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Department photo 2016

Albert Sherman Center

The Program in Bioinformatics and Integrative Biology occupies 7,000 square-feet on the 4th and 5th floors of the Albert Sherman Center (ASC). The ASC cutting edge design integrates research and teaching in an exciting collaborative environment.

Albert Sherman Center

UMass Chan researchers study link between oral microbiome and long COVID

John P. Haran, MD, PhD, is studying neurological long-COVID symptoms in working-age, generally healthy people who were vaccinated prior to infection.

Nature Communications, 12, 73. January 2021

Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes.

The piRNA loci are transcribed by RNA polymerase II in the male germline of placental mammals. Here the authors show that a long first exon or a long unspliced transcript correlates with germline-specific production of piRNA precursor transcripts and mature piRNAs.

Nature, Volume 587 Issue 7833, 12 November 2020

Although genome sequencing is increasingly routine for humans, it remains much less common in most other species, and only a small portion of the diversity of life is represented in genomic databases. In this issue, three papers take steps to redress the balance, exploring uncharted branches of vertebrate evolution. In one paper, Guojie Zhang and colleagues from the Bird 10,000 Genomes Project compare 363 genomes representing more than 90% of avian families, including 267 newly sequenced bird species. In another paper, Elinor Karlsson and her colleagues in the Zoonomia Project describe their analysis of 240 genomes representing more than 80% of placental mammal families, including 122 newly sequenced species. To analyze these massive data sets, both teams used new software called Progressive Cactus, which is described by Benedict Paten and co-workers in the third paper. The software can align thousands of genomes spanning hundreds of millions of years of evolution by reconstructing ancestral genomes using cactus graphs. The cover image reflects this process, using stylized mathematical graphs to highlight the software used and create constellations of some species sequenced in this week’s issue.

Principal Investigators
Andres Colubri, Ph.D.
Manuel Garber, Ph.D.
Elinor Karlsson, Ph.D.
Jill Moore, Ph.D.
Teng-Ting (Elaine) Lim, Ph.D.
Zhiping Weng, Ph.D.

Research Faculty
Alper Kucukural, Ph.D.
Edith Pfister, Ph.D.

Senior Research Scientist
Michelle White, D.V.M., Ph.D.

Postdoctoral Fellows
Carolina Lopes Salomao, Ph.D.
Kathryn Lord, Ph.D.
Artur Manukyan, Ph.D.
Tianxiong Yu, Ph.D.

Bioinformaticians
Pepper Dawes
Natalie Haas
Nishigandha Phalke
Molly Smullen
Onur Yukselen

UX Designer
Yinan Dong

Mobile App Developer
Andonaq Grozdani

Software Engineer
Hung Hong

Research Associates
Kelsey Joyce

Research Data Specialists
Yu Fu
Brittney Kenney

Graduate Students
Greg Andrews
Kelsey Butler
Yuming Cao
Gaurav Chauhan
Shaimae Elhajjajy
Kaili Fan
Mingshi Gao
Thomas Husted
Xue (Shirley) Li
Kathleen Morrill
Henry Pratt
Thomas Reimonn
Shuo (Crystal) Shan
Nicole Shedd
Yuqing Wang

Visiting Scholars