRNA is ultimately anti-inflammatory. We have recently developed mice that are knockouts for the NeST promoter, and these mice show increased susceptibility to the pathogenesis of dengue, poliovirus and Plasmodium infection. BaaS team is helping Kirkegaard lab interpret RNA-seq data on T cells before and after infection. (more)


Type 2 Diabetes and RNA-Seq

Genome wide association studies have identified approximately 400 genes with an increased incidence in type 2 diabetic patients. It is hypothesized that nucleotide polymorphisms within or near the coding region of these ‘candidate’ diabetes risk genes can suppress or enhance gene function resulting in an increased likelihood of developing T2D. Using screening tools in Drosophila, Seung Kim's lab have identified a group of 9 candidate genes which may potentially be involved in maintaining beta cell function. BaaS is helping the project focusing on one of these candidate genes, a repressive transcription factor with no known role in human beta cell function. When this gene was knocked-down in primary human islets Kim Lab observed a significant enhancement in basal and glucose-stimulated insulin secretion. BaaS is helping with RNA-seq analysis in order to understand the pathways/downstream candidates regulated by this gene which would explain the phenotype of enhanced insulin secretion. (more)

BaaS Team

Ramesh Nair, PhD

Ramesh, Associate Director of Bioinformatics at SCGPM, heads up the Bioinformatics-as-a-Service resource for the GBSC, and is the bioinformatician-in-residence for the CIRM-initiated Stem Cell Center of Excellence (CESCG) where he is responsible for diverse bioinformatics needs for the Center Initiated Projects and its extensive collaboration network. Prior to joining SCGPM, Ramesh was a Bioinformatics Analyst at Center for Cancer Systems Biology (CCSB) where among other things, he was sole developer of next-generation sequencing (NGS) pipelines for genome sequencing (Exome-Seq) applied to follicular lymphoma and transcriptome sequencing (RNA-Seq) applied to lung cancer tumor microenvironment. Prior to joining Stanford, he was a Sr. Scientist at various Biotech firms in Bay Area including Cobalt Biofuels, Iconix BioSciences (now Entelos), Lynx Therapeutics (now Illumina) and DuPont. Ramesh has a PhD in Chemical Engineering from Northwestern University and MTech in Biochemical Engineering and Biotechnology from Indian Institute of Technology Delhi.

Yue (Wendy) Zhang, PhD 

Yue is a Bioinformatics Data Scientist dedicated to analyzing the data which comes into the GBSC Bioinformatics-as-a-Service resource. Prior to joining the SCGPM, Yue was a postdoctoral scholar with Prof Mark Kay in the Departments of Pediatrics and Genetics. She has a PhD in Theoretical Physics from Xiamen University in China.

Yue has broad  knowledge and solid experience in different bioinformatics fields, especially in next-generation sequencing data including RNA-seq, single cell RNA-seq, small RNA-seq, Ribosome profiling, ChiP seq, PAR-CLIP seq, ATAC-seq and other cutting-edge sequencing type. She has expertise in statistical modeling, library normalization, classification, programming and visualization. Yue has developed active and close collaboration with dozens of labs at Stanford and is continuing to bring her interdisciplinary knowledge and professional skills to help Stanford researchers achieve their goals. 

Acknowledgement

Genetics Bioinformatics Service Center sincerely thanks Prof Michael Snyder for subsidizing the bioinformatics service for Stanford faculty.

Michael Snyder, PhD, Chair of Genetics and Director of SCGPM

Imagine a world in which you can input your age, lifestyle, and genetic information into an app and obtain personalized recommendations about the food you should eat or avoid and behaviors you should modify to help maintain your health. Moreover, imagine that when you are sick, your physician inputs the same information to determine your customized treatment plan. That world is not 50 years into the future; it is beginning to unfold now.

Fueled by its top-ranked graduate program in genetics, genomics and bioinformatics, Stanford is poised to lead in genomics and other omics. These fields hold the potential to revolutionize medicine by predicting and preventing disease, as well as diagnosing and treating disease with greater precision and personalization. Stanford Center for Genomics and Personalized Medicine​ (SCGPM) is one of Stanford’s nine biomedical platforms that build upon our strengths in fundamental research and translate these discoveries to add specificity and precision to the diagnosis and treatment of diseases in ways that improve patient care and outcomes.