Department of Systems Biology News

Emma Watson has been awarded a Young Investigator Grant from The Breast Cancer Alliance. Congratulations Emma!

Read more about research in the Watson Lab here.

Welcome to Nicholas Genovese who recently joined the Youk Lab as their newest Research Associate!

Read more about Nicholas here

The DSB congratulates Nick Harper who was awarded a Ruth L. Kirschstein National Research Service Award Individual Predoctoral Fellowship from the National Cancer Institute to study mechanisms of cell death upon transcriptional inhibition. Read more about Nick and his research here.   Sept, 2023

The Department of Systems Biology Welcomes Ann Xu a new Research Technician in the Youk Lab   Aug, 2023

Elizabeth Shank recently contributed to this Nature Medicine News article about antibiotic resistance. Read the full article here.

Congratulations to Job Dekker on his induction into the National Academy of Sciences on April 28, 2023.

The Department of Systems Biology Welcomes new Postdoc Arun Kumar to the Walhout Lab   May, 2023

Listen as Job Dekker talks about the 3D genome organization of Dinoflagellates and more.

The DSB Welcomes Our New Rotation Students Hanbing Cao (Dekker Lab) Christopher Jahns (Shank Lab) Arshia Kaur (Shank Lab) Claudia Perez (Watson Lab) Alejandra Rivera Nieves (Watson Lab)

The Department of Systems Biology Welcomes Emma Watson as the Newest Faculty Member September 26, 2022 Cancer Chromosome Genetics What are the functional consequences of chromosomal abnormalities in cancer? Over 90% of tumors are aneuploid, with ploidy ranges from sub-2N to more than 4N. Moreover, tumor-associated chromosomal abnormalities are tissue-specific and often highly recurrent.

Marian Walhout, PhD, was Awarded the Chancellor's Medal for Distinguished Scholarship September 15, 2022 By Pat Sargent UMass Chan Medical School Communications   Marian Walhout, PhD, the Maroun Semaan Chair in Biomedical Research and chair and professor of systems biology, was awarded the Chancellor’s Medal for Distinguished Scholarship. Collins said Dr. Walhout is “known as a most respected member of our scientific community, as a dedicated mentor and an inspiring role model for women in science.” This is most fitting for one who has made such a major impact on science and our community,” Collins said. »Read More

Congratulations to Elizabeth Shank September 16, 2022 Congratulations to Elizabeth Shank, PhD, for receiving a MIRA award titled “Investigating the molecules and mechanisms of bacterial cell-cell interactions".

Congratulations to Job Dekker August 08, 2022 Congratulations to Job Dekker, PhD, for receiving a supplement to his NIH UM1 project titled “4D nucleome studies in a mouse progeria early-onset aging model before and after somatic genetic correction in tissues and cells.”  This is a joint project with another UM1 investigator, Dr. Robert Goldman of Northwestern as well as the Somatic Genome Editing Consortium (Dr. David Liu, Broad Institute of Harvard and MIT & Dr. Francis Collins, NIH) and the Cellular Senescence Network (Dr. Nicola Neretti, Brown University & Dr. Jian Ma, Carnegie Mellon Institute)

Congratulations to Hyun Youk  August 01, 2022 Congratulations to Hyun Youk, PhD for a new NIH MIRA Award: "Dynamics in Eukaryotic Dormancy: Gene Expression and Aging".

The Mitchell Lab Welcomes Jacob Furman as an Intern July 25, 2022

The Department of Systems Biology Welcomes Alyxandra Starbard to the Walhout lab as a Research Lab Tech June, 2022

The Department of Systems Biology Welcomes Elodie Killick to the Brewster Lab as an Undergraduate Intern June, 2022

Congratulations to Amir Mitchell, PhD on Receiving a new RO1 Award: “Mechanisms underlying bacterial sensitivity to host-targeted drugs” from the NIH National Institute Of Allergy And Infectious Diseases. June, 2022

The Department of Systems Biology Welcomes Nezar Abdennur, PhD June, 2022

The Department of Systems Biology Welcomes Juliet Bolduc to the Walhout lab as an Undergraduate Intern May, 2022

The Department of Systems Biology Welcomes Daniel Richards to the Walhout Lab as a Research Associate  May, 2022

The Department of Systems Biology Welcomes a Scientific Writer, Caryn Navarro May, 2022

