Past Lab News
2021
• A very warm welcome to Will Douglas, a new PhD student.
• The lab’s work on developmental gene regulatory networks was recognized by a 4-year, 1.2 million dollar grant from the National Science Foundation (“Analysis of a Model Developmental Gene Regulatory Network”). This award represents a continuation of more than 30 years of funding for the laboratory from the NSF. The lab also continues to be supported by a 4-year, 2.3 million dollar R24 award from the National Institutes of Health (“A Resource for Developmental Regulatory Genomics”) (V. Hinman, co-PI; RA Cameron and A Deiters, co-investigators), and a five-year, 3 million dollar P41 award from the National Institutes of Health (“Extended Echinobase: a Community Genomics Resource for the Future”) (V. Hinman and P. Vize, co-PIs). The NIH R24 award supports the development of experimental resources for the study of the genomic basis of embryonic development, using the sea urchin as a model system. The NIH R24 award supports Echinobase, the principal database and public website for echinoderm genomic data.
• Congratulations to Dr. Jimmy Khor (and his co-authors!), whose genome-wide analysis of enhancer activity during early sea urchin development was published in Genomics Research (PDF).
• Congratulations to Dr. Jen Guerrero-Santoro (and her co-authors!), whose study on the DNA-binding behavior of Alx1, our favorite transcription factors, was published in the Journal of Biological Chemistry (PDF).
• Chuck was invited to organize and edit a special volume of Current Topics in Developmental Biology entitled: “Gene Regulatory Mechanisms in Development and Evolution: Insights from Echinoderms.”
• The lab successfully developed new approaches for light-based control of gene expression in sea urchins and other echinoderms (PDF). This work was made possible through a collaboration with A. Bardhan and A. Deiters in the Department of Chemistry at the University of Pittsburgh.
• We continue to love writing reviews on various aspects of our work (PDF #1) (PDF #2).
• Dr. Toms Beatman’s work on a nomenclature system for echinoderm genes was recently accepted by Database and will be appearing very soon! His paper represents part of our work on Echinobase, the public repository of for genomic data related to sea urchins and other echinoderms (PDF).
2019
• A very warm welcome to two Research Associates- Francisco Delgado and Dr. Thomas Beatman.
• Congratulations to Dr. (!) Jimmy (Jian Ming) Khor, who successfully defended his Ph.D. thesis in August. Fortunately for everyone in the lab, Jimmy will be staying on as a postdoctoral fellow.
• The lab continues to be supported by a three-year, $800,000 grant (“Analysis of a Model Developmental Gene Regulatory Network”) from the National Science Foundation (NSF), a 4-year, 2.3 million dollar R24 award from the National Institutes of Health (“A Resource for Developmental Regulatory Genomics”) (V. Hinman, co-PI; RA Cameron and A Deiters, co-investigators), and a five-year, 3 million dollar P41 award from the National Institutes of Health (“Extended Echinobase: a Community Genomics Resource for the Future”) (V. Hinman and P. Vize, co-PIs). The NSF award represents a continuation of more than 28 years of funding for our laboratory from the NSF. The NIH R24 award supports the development of experimental resources for the study of the genomic basis of embryonic development, using the sea urchin as a model system. The NIH R24 award supports Echinobase, the principal database and public website for echinoderm genomic data.
• Congratulations to Drs. Khor and Santoro, whose genome-wide analysis of Alx1 targets was published in Development (PDF).
• Chuck was an invited, plenary speaker at the 15th International Conference on Biomineralization in Munich, Germany.
• The lab published an exciting new paper in PLOS Biology that examined cell type evolution and the control of embryonic cell fates by competition for a signaling ligand (PDF). This paper was highlighted by The Node, an online community website for developmental biologists.
• Best of luck to Dr. Kate Buckley, who left the lab to begin a tenure-track position at Auburn University.
• The lab contributed two papers to a volume of Methods in Cell Biology devoted to sea urchins and other echinoderms (PDF) and (PDF).
