Sandberg, Elizabeth S Baines, Hayley K Aye, Tandy Harris, Rebecca M Hart-Unger, Sarah Lopez, Ximena Nikita, Maria Eleni Nokoff, Natalie J Persky, Rebecca Roberts, Stephanie A
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Published in
Endocrine and metabolic science
While the field of pediatric endocrinology, and the American Board of Pediatrics, continues expanding training to include gender-affirming care, many pediatric endocrinology fellowship programs do not have formal curriculum for this patient population. Members of the Pediatric Endocrine Society (PES) that have a special interest in transgender heal...
Aydin, Selcan Pham, Duy T Zhang, Tian Keele, Gregory R Skelly, Daniel A Paulo, Joao A Pankratz, Matthew Choi, Ted Gygi, Steven P Reinholdt, Laura G
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Published in
Cell genomics
Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly var...
Rausch, Tobias Snajder, Rene Leger, Adrien Simovic, Milena Giurgiu, Mădălina Villacorta, Laura Henssen, Anton G Fröhling, Stefan Stegle, Oliver Birney, Ewan
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Published in
Cell genomics
Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenet...
Aspden, Julie L Wallace, Edward W J Whiffin, Nicola
Published in
Cell genomics
Exons are regions of DNA that are transcribed to RNA and retained after introns are spliced out. However, the term "exon" is often misused as synonymous to "protein coding," including in some literature and textbook definitions. In contrast, only a fraction of exonic sequences are protein coding (
Ang, Roy Moh Lik Chen, Shi-An A Kern, Alexander F Xie, Yihua Fraser, Hunter B
Published in
Cell genomics
The phenotypic effect of any genetic variant can be altered by variation at other genomic loci. Known as epistasis, these genetic interactions shape the genotype-phenotype map of every species, yet their origins remain poorly understood. To investigate this, we employed high-throughput genome editing to measure the fitness effects of 1,826 naturall...
Marlétaz, Ferdinand Couloux, Arnaud Poulain, Julie Labadie, Karine Da Silva, Corinne Mangenot, Sophie Noel, Benjamin Poustka, Albert J Dru, Philippe Pegueroles, Cinta
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Published in
Cell genomics
Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profi...
Liao, Calwing Moyses-Oliveira, Mariana De Esch, Celine E F Bhavsar, Riya Nuttle, Xander Li, Aiqun Yu, Alex Burt, Nicholas D Erdin, Serkan Fu, Jack M
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Published in
Cell genomics
Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder characterized by deficits in social interactions and communication. Protein-altering variants in many genes have been shown to contribute to ASD; however, understanding the convergence across many genes remains a challenge. We demonstrate that coexpression patterns from 993 h...
Martínez-Zamudio, Ricardo Iván Stefa, Alketa Nabuco Leva Ferreira Freitas, José Améri... Vasilopoulos, Themistoklis Simpson, Mark Doré, Gregory Roux, Pierre-François Galan, Mark A Chokshi, Ravi J Bischof, Oliver
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Published in
Cell genomics
Although oncogene-induced senescence (OIS) is a potent tumor-suppressor mechanism, recent studies revealed that cells could escape from OIS with features of transformed cells. However, the mechanisms that promote OIS escape remain unclear, and evidence of post-senescent cells in human cancers is missing. Here, we unravel the regulatory mechanisms u...
Puigdevall, Pau Jerber, Julie Danecek, Petr Castellano, Sergi Kilpinen, Helena
Published in
Cell genomics
The use of induced pluripotent stem cells (iPSC) as models for development and human disease has enabled the study of otherwise inaccessible tissues. A remaining challenge in developing reliable models is our limited understanding of the factors driving irregular differentiation of iPSCs, particularly the impact of acquired somatic mutations. We le...
Chen, Shi-An A Kern, Alexander F Ang, Roy Moh Lik Xie, Yihua Fraser, Hunter B
Published in
Cell genomics
Gene-by-environment (GxE) interactions, in which a genetic variant's phenotypic effect is condition specific, are fundamental for understanding fitness landscapes and evolution but have been difficult to identify at the single-nucleotide level. Although many condition-specific quantitative trait loci (QTLs) have been mapped, these typically contain...
