LC

Human Genomics

A haplotype map of the human genome

Genomic analyses inform on migration events during the peopling of Eurasia

Genomic analyses inform on migration events during the peopling of Eurasia - Supp

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations - Supp

Genes mirror geography within Europe

Genetic Structure of Europeans: A View from the North–East

Mutational Load and Deleterious Variation in Humans

Direct Evidence of an Increasing Mutational Load in Humans

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

Estimating the mutation load in human genomes

The deleterious mutation load is insensitive to recent population history

Extreme inbreeding in a European ancestry sample from the contemporary UK population

Africa population genetics

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

Static and Moving Frontiers: The Genetic Landscape of Southern African Bantu-Speaking Populations

African signatures of recent positive selection in human FOXI1

The evolutionary history of Southern Africa

Genome-Wide SNP Analysis of Southern African Populations Provides New Insights into the Dispersal of Bantu-Speaking Groups

Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

X chromosome

Signatures of replication, recombination and sex in the spectrum of rare variants on the human X chromosome and autosomes

Extreme selective sweeps displaced archaic admixture across the human X chromosome around 50,000 years ago

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity

Evaluating signatures of sex-specific processes in the human genome

A Pseudohitchhiking Model of X vs. Autosomal Diversity

Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

Why the human X chromosome is less diverse

Neutral genomic regions refine models of recent rapid human population growth

Sex-Averaged Recombination and Mutation Rates on the X Chromosome: A Comment on Labuda et al.

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

Can a Sex-Biased Human Demography Account for the Reduced Effective Population Size of Chromosome X in Non-Africans?

Detecting natural selection by empirical comparison to random regions of the genome

Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans

Genetic Diversity on the Sex Chromosomes

The different levels of genetic diversity in sex chromosomes and autosomes

Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

On the origin of modern humans: Asian perspectives

Explosive genetic evidence for explosive human population growth

Population Genomic Analysis of 962 Whole Genome Sequences of Humans Reveals Natural Selection in Non-Coding Regions

The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection

A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations

America Population Genetics

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

Reconstructing the Population Genetic History of the Caribbean

Melanesian Blond Hair Is Caused by an Amino Acid Change in TYRP1

Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

Y‐chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas

Inferring sex-specific demographic history from SNP data

Bayesian Estimation of Recent Migration Rates After a Spatial Expansion

Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Genome-wide patterns of population structure and admixture among Hispanic/Latino populations

Supp

Genomic Insights into the Ancestry and Demographic History of South America

Understanding the Hidden Complexity of Latin American Population Isolates

Elevated male European and female African contributions to the genomes of African American individuals

EE

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Reconstructing genetic history of Siberian and Northeastern European populations

Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

MX

Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico

Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing

Scyth

137 ancient human genomes from across the Eurasian steppes

The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age Nomads

Ancient genomic changes associated with domestication of the horse

Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe

de Novo Assemblying using long reads

South East Asia

Genomic insights into the peopling of the Southwest Pacific

Language continuity despite population replacement in Remote Oceania

Y Chromosome

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences - Supp

Figure 2: Y-chromosome phylogeny and haplogroup distribution

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

A recent bottleneck of Y chromosome diversity coincides with a global change in culture - Supp

Introduction to the BigY

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

Characterizing the genetic history of admixture across inner Eurasia

Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families - Fig

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Phasing

Michigan Imputation Server

Sanger Imputation Service

The Haplotype Reference Consortium

1000G Project Genetic Maps

Characterizing mutagenic effects of recombination through a sequence-level genetic map

Characterizing mutagenic effects of recombination through a sequence-level genetic map - Supp

Haplotype phasing: existing methods and new developments

Sharon R Browning, PhD

Brian Browning

A reference panel of 64,976 haplotypes for genotype imputation

A reference panel of 64,976 haplotypes for genotype imputation - Supp

Comparison of phasing strategies for whole human genomes

Shapeit

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Population structure

EIGENSOFT

Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

Admixture 1.3 Software Manual

Population history

Efficiently inferring the demographic history of many populations with allele count data

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

Momi2 documentation

Momi2 Github

Momi2 Tutorial

Clustering

CLUMPP 1.1.2

CLUMPAK, version 1.1

Snakemake

Rules

SLURM

Slurm

HPC Tartu

Atlas cluster

Rocket cluster

SLURM (Simple Linux Utility for Resource Management)

