Introducing the Illustris project: The evolution of galaxy populations across cosmic time

We present an overview of galaxy evolution across cosmic time in the Illustris simulation. Illustris is an N-body/hydrodynamical simulation that evolves 2 × 18203resolution elements in a (106.5Mpc)3box from cosmological initial conditions down to z = 0 using the AREPO moving-mesh code. The simulation uses a state-of-the-art set of physical models for galaxy formation that was tuned to reproduce the z = 0 stellar mass function and the history of the cosmic star formation rate density. We find that Illustris successfully reproduces a plethora of observations of galaxy populations at various redshifts, for which no tuning was performed, and provide predictions for future observations. In particular, we discuss (a) the buildup of galactic mass, showing stellar mass functions and the relations between stellar mass and halo mass from z = 7 to 0, (b) galaxy number density profiles around massive central galaxies out to z = 4, (c) the gas and total baryon content of both galaxies and their haloes for different redshifts, and as a function of mass and radius, and (d) the evolution of galaxy specific star formation rates up to z = 8. In addition, we (i) present a qualitative analysis of galaxy morphologies from z = 5 to 0, for the stellar as well as the gaseous components, and their appearance in Hubble Space Telescope mock observations, (ii) follow galaxies selected at z = 2 to their z = 0 descendants, and quantify their growth and merger histories, and (iii) track massive z = 0 galaxies to high redshift and study their joint evolution in star formation activity and compactness. We conclude with a discussion of several disagreements with observations, and lay out possible directions for future research

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Expanded encyclopaedias of DNA elements in the human and mouse genomes

All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.© The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Time to finger point or fix? An invitation to join ongoing efforts to promote ethical authorship and other good publication practices

In this commentary, we present evidence that unethical authorship (eg, guest and ghost authoring) and other publication practices are not restricted to the pharmaceutical industry; they also occur in academia. Such practices are not an industry problem-they are a research problem. To enhance trust in industry sponsored research, companies have made rapid and far-reaching changes to their publication guidelines, policies, and procedures. Professional medical writers have adopted, and continue to implement, these changes. Although evidence indicates that industry practices are improving, there is certainly more to do, both in industry and academia. We invite readers to join ongoing efforts to promote ethical publication practices

Introducing the Illustris project: The evolution of galaxy populations across cosmic time

We present an overview of galaxy evolution across cosmic time in the Illustris simulation. Illustris is an N-body/hydrodynamical simulation that evolves 2 × 18203resolution elements in a (106.5Mpc)3box from cosmological initial conditions down to z = 0 using the AREPO moving-mesh code. The simulation uses a state-of-the-art set of physical models for galaxy formation that was tuned to reproduce the z = 0 stellar mass function and the history of the cosmic star formation rate density. We find that Illustris successfully reproduces a plethora of observations of galaxy populations at various redshifts, for which no tuning was performed, and provide predictions for future observations. In particular, we discuss (a) the buildup of galactic mass, showing stellar mass functions and the relations between stellar mass and halo mass from z = 7 to 0, (b) galaxy number density profiles around massive central galaxies out to z = 4, (c) the gas and total baryon content of both galaxies and their haloes for different redshifts, and as a function of mass and radius, and (d) the evolution of galaxy specific star formation rates up to z = 8. In addition, we (i) present a qualitative analysis of galaxy morphologies from z = 5 to 0, for the stellar as well as the gaseous components, and their appearance in Hubble Space Telescope mock observations, (ii) follow galaxies selected at z = 2 to their z = 0 descendants, and quantify their growth and merger histories, and (iii) track massive z = 0 galaxies to high redshift and study their joint evolution in star formation activity and compactness. We conclude with a discussion of several disagreements with observations, and lay out possible directions for future research