Job Dekker elected to National Academy of Sciences By Colleen Locke UMass Chan Medical School Communications May 04, 2022 UMass Chan Medical School scientist Job Dekker, PhD, was elected to the National Academy of Sciences on May 3 for his contributions to the field of genomics. Dr. Dekker, Howard Hughes Medical Institute Investigator, the Joseph J. Byrne Chair in Biomedical Research, professor of biochemistry & molecular pharmacology and systems biology, is one of 120 newly elected members. »Read More

Congratulations to Dr. Amir Mitchell on Being Promoted to Associate Professor April, 2022

Congratulations to Dr. Johan Gibcus of the Dekker Lab on Being Promoted to Assistant Professor April, 2022

The Department in Systems Biology Welcomes our Newest Rotation Students February, 2022   Jasmine Grasile - Joins the Shank Lab for Rotation Alejandro Felix Mejia - Joins the Youk Lab for Rotation

The Department of Systems Biology Welcomes New Post Doc, Dandan Wang, PhD, to the Walhout Lab! January, 2022   Dandan completed her PhD in the lab of Dr. Rong Zeng at Chinese Academy of Sciences, where she studied mass spectrometry-based proteomics and metabolomics. She is excited to join the Walhout lab to study genetic and metabolic network using C. elegans.

The Department of Systems Biology Welcomes New Post Doc, Rachel Neve, PhD, to the Shank Lab! December, 2021 Rachel completed her PhD in the lab of Dr. Vanessa Phelan at the University of Colorado Anschutz Medical campus, where she studied microbial metabolite production in the context of cystic fibrosis lung infections. She is excited to join the Shank Lab and work with microbial metabolomics to characterize specialized functions carried out by bacteria.

The Department in Systems Biology Welcomes our Newest Rotation Students September, 2021   Ben Clayton - Joins the Lee Lab for Rotation Carmen Li and Gavin Birdsall- Joins the Mitchell Lab for Rotation Amina Bradley - Joins the Shank Lab for Rotation Valeria Sanabria Joins the Youk Lab for Rotation

The Department of Systems Biology Welcomes New Post Doc, Courtney Price, PhD, to the Shank Lab! October, 2021   Courtney completed her PhD in the lab of Dr. George O'Toole at Dartmouth, where she studied microbe-microbe and microbe-host interactions in the context of cystic fibrosis. She is excited to join the Shank lab and begin working with Bacillus subtilis and transparent soil microcosms.

Congratulations to Michael Lee on receiving a 5 year NIH Grant with Pennsylvania State and UMass Amherst:  "Personalization and Failure Testing of Dual Switch Gene Drives in Lung Cancer" October, 2021

The Program in Systems Biology Welcomes our Newest Rotation Students September, 2021   Gavin Birdsall - Joins the Lee Lab for Rotation Vista Sohrab - Joins the Mitchell Lab for Rotation Carmen Li - Joins the Shank Lab for Rotation Lauren Intravaia - Joins the Walhout Lab for Rotation Bradley Class Joins the Youk Lab for Rotation

The Mitchell Lab Welcomes Sydney Schock (Morningside Graduate School of Biomedical Sciences Student) September, 2021

The Youk Lab Welcomes Helen Magana (Morningside Graduate School of Biomedical Sciences Student) September, 2021

The Dekker Lab Welcomes Jiangyuan Liu (Morningside Graduate School of Biomedical Sciences Student) and Xiangru Huo (Bioinformatician) September, 2021

Congratulations to Michael Lee

June, 2021

Michael Lee received a 22 month sponsored research agreement with Hillstream Biopharma. The project is titled “Chemo-genetic profiling to identify mechanisms of action and genetic determinants of sensitivity for novel chemotherapeutics” and this collaboration isto determine the mechanisms of action and chemo-genetic interactions for their novel compound.

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Congratulations to Nicola Minchell on The Marie Curie Global Fellowship!

January, 2021

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We Welcome Nicola Minchell, Visiting Scholar From the University of Cambridge, UK, to the Dekker Lab and Program in Systems Biology

January, 2021

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We welcome Rachel Walker, Research assistant, to the Youk Lab and Program in Systems Biology

January, 2021

Rachel is from Lancaster, MA. She graduated from Brown University, where she studied Biomedical Engineering as an undergraduate. As a Worcester County native, Rachel was lucky enough to get a glimpse of the life of a researcher in high school, when she had an internship over spring break at UMass Chan Medical School itself. That very first experience in a lab sparked a passion for research, and Rachel is excited to begin her professional career at the institution that inspired her. In her spare time, Rachel enjoys reading, puzzles, and scuba diving.

