Alumni Profiles

Siddharth Annaldasula is a Fulbright Fellow at the Max Planck Institute for Molecular Genetics located in Berlin, Germany. He will be working with Dr. Andreas Mayer as part of his Fulbright Study/Research Grant. Specifically, he will looking at the mechanisms behind the RNA Polymerase II pausing in transcription in various cell developmental models using computational methods. These could provide insight into the epigenetic pausing mechanics that may occur in many diseases, including cancer and other disorders. “The experiences from conducting research, as well as knowledge and skills gained from computer science and biology classes, are directly applicable to my future projects and have immensely influenced my future endeavors.”

I use computational tools to analyze genetic and epigenetic information from our labs. We hope to learn how cell type, drug treatments, and environment influence gene expression. Without a solid understanding of biology and experimental motivation, it’s impossible to apply computational methods effectively. In the BSCB program at Carnegie Mellon, I gained not only a fundamental skill set in computer science, but also a strong foundation in genetics and cell biology. The most important skill I learned, however, was how to better understand and communicate scientific ideas.

I entered the MSCB program with a biology background, hoping to gain the computational skills needed to pursue a career in computational biology. This program not only allowed to me learn the computational fundamentals such as algorithms and programming, but it also led me to gain a solid understanding of computational biology in just two years. At CMU, I joined a research group where I applied concepts I learned in class to perform bioinformatics analyses, giving me a taste of the type of work I’d be doing in the future.

Due to the abundance of research and course opportunities offered in this program, I left CMU equipped with all the technical and professional knowledge I needed to succeed in the industry. As a Computational Biologist at Massachusetts General Hospital (MGH) and the Broad Institute, I am now performing genetic and transcriptomics analyses while working with some of the most respected researchers in the field.

Ben is a research associate at Foundation Medicine, the leading company in precision oncology. Foundation Medicine has profiled over 180,000 patients, deep-sequencing tumor biopsies for somatic alterations in over 400 reported genes and giving doctors invaluable insights into deciding targeted therapy regiments.

Currently, Ben is training to perform programmatically customized research and queries on Foundation Medicines’ database of over 180,000 patient samples for Foundation’s 30+ biopharmaceutical partners plus cutting-edge internal development using his group’s Python code-base and knowledge of cancer biology.

“It’s really great! The variety of work we do for our partners is very interesting and I never thought I would get to do my own research as well—in private industry with only a bachelors. Plus the team’s a rather quirky, colorful group which makes going in every day a lot of fun.”

In the coming months, Ben will be working with investigators at Roche – Genentech, and plans on submitting his research for presentation and possibly publication in the spring.

The MSCB program at CMU is interdisciplinary by nature. Coming into the program as a molecular biologist, I acquired lots of knowledge and skills in coding, algorithms and machine learning. Moreover, it introduced these concepts in the context of biology, which taught me how to leverage biology by using computer science.My job at Roche is to analyze the big data generated by prototypes and to optimize their performance at system integration level. Roche is an exciting and interdisciplinary work space where biologists, chemists work with electronic and software engineers to make the dream of personalized medicine true. The MSCB program helped me to advance my career and greatly expanded my horizon.

As a consultant, I have worked in problem solving in a business context. Although the context is different, my work at CMU prepared me well for day-to-day work. As with computational biology research, often multiple iterations are required to derive a solution acceptable to all parties involved. Similarly, the themes of the scientific process – generating a hypothesis, testing, and correcting the hypothesis – carry over from research to consulting.

Because CMU gave me an early grounding in programming, computational modeling and biology, many fascinating research areas and career paths have opened up for me. I especially appreciate the fact that this field is so diverse, allowing me to tailor my research projects to my evolving interests whether they be more biological (i.e. virology and molecular self assembly) or more computational (i.e. machine learning and optimization).

I’m currently working at a Series B startup called Imagen Technologies whose goal is to reduce diagnostic errors from radiology. My role as a Research Engineer on the AI team involves conducting novel research which will directly help build the product. All of my duties can be viewed as making extensive practical use of the skills I acquired during my MSCB course work at CMU. The math and biology courses strengthened my fundamentals due to which my life is easier every day when I’m statistically analyzing our experimental data.

The solid training in computational biology that I earned at CMU helped me transition from an undergraduate degree in biochemistry to a software engineering job in biotech. My life is no different from that of many other software engineers – coffee, meetings, stackoverflow and coding! Yet a lot of my work involves communicating with computational biologists, understanding their needs and finding solutions for their requirements. Thanks to CMU, I understand our scientists better than other engineers do.

I came to CMU without any experience in programming and algorithms. I quickly connected knowledge in these areas, which prepared me for implementing the algorithms and models that I now design. I also received a biology education in both a broad and systematical way so that I have a better understanding of the data I work with every day. My experience at CMU is definitely the most critical factor in my career success so far.

Throughout my childhood I was very interested in programming and problem solving, but it was really my time at CMU that really turned me into a computer scientist with the formal techniques and practical skills to tackle any problem. Today I am very privileged to put these skills to work to advance on some of the most important issues facing society and medicine, including developing novel algorithms and computational systems for studying the genetic basis of autism spectrum disorders and cancer, as well as related problems in agriculture and bioenergy. As biology is becoming an increasingly data-rich and computational field, completing your undergraduate at CMU, especially in the Computational Biology Department in the SCS, will give you the training and opportunities to truly change the world.

Amoolya Singh (BS CS & Bio ’97) is Chief Computing Officer at Calico Labs, an Alphabet company doing research & drug development in the field of age-related diseases such as cancer and neurodegeneration. Before joining Calico, she led a 30-person bioinformatics & software team at Amyris, a synthetic biology pioneer using yeast fermentation to manufacture small molecules of societal & commercial value. During her time at Amyris, she led the development of the Automated Scientist, a closed-loop modeling & machine learning system funded by DARPA to accelerate the design-build-test-learn R&D pipeline. She obtained her MS and PhD at UC Berkeley in CS and Computational Biology respectively, and completed a postdoctoral fellowshp at the European Molecular Biology Lab in Heidelberg, Germany. Between degrees she worked as a software engineer for a web startup, a Wall Street investment bank, and a multinational telecommunications firm.