Git

Cheat sheet

Databases

PopHumanScan

Math

Algebra Cheat Sheet

Programming

How to Design Programs

Modular code development

Latex

Latex Cheat Sheet

Python

PEP 8 – Style Guide for Python Code

yapf - A formatter for Python files

[Data Science Cheat SheetPandas and Numpy Cheat Sheet](https://courses.cs.ut.ee/MTAT.03.183/2017_spring/uploads/Main/pandas-cheat-sheet.pdf)
[Python For Data SciencePandas Basics Cheat Sheet](https://s3.amazonaws.com/assets.datacamp.com/blog_assets/PandasPythonForDataScience.pdf)
[Python For Data SciencePandas Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/9f0f2ae1-8bd8-4302-a67b-e17f3059d9e8)
[Python For Data ScienceScikit-Learn Cheat Sheet](https://s3.amazonaws.com/assets.datacamp.com/blog_assets/Scikit_Learn_Cheat_Sheet_Python.pdf)
[Python For Data ScienceImporting Data Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/50d31142-3de0-4159-89b9-18b718a728ef)
[Python For Data ScienceBokeh Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/f9511cf4-abb9-4f52-9663-ea93b29ee4b7)
[Python For Data ScienceNumpy Basics Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/e9f83f72-a81b-42c7-af44-4e35b48b20b7)
[Python For Data ScienceJupyter Notebook Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/48093c40-5303-45f4-bbf9-0c96c0133c40)
[Python For Data ScienceJupyter Notebook Shortcut Cheat Sheet](https://www.cheatography.com/weidadeyue/cheat-sheets/jupyter-notebook/pdf_bw/)
[Python For Data ScienceScyPy Linear Algebra Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/5710caa7-94d4-4248-be94-d23dea9e668f)
[Python For Data ScienceMatplotlib Cheat Sheet](https://datacamp-community-prod.s3.amazonaws.com/28b8210c-60cc-4f13-b0b4-5b4f2ad4790b)

R

The R Manuals

R FAQ

Books related to R

Color Palette Cheatsheet

Color Palette

ggplot2 reference

Unpacking S4 Objects in R

Tidyverse

The caret package

Markdown

R MarkdownReference Guide

R Markdown Cheat Sheet

R Markdown Extended Syntax

R Markdown Reference

Unix / Linux

Linux command.org

Explain shell.com

Unix/Linux Command Reference

Treebeard’s Unix Cheat Sheet

Screen User’s Manual

Linux screen command

Bash

Advanced Bash-Scripting Guide

BASH Programming - Introduction HOW-TO

Shell Scripting Tutorial

The Bash Guide

Bash scripting Tutorial

A quick guide to writing scripts using the bash shell

Linux Shell Scripting Tutorial v1.05r3

Bash Guide for Beginners

Beginners/BashScripting

AWK

Awk

Simple awk tutorial

SED

Sed

Sed - An Introduction and Tutorial by Bruce Barnett

EIGEN

convertf

BCFTOOLS / VCF

The Variant Call Format (VCF) Version 4.1 Specification

The Variant Call Format (VCF) Version 4.2 Specification

The Variant Call Format (VCF) Version 4.3 Specification

Bcftools

BCFtools HowTo

Statistics

The Elements of Statistical Learning

An Introduction to Statistical Learning

Modern Statistics for Modern Biology

SticiGui - Philip B. Stark

Statistics for Genomic Data Science - Jeff Leek

Mutational Signatures

Smaug Genetics

Jedidiah Carlson Web page

Mutation Rate Browser

International Standard ISO 80000-2

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Complete Genomics

Documentation Portal

Standard Sequencing Service 2.4 - 2.5

Standard Sequencing Service 2.2

Standard Sequencing Service 2.0

Data File Formats 2.5

Data File Formats 2.4

Data File Formats 2.2

Data File Formats 2.0

CGATools

CGATools release Notes

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Illumina

NovaSeq 6000 Sequencing System

Human Whole-Genome Sequencing with the HiSeq X Sequencing System

HiSeq X Series of Sequencing Systems

NextSeq 500 Sequencing System

HiSeq 2500 Sequencing System

HiSeq 2000 Sequencing System

Illumina Two-Channel SBS Sequencing Technology

Genome-Wide DNA Analysis BeadChips

Combinatorics

Combinatorics

Applications of Combinatorics to Molecular Biology

Combinatorial Pattern Matching

ASCII

ASCII Code - The extended ASCII table

The Future Under a Microscope

Scientists Turn Bacteria Into Living Hard Drives

Molecular recordings by directed CRISPR spacer acquisition

Next-Generation Digital Information Storage in DNA

Long-Term Storage of Information in DNA

Text Of A Full Book Encoded In DNA

C Program to Find ASCII Value of a Character

Drosophila

Latitudinal clines in gene expression and cis-regulatory element variation in Drosophila melanogaster

Gene expression changes in male accessory glands during ageing are accompanied by reproductive decline in Drosophila melanogaster

Rapid evolution of male-biased gene expression in Drosophila

GEO

Effects of temperature on cuticular lipids and water balance in a desert Drosophila: is thermal acclimation beneficial?

Involvement of chitin in exoskeleton morphogenesis in Drosophila melanogaster

Dr. Itai Yanai - Evolution of developmental gene expression programs

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution

Functional genomics of cactus host shifts in Drosophila mojavensis

Genomics of Ecological Adaptation in Cactophilic Drosophila

The cuticle proteins of Drosophila melanogaster: Stage specificity

Cuticle Preparation of Drosophila Embryos and Larvae

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

Gene expression divergence recapitulates the developmental hourglass model

Developmental Constraints on Vertebrate Genome Evolution

The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates

Unmodern Synthesis: Developmental Hierarchies and the Origin of Phenotypes

Positional information and reaction-diffusion: two big ideas in developmental biology combine

Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors

Black Death

Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period

Population Size Recontruction

Ancestry-specific recent effective population size in the Americas

SwedGen

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population