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Congratulations to Dr. Elizabeth Shank on Receiving Tenure

January, 2021

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Hyun Youk, PhD, has received the CIFAR AI Catalyst Grant

November 2, 2020

 

This grant will support of his collaborative project, “Mechanisms of bacterial spatial localization in response to oxidative stress in the gut.”This is a joint award with Professor Carolina Tropini, School of Biomedical Engineering, University of British Columbia.

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Hyun Youk, PhD, has been selected as a member for the EMBO Young Investigator Programme

November 2, 2020

 

EMBO identifies and supports some of the best young researchers in the life sciences. EMBO Young Investigators are group leaders in the early stages of setting up an independent laboratory and the programme helps them develop skills and connections that will help them during this career stage.

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Hyun Youk, PhD, joins the Program in Systems Biology

November 2, 2020

We welcome Dr. Hyun Youk to UMass Chan Medical School as an Associate Professor in the Program in Systems Biology. Hyun and his lab study how living systems transition between being alive and being either truly dead or seemingly dead. They hope to discover common, quantitative principles that underlie life or death transitions. The Youk Lab is particularly eager to unveil principles that allow life to be restarted after it has nearly ceased. Their studies use microbes and mammalian cells (e.g., yeasts and mouse embryonic stem cells), and combine experimental approaches, mathematical models, and ideas rooted in statistical physics to achieve their goal.

Despite the remarkable advances in science, "what is life?" is a long-standing, deceptively simple-to-state question that still remains difficult to address at a deep level. The same is true for the related questions, "what is death?" and "can we revive any dead things?". Every molecule in a cell (e.g., DNA, RNA, protein) is governed by the same laws and principles of physics and chemistry as non-living systems. Yet, unlike non-living systems such as rocks and metals, biomolecules can interact amongst themselves to somehow endow a cell with "life" and all the remarkable behaviors associated with a living state (e.g., making decisions, processing information, cognition). Microscopic cells, too, can interact amongst them to endow life to macroscopic beings. How does a state of living emerge from interacting molecules and cells? The Youk Lab hopes that their work can reveal how small and large-scale networks of molecules and cells engender life, death, and revival. Beneath the molecular mechanisms that are specific to each organism, they believe that there may be quantitative principles that are common to many different cell types and organisms.

Welcome to the PSB!

• Youk Lab Website ≫

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UMass Chan scientists to expand 4D nucleome research with $13 million NIH grants

Job Dekker and Paul Kaufman to investigate architecture of genome as it changes over time

October 23, 2020

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Job Dekker elected to European Molecular Biology Organization

July 07, 2020

 

The European Molecular Biology Organization (EMBO) has elected Job Dekker, PhD, Howard Hughes Medical Institute investigator, the Joseph J. Byrne Chair in Biomedical Research, professor of biochemistry & molecular pharmacology, and co-director of the Program in Systems Biology, to lifetime membership in the organization. Dr. Dekker and 62 other leading scientists from around the world were elected in recognition of their remarkable achievements in the life sciences.

“The new members have contributed to the success of research in the life sciences in Europe and around the world,” said EMBO Director Maria Leptin. “As EMBO members, they can help to shape     the future through EMBO’s work to support talented researchers, bring ideas together, and   promote an international research environment conducive to excellent science.”

• Read More ≫

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UMass Chan students produce hand sanitizer for nearby hospitals amid COVID-19 pandemic

April 10, 2020

In a time of dire need, as medical professionals are working to care for patients during the COVID-19 pandemic and critical supplies of protective gear are running low, students in the Morningside Graduate School of Biomedical Sciences at UMass Chan Medical School produced nearly 130 gallons of hand sanitizer in less than three days to help sustain local hospitals. 

“We wanted to find a way to get the graduate students involved in this effort,” said MD/PhD student Peter Cruz-Gordillo, a member of the UMass Chan COVID-19 student task force. “By the day, COVID-19 cases are increasing. There’s a great need for sanitizer not just for hands, but also to clean off the PPE. We thought this would be a great opportunity to help.”

