Welcome to the Baker Lab!

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The Baker laboratory examines the genomics underlying the differentiation and evolution of fetal cell types. We use multiple model systems, including frog and mouse embryos, embryonic stem cells, trophoblast stem cells and human tissues, to ask how cell types in the fetus form, how these cell types are regenerated, how particular lineages evolved and how these processes might lead to human disease.

Much of our work has focused on the establishment of the early germ layers, the ectoderm, mesoderm, endoderm and – in mammals – the trophectoderm.

Scroll down for highlights of some recent findings!

Research Interests

How do cells become endoderm and mesoderm?

We have discovered that the formation of mesoderm and endoderm depends on the interaction between the role of the HLH proteins, E2A and HEB, and the Nodal signaling pathway. Importantly, we have found that HEB also associates with the histone repressive mark, H3K27me3, to regulate developmental genes (Yoon et al., 2015). We also have shown that E2a is required for endoderm and mesoderm formation in the frog embryo and its role is both to activate developmental transcription factors and to repress the molecule Lefty (Wills et al., 2015).

 

 

 

Transposons guide evolution of trophectoderm.

In examining the genomics of trophoblast stem cells and placenta, we have been elucidating how this critical mammalian organ evolved. We find that a single transposable element has contributed 30% of the binding sites for the key transcription factors Cdx2, Eomes and Elf5 – all three being essential for establishment of the trophectodermal lineage in mammals (Chuong et al., 2013). We are continuing to examining the role of transposable elements in placentation.

 

 

 

 

The placental genome has regions of under and over amplification.

Placental cells are typically polyploid or multinucleated in all species and tolerate a significant amount of moisacism. In examining mouse polyploid placental cells, we find specific regions of under and over represented regions. Under amplified regions are highly enriched for sensory and adhesion genes whereas over represented regions are mainly placental hormones. Overall, we suggest that genomic copy number variation may be responsible for regulating specific classes of genes in the placenta (Hannibal et al., 2014).

 

 

 

 

Egg Reprogramming

The egg is the only cell that internalizes a foreign nucleus and efficiently and rapidly reprograms it to pluripotency. We have taken a genome wide approach to define how the egg reprograms cells. Transcriptomics and proteomics have revealed that the egg is a highly organized cell and this organization drives efficient reprogramming. Current work is focused on drawing parallels between somatic reprogramming and fertilization.

 

 

 

 

Tail regeneration in the tadpole

While pathways guiding cell fate specification in the embryo have been explored over the past 20 years, very little is known about how tissue regeneration occurs – particularly in the spinal cord. We have been examining the chromatin and transcriptome context of the regenerating spinal cord during a timeseries spanning hours post injury.

 

 

 

 

 

 

Diseases of pregnancy

We are investigating the genetics of preeclampsia in the Peruvian Altiplano and the disease accreta using genomic technologies.

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transposon

 

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2C5CA978-145C-42BE-98B3-C5F876A68CFC@stanford.edu

 

 

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Lab Members

Julie Baker

Julie Baker

Principal Investigator

Hi, my name is Julie!

jbaker@stanford.edu

 

Guillaume Cornelis

Guillaume Cornelis

Postdoctoral Scholar

I am interested in the molecular and cellular mechanisms that can influence pace of life of organisms, as well as their evolutive history. More particularly, I am studying the impact of transposable elements (TEs) on the development of the mammalian placenta. TEs are mobile genetic elements scattered across vertebrate genomes. They have been shown to play critical roles in placentation, including as protein coding genes necessary for placental morphogenesis and as important enhancer elements that rewire the placental transcriptional circuitry. This active TE environment is entirely novel to the placental landscape as adult somatic tissues tightly repress TEs using specific epigenetic marks to specifically shut down these highly mutagenetic agents. The consequence, however, is extreme – inducing rapid evolution and potentially allowing for significant diseases associated with this organ, including cancer. My goal is to characterize the role of TEs cooptation in normal and pathological placenta, leading toward a better understanding of the development and evolution of placentation.

Outside of work, I like photography, movies and experimenting new cake recipes on my fellow labmates!

gcorneli@stanford.edu

Roberta Hannibal

Roberta Hannibal

Postdoctoral Scholar

I am interested in understanding the development and evolution of the placenta, a mammalian specific organ crucial for fetal well-being.  A key feature of the placenta are polyploid trophoblast cells that invade and remodel the mother’s uterus in order to promote blood flow and nutrient delivery to the fetus.  In rodents, these cells are called trophoblast giant cells (TGCs) and have up to 1,000N DNA content due to endoreplication.  As recent work has shown that TGC endoreplication is essential for fetal health, my research uses mouse knock-outs and genomics to elucidate the function of endopolyploidy.  In addition, I am studying human trophoblast cells, as defects in these cells have drastic consequences for both fetal and maternal health, including preeclampsia and preterm birth, yet very little is understood about the molecular mechanisms behind these diseases. 

robertah@stanford.edu

Qin Li

Qin Li

Postdoctoral Scholar

The placenta is one of the defining characteristics of placental mammals. It is also a novel and recent evolution event occurring in eutherians and marsupials. My research currently uses functional and comparative genomic approaches to investigate the genetic networks of eutherians and marsupials placenta. I am mostly interested in identifying genomic milestones in the evolution events of placenta, such as novel genes/pathways, genomic variation, etc. I am also interested in the polyploidy nature of Xenopus laevis genome. Although polyploidy is widespread in plant kingdom, it is relatively rare amongst animals. X. laevis is an ideal model system to study the regulatory network of allotetraploid genome, in hopes of understanding the specific roles of sub-genomes throughout development stages of germ cells.

