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Cancer Computational Methods Expert Martin Aryee, PhD Joins Data Science Faculty

The Department of Data Science at Dana-Farber Cancer Institute is excited to announce that Martin Aryee, PhD joins our faculty on January 1, 2022.

Dr. Aryee’s research involves the development and application of statistical methods for genomics. Most of his work centers on cancer epigenomics, with a focus on the role of spatial organization within tumors at scales ranging from DNA folding to the tumor microenvironment. He is also involved in the development of tools to ensure the safe translation of CRISPR-based genome editing technologies into clinical use. His research contributions include several methods for the analysis of DNA methylation data and insights into the role of disordered chromatin organization in cancer.

Dr. Aryee will be Associate Professor, Pathology Department at Harvard Medical School and an independent faculty member in Data Science. He will also lead a team of staff scientists as the Director of Hematologic Malignancies, Biostatistics and Computational Biology at Dana-Farber. He received his PhD in Biostatistics from the Harvard T.H. Chan School of Public Health, and completed his post-doctoral work at Johns Hopkins University School of Medicine.

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The American Society of Hematology Honors Donna S. Neuberg with the 2021 Exemplary Service Award

(WASHINGTON, Oct. 5, 2021) – The American Society of Hematology (ASH) will recognize Donna S. Neuberg, ScD, senior statistician for the Leukemia, Lymphoma, and Benign Hematology Programs at Dana-Farber Cancer Institute, with the 2021 Exemplary Service Award for her years of service and dedication to ASH and to hematology.

The Exemplary Service Award was established in 1998 to recognize an individual whose outstanding service, extending over a period of years, has significantly advanced the interests of the Society. ASH President Martin S. Tallman will present this award during the 63rd ASH Annual Meeting and Exposition this December that will take place both in-person in Atlanta, Georgia, and virtually.

“Dr. Neuberg is an outstanding colleague and mentor as well as a world-class statistician with an encyclopedic knowledge of hematology. Through her decades of dedicated service in ASH training programs such as TRTH and CRTI, Dr. Neuberg has empowered innumerable investigators to design clinical trials with the highest standards of scientific rigor and statistical methodology,” said ASH President Martin S. Tallman of Memorial Sloan Kettering Cancer Center. “We value Dr. Neuberg’s contributions to shaping the future of hematology and of ASH.”

After receiving her ScD in Biostatistics from the Harvard School of Public Health, Dr. Neuberg joined the Dana-Farber Cancer Institute as a biostatistician. She currently serves as the senior statistician for the Leukemia, Lymphoma, and Benign Hematology Programs at Dana-Farber, where her research interests focus on the planning and analysis of studies that integrate laboratory outcomes at the genome, transcriptome, or proteome level with clinical and demographic information.

From 2014 to 2017, Dr. Neuberg served on the editorial board of Blood, ASH’s peer-reviewed journal. She has also demonstrated her commitment to ASH through her service as a statistician for the ASH Research Collaborative (ASH RC) Data Hub. Her expertise was integral in the development of the ASH RC COVID-19 Registry for Hematology data summaries, figures, and publications.

Dr. Neuberg has served as a dedicated mentor for the ASH-European Hematology Association (EHA) Translational Research Training in Hematology (TRTH), a year-long training program helping early-stage researchers build successful hematology research careers, since its inception in 2010. Dr. Neuberg is celebrated by TRTH participants for empowering trainees to take steps toward becoming not only rigorous scientists, but also thoughtful citizens of the international hematology community. In addition to celebrating the help they received in bringing their research to exceptional standards, trainees laud Dr. Neuberg for her generosity with her time and energy, and her ability to inspire them personally and professionally.

Dr. Neuberg’s deep passion for training the next generation of scientists is also reflected in her long-standing service as a mentor in the ASH Clinical Research Training Institute (CRTI), a year-long education program for hematology fellows and junior faculty at academic medical centers. She has shared her expertise as CRTI faculty from 2010 to 2016, and has participated in the study sections for the CRTI and the ASH Scholar Award. Her mentees and scholars credit her with imbuing them with her own unmistakable passion for sensible study design, experimental rigor, and enjoyment of a life in biomedical investigation.

Full press release from ASH Hematology

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Heng Li, PhD Receives 2021 Sloan Fellowship

Heng Li, PhD, Assistant Professor of Biomedical informatics, Dana-Farber Cancer Institute and Harvard Medical School, is the recipient of a 2021 Sloan Fellowship from the Alfred P. Sloan Foundation.

From the Sloan Foundation press release: “Awarded annually since 1955, Sloan Fellowships honor extraordinary U.S. and Canadian researchers whose creativity, innovation, and research accomplishments make them stand out as the next generation of scientific leaders. A Sloan Research Fellowship is one of the most prestigious awards available to young researchers, in part because so many past Fellows have gone on to become towering figures in the history of science.”

“Heng is one of the most prolific idea generators and tool builders in computational biology,” says Rafael A. Irizarry, PhD, department chair, and professor of Applied Statistics at Harvard T.H. Chan School of Public Health. “He is also one of the most humble academics I know, so I am particularly delighted that he has been honored with this prestigious award.”

