Javascript is disabled/outdated. Please enable Javascript/use updated browser to load site navigation and frame.

Browser needs ECMAScript 6 support.

The world is a dangerous place, not because of those who do evil, but because of those who look on and do nothing.
--- Albert Einstein

Beginner's Readings

Program/Department links

Upstate Neuroscience Graduate Program
Upstate Psychiatry Research Division

ABC as a scientist

UH333 for lab safety; UH8794 for Bloodborne pathogenes UH8794_2020: Bloodborne Pathogens/Infection Control Training 2020 135: Cyber Security Training 162: Keeping the Upstate Community Safe: What You Need To Know;	Blackboard courses
Conflict of interest Responsible conduct of research IRB and Western Institutional Review Board (WIRB) for industry-sponsored clinical trials protocol submissions.	IRB CITI training
Ethical Issues in Genetic Studies	AHG Editorial: Topical ethical issues in the publication of humangenetics research
IRBnet	IRBnet for submitting IRB protocol
General online courses	Khan Academy edX Coursera Harvard free courses MIT OpenCourseWare Princeton Online courses Georgia Institute of Technology

Bioinformaticians

Unix/Linux basic.	Ubuntu Linux Redhat Linux Fedora Linux
The use of supercomputer clusters/grid/cloud computing	Introduction to our supercomputer use
R or other statistical tools, like SPSS, SAS, MatLab	http://cran.r-project.org/doc/manuals/R-intro.pdf
Python or Perl, for text manipulation	Python 3 Perl
SQL database (MySQL)	MySQL for managing data
Graph database	Graph database, Neo4j
REDCAP database	Upstate REDCAP
Cloud computing and data migration	Internet 2 Google cloud platform Amazon Web Service Microsoft Azure Terra Bio on GCP and Azure Globus Online Aspera NIH STRIDES
GO and geneset analyses	DAVID, GO and pathway GSEA GOrilla Enrichr PANTHER gProfiler webgestalt Cytoscape app GeneMANIA Bioconductor Piano Bioconductor SPIA
Network, pathway analyses	MetaboAnalyst, networkAnalyst, MicrobiomeAnalyst, miRNet, OmicsNet (Xia Lab @ McGill) Pathway Studio from Elsevier SIGNAL, combining pathways with PPI networks Ingenuity Pathway Analysis from Qiagen Reactome Pathway
Gene sets, gene lists for enrichment analyses	Literature inclusion criteria (tbp) Update plan (tbp) Gene lists (tbp)

Basic genetics & epigenetics

Basic concepts of population genetics	(from IPGRI, Cornell)
Population genetic inference from genomic sequence variation	(John E. Pool, et al. 2010)
Genetic architectures of psychiatric disorders: the emerging picture and its implications.	(Patrick F. Sullivan, Mark J. Daly, and Michael O'Donovan, 2012)
QTL Mapping of Molecular Traits for Studies of Human Complex Diseases	(Liu 2012)
Epigenetics in humans: an overview,	(RM. Rivera and LB. Bennett, 2010)
The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders.	(Dennis R Grayson and Alessandro Guidotti, 2012)
Psychiatric Genetics, Epigenetics, and Cellular Models in Coming Years	(Chunyu Liu, Stephen V. Faraone, Stephen J. Glatt, 2019)
Current Practices in Genetics Research of Psychiatric Disorders	(Chunyu Liu, Kay S. Grennan, Elliot S. Gershon, 2016)
A decade in psychiatric GWAS research	(Tanya Horwitz, Katie Lam, Yu Chen, Yan Xia & Chunyu Liu, 2019)
DNA Methylation and Psychiatric Disorders	(Chunyu Liu, Chuan Jiao, Kangli Wang, Ning Yuan, 2018)
microRNA book chapter	()
From brain bank to statistical and experimental methods	(Le Wang, Yan Xia, Yu Chen, Rujia Dai, Wenying Qiu, Qingtuan Meng, Liz Kuney, Chao Chen, 2019)
Search for genetic roots of psychiatric disorders	Introduction of Liu Lab (2021)
PGC GWAS Summary 2021	PGC (2021)
Broad GWAS RICOPILI PIPELINE	Broad Inst
Meta-analytical methods	Nicholas Mikolajewicz1 and Svetlana V. Komarova (2019)
International Statistical Genetic Workshop	ISGW workshop

Scientific writing

Writing	Writer's handbook about reverse outlines Biorender for Science Figures Graphviz turns text of relationships into graph Plagiarism tools: Turnitin and iThenticate cerebroViz for visualizing spatiotemporal data in the brain
Choice of Journals	Nature Family Cell Family Science Family Science Editors BMC Family PloS Family Journal of Psychiatry and Brain Science American Journal of Medical Genetics Part B SCI IF list for 2019
Pre-print Journals	Biorxiv Medrxiv
Data deposit and sharing	DMPTool, for NIH data management and sharing protocol Dryad, data deposit Dataverse, data deposit Zenodo, data deposit Protocol DOI RRID, resource ID

Funding Opportunities & Publications

Funding Opportunities	Upstate Research Pivot RP NIH Reporter Matchmaker	Publications & expertise	Dimensions AI

AI tools

General uses	OpenAI ChatGPT Google Gemini Bing Copilot Anthropic Claude 3 Moonshot Kimi Ali Tongyi Qianwen Baidu Wenxin Yiyan Perplexity ai	Literature reading	txyz ai SciSpace, search for literature Research Rabbit Scite Consensus OpenRead Elicit
Video and Other production	Invideo for video SUNO for music	Local AI	ollama NotebookIlama Nvidia ChatRTX
Others	Hume AI, Empathic AI chatbot	Omics LLMs	scGPT, scBERT, TOSICA, Geneformer, scFoundation,
Coding	Replit	News & Views	The gradient, sc The gradient, Mamba/SSM
AI assist writing	Jenni AI MediPen		ChatGPT Academic