qinl@stanford.edu

Christine Reid

Christine Reid

Postdoctoral Scholar

I’m originally from Southern California, and I went to University of Pennsylvania in Philadelphia for my PhD. I came to Stanford as a postdoc in the Baker Lab in late 2012, where I began work on reprogramming somatic cells using the Xenopus laevis oocyte. The oocyte reprograms cells efficiently and rapidly, but little is know about the factors that reprogram foreign nuclei. To define how the oocyte reprograms nuclei, I have characterized both proteins and transcripts within the oocyte. Current work is focused on profiling the chromatin state of the oocyte and the nuclei being reprogrammed. When I’m not in lab, I like hiking in the redwoods, hanging out at the beach and bike riding with my family.

cdreid@stanford.edu

Andrea Wills

Andrea Wills

Postdoctoral Scholar

I spend a lot of my time puzzling over some big questions. Why do humans have such limited regeneration capacities, when other vertebrates like amphibians are readily able to regenerate structures like the heart, spinal cord, or limbs? Is regeneration of these tissues in amphibians basically a recapitulation of embryonic patterning events? What are the events in early embryogenesis that ultimately govern whether a cell will differentiate into one tissue like liver, while neighboring cells instead become another tissue like heart? I tackle these questions using a combination of genomics and embryology in the frog Xenopus tropicalis. I have been using genomics and transcriptomics approaches to identify how transcription factors interface with chromatin modifications during early embryogenesis to drive cell differentiation. More recently, I have applied these approaches to understand how chromatin and gene expression are remodeled during regeneration, and how these processes compare to early embryogenesis.

Outside of these puzzles, I spend my time running, reading old science fiction, and honing my toddler-wrangling skills.

aewills@stanford.edu

Se-Jin Yoon

Se-Jin Yoon

Postdoctoral Scholar

I am investigating the Nodal signaling pathway including the transcriptional factor complex containing Smad2/3 and FoxH1 required for the establishment of endoderm as well as the maintenance of pluripotency in hESCs. An understanding of the Nodal pathway and its downstream targets is critical for unraveling the interlocking mechanisms underlying both pluripotency and early cell fate commitment. To identify Nodal signaling targets in hESCs and endodermal cells, I have accomplished the genome-wide screening of Smad/FoxH1 downstream targets in undifferentiated hESCs and endoderm differentiated hESCs via ChIP with ultra high throughput sequencing. The analysis of the Smad/FoxH1 transcription factor binding network in this two different cell types will provide a glimpse at the genomic mechanism behind the early stages of differentiation in human.

sjyoon@stanford.edu

Keyla Badillo-Rivera

Keyla Badillo-Rivera

Graduate Student

I am interested in how different aspects of gene regulation alter placental tissue differentiation and function, and how that affects fetal development and puts the mother in risk. For this, I’m studying both mouse models and human cohorts. Right now, I am particularly looking at factors that affect the invasiveness of the placenta, such as endoreplication in trophoblast giant cells in mice, and previous uterine damage in humans.

Outside of lab, I mainly enjoy staying active. I’ve been dancing salsa for 6 years, and I am currently the director of Los Salseros de Stanford. I recently found a new hobby in rock climbing, and I love just being outdoors and enjoying the sun.
kbadillo@stanford.edu

Sharon Briggs

Sharon Briggs

Graduate Student

I am interested in understanding human reprogramming to iPSCs. I focus specifically on X chromosome inactivation, and tracking changes to the X chromosome over reprogramming and time in culture. In addition, I’ve taken a single cell, gene expression approach to try to uncover predictive patterns of expression that signify a certain cell fate. 

Outside of lab I love soccer, baking, craft beer, weight lifting, and hosting dinner parties!

sfbriggs@stanford.edu

Jessica Chang

Jessica Chang

Graduate Student

Since my time in the Baker Lab, I have been deeply engrossed in the remarkable capacity for Xenopus tropicalis tadpoles to regenerate.  I am broadly interested in understanding how collections of genes interact over such a developmental time series.  As such, I have been involved in utilizing large scale sequencing approaches to systematically identify and characterize patterns of activity that may characterize key biological processes involved in regeneration.

Outside of lab, I’m a huge fan of photography, tennis, and really incredible reality television!

jchang8@stanford.edu

Eduardo Gonzalez-Maldonado

Eduardo Gonzalez-Maldonado

Graduate Student

Hi, I’m Eduardo!

I am interested in how major developmental pathways such as the Nodal signaling pathway diversify their downstream effects on gene activation and morphogenesis using a limited amount of effectors depending on different developmental contexts. In Xenopus, the Nodal signaling pathway is involved in specification of mesendoderm, gastrulation and left-right asymmetry. Several Nodal ligands act through type I and type II receptors, resulting in phosphorylation and activation of receptor-activated SMADs. Once activated, the SMADs enter the nucleus and associate with other binding partners such as FOXH1, E2A and HEB, which modify the affinity of the SMAD complex for different sites in the genome. Currently, I am using ChIP-Seq to assess changes in the occupancy of SMAD binding sites in the genome after individual knockdown of Nodal ligands and SMAD binding partners like E2A. Research suggests that changes in the kinetics of SMAD shuttling between cellular compartments results in differential gene expression. Along with Andrea Wills, I am planning to use GFP fusion and bimolecular fluorescence complementation experiments to study the effects or different Nodal ligands on the shuttling of SMADs and their binding partners between the cytoplasm and the nucleus.

egm25001@stanford.edu

Chris Kaelin

Barsh Lab Member

Hi, I’m Chris!

kaelin@stanford.edu

Hermie Manuel

Hermie Manuel

Barsh Lab Member

Hi, I’m Hermie!

hermie@stanford.edu

Kelly McGowan

Kelly McGowan

Barsh Lab Member

Hi, I’m Kelly!

smells@stanford.edu