• The lab received supplemental funding from the NIH to obtain a state-of-the-art microinjection workstation. This will have a major impact on our work by facilitating the introduction of DNA constructs (BACs and plasmids), mRNAs, lineage tracers, CRISPR reagents, and other molecules into fertilized eggs.
• Congratulations to recent lab graduates on their new successes: Nathalie Chen (former undergraduate researcher) has been accepted into the MD/PhD program at the University of Pittsburgh. Dr. Tanvi Shashikant will be moving from McKinsey and Company to Ginkgo Bioworks, a biotechnology company. Dr. Ashrifia Adomako-Ankomah has started a new position at Palladian Partners, a science communication company.
2018
• A warm welcome to four new members of the lab: Dr. Jennifer Guerrero Santoro (Research Associate), Dr. Katherine Buckley (Principal Research Biologist), Dr. Daniel Samorodnitsky (Postdoctoral Fellow), and Cam LaJeunesse (first-year Ph.D. student).
• The lab continues to be supported by a three-year, $800,000 grant (“Analysis of a Model Developmental Gene Regulatory Network”) from the National Science Foundation (NSF) and by a 4-year, 2.3 million dollar grant from the National Institutes of Health (“A Resource for Developmental Regulatory Genomics”) (V. Hinman, co-PI; RA Cameron and A Deiters, co-investigators) The NSF award represents a continuation of more than 28 years of funding for the laboratory from the NSF. The NIH award support the development of experimental resources for the study of the genomic basis of embryonic development, using the sea urchin as a model system.
• Congratulations to Dr. Tanvi Shashikant and Jimmy (Jian Ming) Khor, whose work on the genome-wide identification of PMC enhancers was published in BMC Genomics (PDF).
• Chuck was invited to assemble a special volume of Current Topics in Developmental Biology devoted to echinoderm regulatory genomics.
• Congratulations to Jimmy (Jian Ming) Khor, who was awarded a Glen de Vries Presidential Fellowship for Biological Sciences.
• Welcome to Maxwell Martin and Emily Schneider, Carnegie Mellon students who will be carrying out Summer Undergraduate Research Apprenticeships in the lab.
2017
• Congratulations to Jimmy (Jian Ming) Khor, whose work on the evolution of Alx1 structure and function was published in eLife (Khor and Ettensohn, 2017) (PDF). This paper was highlighted by eLIfe in a special INSIGHT article .
• Congratulations to Dr. Tanvi Shashikant and Jimmy (Jian Ming) Khor, whose work on the genome-wide identification of PMC enhancers was recently accepted by BMC Genomics.
• The lab (with Dr. Veronica Hinman as co-PI, and R. Andrew Cameron and Alexander Deiters as co-investigators) was awarded a 4-year, 2.3 million dollar grant from the National Institutes of Health to establish a Resource for Developmental Regulatory Genomics. This award will support the development of powerful new experimental technologies and community resources for the study of the genomic basis of embryonic development, using the sea urchin as a model system.
• The lab was awarded a three-year, $800,000 grant (“Analysis of a Model Developmental Gene Regulatory Network”) from the National Science Foundation (NSF). The award represents a continuation of more than 28 years of funding for the laboratory from the NSF.
• Chuck contributed an invited article (“Sea urchins as a model system for studying development”) to the Elsevier Reference Module in Biomedical Sciences. (PDF)
• Congratulations to Nathalie Chen, who presented her analysis of PMC enhancers in a poster at the “Meeting of the Minds” symposium on May 2.
• The transfer of genomic resources from the Center for Regulatory Genomics at Caltech (formerly housed in the laboratory of E.H. Davidson) to Carnegie Mellon was completed in April, with the help of Dr. Andy Cameron.
• Congratulations to Dr. Tanvi Shashikant, who successfully defended her Ph. D. thesis (“From genome to morphology: the dissection of a developmental gene regulatory network”) on April 21st.
• Two new papers from the lab were published (Sun et al., 2017 (PDF) and Ettensohn and Dey, 2017 (PDF)).