Essential/core Databases and Tools (linkers see below)

Categories	Databases	Tools
Genome sequence and annotation	Genome Browser NCBI Ensembl GENCODE	Galaxy
Genetic variants	dbSNP dbVar dbGaP
GWAS	GWAS catalog PGC LD-hub GWAS Atlas
Epigenetic features	RegulomeDB Human Epigenome Atlas Enhancer DB Epigenomic browser ENCODE
Gene expression	GTEx GEO ArrayExpress
eQTL and other QTLs	GTEx xQTL

Online Databases with linkers

Commonly used genomics websites	Genome Browser 3D genome browser, Hi-C, http://www.ncbi.nlm.nih.gov/ GWAS Atlas GWAS Catalog Open targets, for SNP, gene association with drugs, traits and diseases Drug-Gene Interaction Database LD Hub DisGeNet disease gene database VarCards: an integrated genetic and clinical database for coding variants in the human genome Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans Development disorder genotype to phenotype database TargetGene: Relating SNPs to their target genes others particularly dbSNP, dbVar, dbGaP, GEO,	Spatiotemporal Gene Expression	*Brain Bulk-tissue* PsychENCODE Knowledge Portal GTEx Portal GTEx multi-gene query BrainEXP BrainEXP-NPD: DEG/coexpression in neuropsych brains HBT (Human Brain Transcriptome) from Sestan's lab at Yale *Human sorted cell expression* Human Ensemble Cell Atlas *Brain single-cell or cell-type-specific* Brain Cell Atlas myeloid sc RNA-seq, microglia and macrophage cells Human and mouse brain sc RNA-seq UCSC Cell Browser for sc RNA-seq data, for brain-related UCSD Single-cell methylome and cell types, by Eran A. Mukamel CoDex Viewer, Cortical development, cell specific expression Allen Brain Map, human/mice, major cell types by SMART-seq and 10x GTEx single cell data (non-brain) Protein Atlas (all tissues) MCA: Mouse developmental cell atlas (all tissues) spatialLIBD: Spatial transcriptome of DLPFC *Brain isoforms* single cell isoform from fetal brain *Brain omics data archive* Human Cell Atlas, Data portal: Single cell RNA-seq archive Nemo: The Neuroscience Multi-omic Archive *Brain organoids* Gene Expression in Cortical Organoids EpiMap OrganoidDB, transcriptome of 16218 samples *iPSC-derived brain cells* LIBD Stem Cell Browser iPSC (TBD) NPC (TBD) Neuron (TBD) Microglia (TBD) Endo (TBD) *Other relevant data* Endothelial cell db
Brain eQTL and pQTL	Meta Brain, eQTL of 7 brain regions, MR, and coloc Brain xQTLServe xQTL database, of 253 studies ROSMAP/Banner/control pQTL from 139- 330 subjects cerebral cortical and cerebellar brain eQTL, 1433 samples available from four cohorts, AMP-AD, including ROSMAP (DLPFC), Mayo (TCX), and Mayo (Cerebellum). cerebral cortical and cerebellar brain eQTL, 1433 samples available from four cohorts, meta-analysis eQTL CMC (N=467) and PsychENCODE (N=1866) eQTL query provided by SZDB PsychENCODE eQTL, cQTL, fQTL, isoQTL GTEx portal with up to 209 subjects for 11 brain regions The Brain eQTL Almanac, by UK Brain Expression Consortium (UKBEC), frontal cortex and cerebellum, around 400 subjects Brain Catalog: Brain-related Traits, including QTLs and other triats	miRNA	miRNASNP-v3, SNPs in miRNA or mRNA targets
DNA methylation and mQTL	Developing Brain mQTL MeQTL EPIC Database: UKB blood mQTLdb: blood mQTL of lifespan	Brain imaging genetics	Brain Imaging Genetics Knowledge Portal
SNP-related Epigenetic regulators	RegulomeDB: co-localized epigenetic markers for SNPs	Subcellular location	LocDB: Protein subcellular location Compartments
Brain Cell Morphology	NeuroMorpho, a centrally curated inventory of digitally reconstructed neurons and glia	non-Brain eQTL	eQTLGen Consortium, blood, cis and trans e(s)QTL Catalogue

iPSC/ESC and derived neural cells

iPSC and derived	HipSci, iPSC lines Fujifilm neural cells Hopstem BrainXell NIMH Repository	ESC	NIH Human Embryonic Stem Cell Registry

Essential concepts for this lab:

Quantitative traits; GWAS; TWAS; LD; QTL mapping; association, correlation, colocalization, and causality; effect size; coexpression networks; intermediate phenotypes; endophenotypes; central dogma; epigenetics; -omics; sanger sequencing, NGS and TGS (WGS, WES, RNAseq, riboseq, ATACseq, ChIP-seq, etc.); spatial transcriptome; In situ hybridization; cell sorting; Mendalian randomization; population structure; splicing isoforms and exons; pseudogene; expression regulators and targets; significance level and multiple testing correction; types of genetic variants; allele frequency; major psychiatric disorders; power estimate; internal validity and external validity; Batch effect and positional effect; covariable and confounding factors; meta-analysis and network meta-analysis (confidence interval, predictive interval, heterogeneity, publication bias, inconsistency, incoherence); specificity, accuracy, and precision; enrichment test (hypergeometric test, Chi-square test); mega-analysis; major brain regions; neural and immune cell types: PBMC, leukocyte, saliva, neuron & glia, progenitor cells; brain development; cell cycle and differentiation; Analysis of variation and regression; factor analysis, mediation, and PCA; latent variable; standarize, normalize, and residulize