Lab Members

Anasuya Dighe, Postdoc

Eric Erkenbrack, Postdoc

Lonjun Wu, Postdoc

Daniel Stadtmauer, Graduate Student
Pranav Kantroo, Graduate Student

Jamie Maziarz, Research Associate

Rachel Bobo, Undergraduate Researcher

Irene Pak, Undergraduate Researcher
Elaine Kosowsky, Lab Assistant
Amy Mulholland, Senior Administrative Assistant

The Boss

Günter P. Wagner

My research program aims at understanding the evolution of complex characters. This problem has many dimensions, including the question how complex characters can evolve by random mutation and selection (i.e. evolvability, the evolution of evolvability, the role of modularity etc), the biological nature of character identity (homology) and the genetic mechanisms for the origin of novel characters. Most of the effort in my lab focuses on the evolution of the gene regulatory network underlying the origin of a novel cell type, the endometrial stromal cells of placental mammals. This research led us towards an investigation of the role of transcription factor protein evolution in particular the origin of novel protein-protein interactions. The second focus is the developmental basis of avian digit identity. Ever since the discovery that birds are dinosaurs we face the problem whether avian wing digits are 1,2, 3, or 2, 3, 4. All these empirical research problems bring with them a host of conceptual and theoretical problems that I also like to address, such as the nature of character individuation, the structure of the homology concept and the role of measurement theory in formulating evolutionary models.

Contact Information

Yale University Department of Ecology & Evoultionary Biology
165 Prospect Street, Osborn Memorial Lab 327A, New Haven, CT 06520
850 West Campus Drive, Integrated Science & Technology Center, 108, West Haven, CT 06516
Phone Number: (203) 737-3091
e-mail address: gunter.wagner[at]yale.edu

Postdocs

Eric Erkenbrack

Gene regulatory networks (GRNs) are assemblages of regulatory genes that cross-regulate each other via protein-protein interactions and cis-regulatory control of transcription encoded in the genome. DNA linkages and post-transcriptional/translational interactions of regulatory genes direct cell-fate decisions in developmental systems. I am interested in how these systems are wired, how they give rise to differentiated cell types and ultimately how they evolve. In the Wagner Lab, I approach these systems-level problems by studying mammalian pregnancy. To better understand how GRNs are wired and the molecular mechanisms driving cell fate decisions, I study the terminal differentiation of decidual cells from their progenitor cell type, endometrial stromal fibroblasts, in the human uterus. We aim to construct a predictive GRN that provides a causal explanation of this cellular differentiation event. Studying mammalian pregnancy also allows us to approach the conceptual problem of how GRNs and cell types evolve. We approach these biological problems comparatively by studying pregnancy in diverse mammalian systems. Importantly, we are studying pregnancy in a marsupial mammal, an outgroup of placental mammals and a system which lacks the terminal differentiation event of endometrial stromal fibroblasts into decidual stromal cells. By comparing and interrogating development of cell types and GRNs in diverse mammalian taxa, we hope to get at the fundamental features of the important concepts of regulatory and developmental evolution.

Anasuya Dighe

I am intrigued by the relation between sequence and structure of biomolecules that elegantly orchestrates complex physiological processes in all life forms. As a computational biologist, my doctoral work at Indian Institute of Science, Bangalore (India) explored the structure of biomolecules. I analyzed the three dimensional organization of proteins from a mathematical perspective by applying concepts of network biology to study the dissemination of information through structure of signaling proteins.

As a post-doctoral associate in the Wagner lab, I am interested in exploring the other aspect i.e. sequence. Among mammals, the degree of placental invasion correlates with vulnerability to malignancy. My research aims to explore this link from an evolutionary standpoint. Specifically, I am interested in performing mathematical analyses on sequence data contained in the transcriptomes of endometrial stromal fibroblasts (ESFs) and skin fibroblasts (SFs) from diverse species in order to elucidate evolutionary determinants governing invasiveness.

Longjun Wu

[in prep.]

Graduate Students

Daniel Stadtmauer

I joined the Wagner lab in 2016 for a senior thesis (Yale College ‘17)

and continued into PhD research. I am interested in studying the

genetic and developmental changes behind evolutionary innovations. My

current research in the lab is focused on the evolution of pregnancy

in mammals, at the intersection of evolutionary biology, reproductive

biology, and immunobiology. My approach to understanding the complex

interactions between fetal and maternal cells is by reconstructing how

they were modified over the course of evolution. Questions I aim to

address are how uterine gene expression has been uniquely modified to

support extended gestation in placental mammals, and in which ways

genes that originally evolved as parts of other pathways, such as the

immune system, stress, and inflammation, have been incorporated into

normal physiology. I am working to apply technology such as

single-cell RNA sequencing to study gene expression in the pregnant

uterus and to characterize the diversity of cell types within the

decidua of placental mammals, the maternal tissue that supports the

fetus during extended gestation.

Pranav Kantroo

I studied mathematics and biology as an undergraduate at the Indian Institute of Science, Bangalore. Over the course, I developed an appreciation for abstraction as a problem-solving tool, especially in the empirical sciences. Drawing the parallels between seemingly unrelated phenomena and appreciating their linkages has been an integral part of my learning experience. This style of learning has molded my research interests — I have gravitated towards areas that draw from each other in search of recurrent motifs. For this reason I am interested in studying the general overarching principles behind how biological systems process information to give rise to complexity, by developing mathematical models and simulations.