• Read More ≫

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Elizabeth Shank, PhD, joins the Program in Systems Biology

January 2, 2020

PSB welcomes Dr. Elizabeth Shank to UMass Chan Medical School as an Associate Professor of Microbiology & Physiological Systems. Beth and her lab study microbiolal activities and how they impact their hosts and ecosystem. They are particularly fascinated by the idea that microbes are able to generate and secrete chemical cues (specialized or secondary metabolites) that can act as interspecies signals to influence the physiology and metabolism of their microbial neighbors, and thus contribute to the stability and functioning of complex microbial communities.

The Shank lab's research dissects microbial interactions using traditional microbiology, fluorescent co-culture, bioinformatics, mass spectrometry imaging, and native-like microcosms. They aim to define the molecular basis of how microbial specialized metabolites impact bacterial cellular differentiation, discover chemical tools to kill and modulate pathogens, and dynamically visualize microbial interactions at the single-cell level. Their goal is to gain insights into microbial ecology as well as identifying novel bioactive compounds as potential therapeutics and chemical tools to achieve our long-term goal of manipulating microbial communities to improve host health and the environment.

Welcome to PSB!

• Shank Lab Website ≫

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Amir Mitchell to study cellular decoding of extracellular information with new NIH grant

October 9, 2019

Amir Mitchell, PhD, assistant professor of molecular medicine in the Program in Systems Biology, has received the Maximizing Investigators' Research Award from the National Institute of General Medical Sciences to support research into cellular decoding of signaling dynamics.

Dr. Mitchell will use the five-year, nearly $2.1 million grant to study how intracellular dysfunctions, as mutations, corrupt information encoding and which cellular processes need to be targeted in order to restore proper encoding.

“Healthy cells in the human body use temporal patterns of activity in signaling pathways to encode information about the extracellular environment. Many diseases, foremost cancer, stem from corruption of these temporal signaling patterns which culminates in maladaptive outcomes as uncontrolled cell proliferation,” Mitchell said.

• Read More ≫

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Job Dekker receives the Chancellor’s Medal for Distinguished Scholarship at the 2019 Convocation

September 13, 2019

Job Dekker, PhD, Howard Hughes Medical Institute Investigator, the Joseph J. Byrne Chair in Biomedical Research, professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology, received the Chancellor’s Medal for Distinguished Scholarship. As recipient of the honor, Dr. Dekker will present the plenary lecture at the 20th Annual Research Retreat next month.

Chancellor Michael Collins (pictured right with Dr. Dekker) said Dekker was described by his peers as an “unselfish collaborator,” an “intellectual leader,” and as one who “inspires loyalty in his collaborators.”

• Read More ≫

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Amir Mitchell lab engages high school classes in superbug research via online portal

May 14, 2019

Under the guidance of Amir Mitchell, PhD, assistant professor of molecular medicine in the Program in Systems Biology, 250 high school students from Massachusetts, California and Israel have had the opportunity to research one of medicine’s biggest challenges today—the emergence of superbugs. While students often learn about strains of drug-resistant bacteria in school, Dr. Mitchell’s innovative program is allowing these students to conduct their own investigations into the phenomenon. Mitchell’s lab collaborated with Anat Yarden, PhD, of the Weizmann Institute of Science in Israel, to develop an approach to educate high school students on the emergence of antibiotics resistance through natural selection and rapid evolutionary adaptation. This year, Worcester Tech students (pictured left) were joined by peers in Brockton and San Francisco to monitor, in real-time through live video streams on YouTube and the project’s website, how drug resistance gradually emerged. The educational framework for this project was published in PLoS Biology.

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Job Dekker and colleagues develop new model to examine large mutations in cells

September 11, 2018

Scientists at UMass Chan Medical School, Pennsylvania State University and Florida State University have developed a new computational framework combining three methods of finding large mutations in cancer cells into a single, more complete model. The new method, described in a study published in Nature Genetics, will help researchers find what are called “structural variants” within cancer genomes and learn more about how such cancers begin.

Each of the three methods alone only reveals a portion of the structural variations found in cancer cells, but when the results of all methodologies are integrated using the new model, a more comprehensive view of the genome emerges, said study authors Job Dekker, PhD, Howard Hughes Medical Institute Investigator, the Joseph J. Byrne Chair in Biomedical Research, professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology at UMass Chan, and Feng Yue, PhD, assistant professor of biochemistry and molecular biology at Penn State.

