Welcome to BIB

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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 MIND awarded drama therapy grant by National Endowment of the Arts

Xiaoduo Fan, MD, MPH, is principal investigator of a collaboration between UMass MIND and Lesley University to investigate virtual drama therapy for individuals recovering from serious mental illness, who often do not respond to conventional treatment methods.

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.
Teng-Ting (Elaine) Lim, Ph.D.
Zhiping Weng, Ph.D.

Research Faculty

Alper Kucukural, Ph.D.

Senior Software Engineer
Nathan Novod

Postdoctoral Fellows
Kathryn Lord, Ph.D.
Artur Manukyan, Ph.D.
Pranitha Vangala, Ph.D.

Bioinformaticians
Jill Moore, Ph.D.
Nishigandha Phalke
Onur Yukselen

Research Associates
Mannix Burns

Lab Technicians
Brittney Logan

Graduate Students
Greg Andrews
Yuming Cao
Gaurav Chauhan
Kaili Fan
Mingshi Gao
Kyle (Jake) Gellatly
Jack Huey
Xue (Shirley) Li
Kathleen Morrill
Henry Pratt
Thomas Reimonn

Visiting Scholars