Juri A. Miyamae

Inspired by the wiggling snout of a charming African animal called the sengi, my PhD research seeks to understand this specialized structure by exploring larger questions about the evolutionary origins of facial musculature in all mammals and their subsequent modification into amazing structures like mobile nasal probosces. My work aims to synthesize data from the fossil record, development, comparative anatomy, and function to address these questions — which is how I find myself generously co-advised by both the Wagner Lab and the Bhullar Lab in the Department of Geology & Geophysics.

Undergraduate Researchers

Rachel Bobo

Irene Pak

I am a first-year undergraduate student at Yale University. I am interested in studying either Molecular, Cellular, and Developmental Biology (including Biotechnology) or Ecology and Evolutionary Biology. In particular, I would like to delve into organismal biology, physiology, and biotechnology/artificial intelligence. I aim to apply this knowledge to further understand the human body and push the fields of medicine and public health forward. I aspire to attend medical school after graduation, pursuing either an MD or MD/PhD, in the hopes of bridging the gap between research, medicine, and technology.

Research Associates

Jamie Maziarz

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: jamie.maziarz[at]yale.edu

Lab Assistants

Elaine Kosowsky

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: elaine.kosowsky[at]yale.edu

Administrative

Amy Mulholland

Yale University, West Campus – Systems Biology Institute
850 West Campus Drive, Integrated Science & Technology Center, 106, West Haven, CT 06516
e-mail address: amy.mulholland[at]yale.edu

Former graduate students

Andreas Wagner (91-95), Department for Biochemistry, University of Zürich, Switzerland

Bruce Rannala (91-96), Univ. of Alberta, Canada

Bernhard Misof (91-97), Zoologisches Forschungsinstitut und Museum Alexander König, Bonn, Germany

Martin Baatz(91-97), Definiens Imaging GmbH, Germany

Manfred Laubichler(91-97), School of Life Sciences, Arizona State University, AZ

Christian Pazmandi (91-00), University of Innsbruck, Austria

Jason Mezey(95-00), Department of Biological Statistics and Computational Biology, Cornell University, NY

Homayoun Bagheri(95-01), Institute of Zoology, University of Zurich, Switzerland

Ashley Carter (97-02), California State University Long Beach, CA

Maxim Shpak (97-03), University of Texas at Auston, TX

Casey W. Dunn (00-05), Department of Ecology and Evolutionary Biology, Yale University, CT

Jutta Roth (01-05), National Institute for Medical Research, Division of Developmental Biology, UK

Geffrey Stopper(02-06), Sacred Heart University, Fairfield, CT

Deena Emera, (-12), The Buck Institute for Research on Aging, Center for Female Reproductive Longevity and Equality.

Mary Rorick, (-12), Department of Ecology and Evolutionary Biology, University of Michigan.

Jacob Musser, (-15) EMBL Heidelberg, Germany

Koryu Kin, (-15) Cell and Developmental Biology, University of Dundee, UK

Yeonwoo Park, (Undergrad -15), University of Chicago, IL

Former postdocs and visiting faculty

Xinghong Ma

Tom Stewart

I am interested in explaining patterns of biological diversity. My research focuses on vertebrate appendages—their origin and diversification—and attempts to integrate genetic and generic models of development. In particular, I am studying how digit identity is established and how it evolves by employing in vitro and in vivo experimental approaches.

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: tom.stewart[at]yale.edu

Oliver Griffith

My research aims to identify the mechanisms that underpin the evolution of complex phenotypes, such as placentation. My research program integrates genomics, developmental biology, and ecophysiology to understand the mechanism that give rise to the selectable variation that has resulted in the evolution of complex traits.

At Yale I aim to identify the genetic basis for placental functions in lizards, and to identify how the placenta impacts the ecophysiology of lizards in a changing climate. In particular I will show whether placentae can facilitate reproductive plasticity in lizards, identify the genetic basis of this plasticity, and identify if placental plasticity offers a fitness advantage in the warmer, less predictable environments predicted by climate models.

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: oliver.griffith[at]yale.edu

website: www.oligriffith.com

Yujie Zou, Wuhan University, China

Kalle Rytkönen, University of Turku

Peter Krall (93-97), private company

Maria-Jose Blanco (93-95), Madrid, Spain

Rafaelle Callabretta (97-98), CNRS, Rome, Italy

Gavin Naylor (96-97), The School of Computational Science and Information Technology, Florida State University, FL

Thomas Hansen (98-99), University of Oslo, Norway

Xue Liangy (99-00), Ningbo University, PR China

Elena Kramer (99-00), Harvard University, MA

Chi-hua Chiu (97-01), Department of Genetics and Anthropology, Rutgers University, NJ

August Hämmerli (03-04)

Hans Larsson (01-02), Department of Biology, McGill University, Montreal, Quebec, Canada

Tiana Kohlsdorf (04-06), Departamento de Biologia, FFCLRP, Universidade de Sao Paulo, Brazil

Matthew Brandley (08-10), University of Sydney Postdoctoral Fellow, School of Biological Sciences.

Rebecca Young Brim (-12), University of Texas at Austin, Visiting Scientist.

Vincent Lynch (-12), Department of Genetics, University of Chicago, Assistant Professor.

Kathryn Brayer (-12), Cancer Research, University of New Mexico, Post-Doc.

Zhe Wang (-12), East China Normal University, Shanghai.

Mauris Nnamani (-15), Seres Theraputics, Boston MA