An expert in analyzing next-generation genomic sequencing data, Li is the principal developer of several software projects. His portfolio includes: SAMtools, the Burrows-Wheeler Aligner, the Mapping and Assembling with Quality (Maq) alignment tool, Treesoft, and TreeFam. The Li Lab at Dana-Farber Cancer Institute studies advanced computational methods to analyze large-scale biological sequence data and to solve practical problems in biomedical research.

“Heng was one of the first people to develop fast and memory-efficient software for processing genomic data sets,” says Irizarry. “His technology took cancer research to a whole new level. It allows us to process in minutes what previously took months.”

Li earned his doctorate from the Institute of Theoretical Physics at the Chinese Academy of Sciences in 2006. Prior to his appointment at Dana-Farber, he investigated genetic causes of disease at the Broad Institute of MIT and Harvard.

Alejandra Avalos-PachecoDana-Farber
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Alejandra Avalos-Pacheco, PhD Wins 2020 Savage Award

Alejandra Avalos-Pacheco, PhD, a postdoctoral fellow in the Lorenzo Trippa lab and the Harvard Program in Therapeutic Science (HiTS) within the Harvard-MIT Center for Regulatory Science (CRS), has won the 2020 International Society of Bayesian Analysis Savage Award. The Savage Award, named for pioneering statistician Leonard J. Savage, recognizes two out-standing doctoral dissertations in Bayesian econometrics and statistics, one each in Theory & Methods and Applied Methodology.

Dr. Avalos-Pacheco won in the category Applied Methodology for her PhD thesis on“Factor regression for dimensionality reduction and data integration techniques with applications to cancer data.” She defended her thesis on March 2019 at the University of Warwick as part of her PhD studies in the joint Oxford-Warwick PhD program on Big Data, and was supervised by Richard Savage (University of Warwick) and David Rossell (Universitat Pompeu Fabra). “My thesis develops a practical solution to address heterogenous high-dimensional data integration using Bayesian techniques, while also offering practical foundational and computational developments,”  says Dr. Avalos-Pacheco. “ My results show that batch effects and data integration are practically-relevant in cancer genomics and applies the methodology to ovarian, lung and pancreatic datasets.”

Congratulations, Dr. Avalos-Pacheco!

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Collin Tokheim, PhD Wins New Damon Runyon Cancer Research Foundation Quantitative Biology Fellowship

Collin Tokheim, PhD, a postdoc in the X. Shirley Liu lab, has been awarded a Damon Runyon Cancer Research Foundation Quantitative Biology Fellowship. Dr. Tokheim’s mentors are X. Shirley Liu, PhD, and Eric S. Fischer, PhD, at Dana-Farber Cancer Institute, Boston.

“The first class of Damon Runyon Quantitative Biology Fellowship Awardees launched their research in novel directions that may lead to the next breakthroughs in cancer research. Nine brilliant young scientists will apply their quantitative skills to design innovative experiments and interpret massive data sets that may help solve important biological and clinical problems. The awardees were selected by a distinguished committee of leaders in the field.

Dr. Tokheim is developing computational models that can identify degradable proteins that are linked to the development of human cancers. Unlike traditional drugs that bind and block the activity of key proteins in cancer cells, a new generation of drugs can eliminate proteins by hijacking the protein degradation machinery within cells. By leveraging big data from thousands of tumor profiles and a novel statistical and deep learning model, he will conduct an unbiased search for candidate proteins that can be verified experimentally. This research may lead to the development of drugs targeting protein degradation as a potent and selective way to treat a variety of human cancers.

Each postdoctoral scientist selected for this unique three-year award will receive independent funding ($240,000 total) to train under the joint mentorship of an established computational scientist and a cancer biologist. Damon Runyon has created this new funding mechanism to encourage quantitative scientists (from fields such as mathematics, physics, computer science and engineering) to pursue careers in cancer research. This support will help create an elite cadre of computational biology leaders trained in quantitative and biological sciences—scientists who are capable of traversing both worlds with ease and are comfortable speaking both languages fluently.

“Because this is in essence a new field at the nexus of traditional cancer research and data science, it is critical to draw fearless and brilliant young computational scientists to these problems to drive the field forward,” said Aviv Regev, PhD, of the Broad Institute and inaugural Chair of the Quantitative Biology Fellowship Award Committee.”

Full release: Damon Runyon Cancer Research Foundation

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Rafael Irizarry, PhD Elected International Society of Computational Biology Fellow

Rafa Irizarry, PhD, Professor of Biostatistics at Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, has been elected a 2020 International Society of Computational Biology Fellow.

From ISCB:

“The ISCB Fellows program was created to honor members who have distinguished themselves through outstanding contributions to the fields of computational biology and bioinformatics. Begun in 2009, 2020 marks the 11th anniversary of the program. In early December of each year, ISCB has sought Fellow’s nominations from our members, with eligibility restrictions based on selection criteria focused most heavily on the significance of scientific contributions.

Dr. Irizarry was selected for his pioneering work in expression analysis and development of statistical methods for expression analysis, which are some of the most impactful in the entire field.”