2016
• Congratulations to Tanvi Shashikant, who has accepted a position with McKinsey and Company, a global consulting firm. She’ll start there shortly after her Ph. D. thesis defense.
• Zhongling’s paper on the role of TGF-beta signaling in skeletogenesis was accepted by Developmental Biology (Link).
• Xian Chang and Nathalie Chen received Carnegie Mellon Small Undergraduate Research Grants (SURGs) to support their research projects.
• The lab’s work on kirrelL, a gene that plays an essential role cell-cell fusion, was published in Developmental Biology (Link).
• Congratulations to (Dr.) Zhongling Sun, who successfully defended her Ph. D. thesis on July 19!
• The 23rd Meeting on the Developmental Biology of the Sea Urchin, co-organized by Chuck, Gary Wessel, Ina Arnone, and Robert Burke, was held at the Marine Biological Laboratory in Woods Hole, MA.
2015
• Welcome to Jian Ming (Jimmy) Khor, a new Ph. D. student, and to Manar Naboulsi, an undergraduate researcher from CMU-Qatar.
• Tanvi Shashikant, was awarded the 2015 Department of Biological Sciences Stupakoff Fellowship for her paper with Kiran Rafiq. (Link)
• Apeksha Atal, Xian Chang, and Nathalie Chen received Carnegie Mellon Small Undergraduate Research Grants (SURGs) to support their research.
• Zhongling’s paper on the signal-dependent regulation of the skeletogenic network was accepted by Gene Expression Patterns. (PDF of MS)
• The lab was awarded a three-year grant (“Analysis of a Model Developmental Gene Regulatory Network”) from the National Science Foundation (NSF). The award is a continuation of more than 25 years of funding from the NSF.
• Kiran and Tanvi’s collaborative work on the architecture of the skeletogenic gene regulatory network was published in Development. (PDF of MS)
• Chuck’s paper on the evolution of the msp130 gene family was published in Evolution and Development. (PDF of MS)
• Welcome to Debbie Dey, a new postdoctoral fellow, and to Iris Yang, a Master’s student in Biomedical Engineering.
• Ashrifia’s review on the role of growth factors in early embryonic cell migration was published in Genesis. (PDF of MS)
• Planning began for the 23rd Meeting on the Developmental Biology of the Sea Urchin, co-organized by Chuck, Gary Wessel, Maria Arnone, and Robert Burke.
• Tanvi’s web-article, “A Day in the Life of a Sea Urchin Lab,” was posted on The Node.
2014
• Zhongling’s paper on the signal-dependent regulation of the skeletogenic network was accepted by Gene Expression Patterns.
• The lab was awarded a three-year grant (“Analysis of a Model Developmental Gene Regulatory Network”) from the National Science Foundation (NSF). The award is a continuation of more than 25 years of funding from the NSF.
• Kiran and Tanvi’s collaborative work on the architecture of the skeletogenic gene regulatory network was published in Development. (PDF of MS)
• Chuck’s paper on the evolution of the msp130 gene family was published in Evolution and Development. (PDF of MS)
• Welcome to Debbie Dey, a new postdoctoral fellow, and to Iris Yang, a Master’s student in Biomedical Engineering.
• Ashrifia’s review on the role of growth factors in early embryonic cell migration was published in Genesis. (PDF of MS)
• Planning began for the 23rd Meeting on the Developmental Biology of the Sea Urchin, co-organized by Chuck, Gary Wessel, Maria Arnone, and Robert Burke.
• Tanvi’s web-article, “A Day in the Life of a Sea Urchin Lab,” was posted on The Node.
• Stephanie Guerra, a former undergraduate researcher now working on her Ph. D. at Harvard University, was awarded a NSF Graduate Fellowship.
• Kiran Rafiq, a former Ph. D. student, accepted a position at Sun Pharma.
• Chuck joined the editorial board of BMC Genomics.
• A prototype of our new Virtual Urchin tutorial (a collaboration with Jason Hodin of Stanford University) went live.