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Ben Landry, Mike Lee and colleagues publish their findings on the diversity in tumor-stromal cell interactions that modulate chemotherapeutic drug sensitivity in Molecular Systems Biology

June 28, 2018

Due to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear, however, what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor microenvironment. Using a large‐scale coculture assay optimized to measure drug‐induced cell death, we identify tumor-stroma interactions that modulate drug sensitivity. Our data show that the chemo‐insensitivity typically associated with aggressive subtypes of breast cancer is not observed if these cells are grown in 2D or 3D monoculture, but is manifested when these cells are cocultured with stromal cells, such as fibroblasts. Furthermore, we find that fibroblasts influence drug responses in two distinct and divergent manners, associated with the tissue from which the fibroblasts were harvested. These divergent phenotypes occur regardless of the drug tested and result from modulation of apoptotic priming within tumor cells. Our study highlights unexpected diversity in tumor-stroma interactions, and we reveal new principles that dictate how fibroblasts alter tumor drug responses.

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PSB faculty receive award for outstanding contribution to curricular development for the Systems and Computational Biology course

April 19, 2018

The faculty members of the Program in Systems Biology received an award for outstanding contribution to curricular development at the 20th annual Educational Recognition Awards ceremony. The Systems and Computational Biology course was cited for excellence in teaching concepts and ideas needed for modern biological analysis. All faculty members from the program contributed to the course development: A.J. Marian Walhout, PhD, Robert C. Brewster, PhD, Job Dekker, PhD, Michael J. Lee, PhD, Amir Z. Mitchell, PhD, and Lutfu Safak Yilmaz, PhD.

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Job Dekker receives 2018 Edward Novitski Prize

February 9, 2018

The Genetics Society of America (GSA) has named Job Dekker, PhD, the recipient of the 2018 Edward Novitski Prize. The award honors investigators who have exhibited “an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research.”

Dr. Dekker, Howard Hughes Medical Institute Investigator, the Joseph J. Byrne Chair in Biomedical Research, professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology at UMass Chan Medical School, is recognized for scientific contributions that include the development of chromosome conformation capture—a technique that has revolutionized chromosome research.

Chromosome conformation capture, or 3C, allows researchers to study the interactions of chromosomes at resolutions and scales previously impossible to attain. In 3C, chromatin is treated with a crosslinking chemical that causes chromosomal regions that are near each other to be chemically linked together. By isolating these crosslinked regions of chromatin and determining their DNA sequences, geneticists can deduce which parts of the genome are in proximity to each other. Although the foundation of the technique seems simple, no one before Dekker had formulated a practical way to take advantage of it for a high-throughput molecular assay like 3C.

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Study from the Dekker lab and colleagues answers 100-year-old question about how chromosomes get their distinctive X-shape

January 18, 2018

A multi-disciplinary team at UMass Chan Medical School led by Job Dekker, PhD, has unraveled how chromosomes are packaged into their iconic X-shape during cell division. Packaging the genome inside mitotic chromosomes is critical to the faithful transmission of DNA from parent to daughter cells; these findings shed new light on the inner workings of cell division and may provide novel targets for potential cancer treatments.

“Cancer cells are experts at dividing. They do it well, and they do it very fast,” said Dr. Dekker, Howard Hughes Medical Institute Investigator, the Joseph J. Byrne Chair in Biomedical Research, professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology at UMass Chan. “Many cancer therapies take advantage of this fact and attack dividing cells specifically in the hopes of eliminating the cancer. The more we understand about how this process works, the more ways we have to throw a wrench into this machine and disrupt this process.”

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Job Dekker appointed inaugural Joseph J. Byne Chair in Biomedical Research

July 17, 2017

Two newly established endowed chairs at UMass Chan Medical School—the Joseph J. Byrne Chair in Biomedical Research and the Herman G. Berkman Chair in Diabetes Care Innovation—were approved by the UMass Board of Trustees on Monday, July 17, according to Chancellor Michael F. Collins.

Job Dekker, PhD, Howard Hughes Medical Institute Investigator, professor of biochemistry & molecular pharmacology and co-director of the Program in Systems Biology, and Michael J. Thompson, MD, clinical professor of medicine and chief of adult diabetes clinical research, were appointed to the positions, respectively.

The purpose of The Joseph J. Byrne Chair in Biomedical Research is to support the research activities of an accomplished faculty member whose work is advancing the fundamental understanding of human biological systems and offering new and innovative pathways to treat human disease. Dr. Dekker is one of the medical school’s most dynamic and cutting-edge researchers and is the inaugural holder of The Joseph J. Byrne Chair in Biomedical Research.

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