Phillip is an Associate Teaching Professor and Assistant Department Head in the Computational Biology Department at Carnegie Mellon University, where he teaches a variety of courses across mathematics, computer science, and computational biology. He received a Ph.D. in mathematics from UC San Diego, where he co-founded Rosalind, an online platform for learning bioinformatics. He loves building projects in online education and is also the founder of Biological Modeling and Programming for Lovers.
Pavel is Ronald R. Taylor Professor of Computer Science at the University of California, San Diego. He holds a Ph.D. from Moscow Institute of Physics and Technology, Russia. He is a Howard Hughes Medical Institute Professor (2006-present), an Association for Computing Machinery Fellow (2010), and an International Society for Computational Biology Fellow (2012). In addition to Bioinformatics Algorithms, he has authored the textbooks Computational Molecular Biology: An Algorithmic Approach (2000) and An Introduction to Bioinformatics Algorithms (2004) (jointly with Neil Jones).
Meet the development team
Olga works as a Bioinformatics Data Scientist at the Chan Zuckerberg Biohub. She received her Ph. D. in Bioinformatics and Systems Biology from the University of California, San Diego. She holds an M.S. in Bioinformatics from the University of California, Santa Cruz and B.S. degrees in Mathematics and Biological Engineering, from the Massachusetts Institute of Technology. She enjoys blogging about open-source software, dance, and playing cello.
Niema is an Assistant Teaching Professor in the Computer Science & Engineering Department at the University of California, San Diego (UCSD). He works on computational biology, with a research focus on HIV phylogenetics and epidemiology. He also places a heavy emphasis on teaching, namely on the development of online educational content, primarily Massive Adaptive Interactive Texts (MAITs).
Son is the founder and Chief Scientific Officer at BioTuring. He previously completed postdoctoral research at Salk Institute. He received his Ph. D. in Computer Science and Engineering from the University of California, San Diego. His research interests include graph theory, genome assembly, comparative genomics, and neuroscience. Besides research, he enjoys walking meditation and gardening.
Mike is a postdoctoral researcher in the Computer Science & Engineering department at the University of California, San Diego. He holds a Ph. D. in Biology from Komarov Botanical Institute. His research interests include comparative genomics, species conservation, and molecular evolution. He has contributed to several MOOCs and won a 23andMe Education Honorable Mention Education Grant. He enjoys raising his child and volunteering in social programs.
Kai is a postdoctoral fellow at the Ludwig Institute for Cancer Research, San Diego. He received his Ph.D. in Bioinformatics from the University of California San Diego. His research interests include network biology, single-cell genomics, and transcriptional regulation. He enjoys programming, basketball, and badminton.
This textbook was greatly improved by the efforts of a large number of individuals, to whom we owe a debt of gratitude.
The development team, as well as Laurence Bernstein, Ksenia Krasheninnikova, Max Shen, and Jeffrey Yuan, implemented coding challenges and exercises, rendered figures, helped typeset the text, and offered insightful feedback on the manuscript. Glenn Tesler provided thorough chapter reviews and even implemented some software to catch errors in the early version of the manuscript!
Robin Betz, Petar Ivanov, James Jensen, and Yu Lin provided insightful comments on the manuscript in its early stages. David Robinson was kind enough to copy edit a few chapters and palliate our punctuation maladies.
Randall Christopher brought to life our crazy ideas for illustrations throughout the book, including the chapter header cartoons and the textbook cover. Andrey Grigoriev and Max Alekseyev gave advice on the content of Chapter 1 and Chapter 6, respectively. Martin Tompa helped us develop the narrative in Chapter 2 by suggesting that we analyze latent tuberculosis infection.
Nikolay Vyahhi led a team composed of Andrey Balandin, Artem Suschev, Aleksey Kladov, and Kirill Shikhanov, who worked hard to support an online, interactive version of this textbook used in our online courses on Coursera.
To help with solving homework problems, Parker Côté and Ryan Eveloff have helped compile a collection of test datasets for our programming assignments.
Our students on Coursera, especially Mark Mammel, Isabel Lupiani, Erika Ramírez and Dmitry Kuzminov, found hundreds of typos in our preliminary manuscript. Mikhail Gelfand, Uri Keich, Hosein Mohimani, Son Pham, and Glenn Tesler advised us on some of the book’s “Open Problems” and led Massive Open Online Research projects (MOORs) in the first session of our online course.
The Big Data to Knowledge Program at the National Institutes of Health, as well as Howard Hughes Medical Institute and the Russian Ministry of Education and Science generously gave their support for the development of the online courses accompanying this textbook. The Bioinformatics and Systems Biology Program and the Computer Science & Engineering Department at the University of California, San Diego provided additional support.
Finally, our families gracefully endured the many long days and nights that we spent poring over manuscripts over the last several years; they helped us preserve our sanity along the way.
Phillip and Pavel