How to do Research Part 2: Writing & Publishing
This session will cover writing and publishing papers and code. How to write a paper; How to publish -- conferences, journals, open access; what is and isn’t plagiarism (including self-plagiarism), how/when to cite other references, dual submissions, and author ordering; How to publish code and how you can use the code of others. It will also cover common ethical issues, e.g., what to do if you find a mistake in a paper you published.
Panelists:
Luther Tychonievich he/him/his
Teaching Associate Professor
Luther Tychonievich began at Illinois in August 2022; prior to that he spent 9 years as teaching faculty at the University of Virginia. His primary academic activity is education: education of students, teaching assistants, faculty, and computer science educators at every level. He has taught across the CS curriculum (computer organization, data structures, discrete mathematics, graphics, programming, software development, theory of computation) as well a about equity and inclusion (active recruiting, inclusive pedagogy, stereotype threat) and education (assessment, tutoring and teaching methods).
Luther was the 2017 recipient of the Harold S. Morton Jr Award for Teaching and the 2015 and 2019 UVA ACM student chapter's Professor of the Year award winner. He currently serves on Illinois CS's Broadening Participation in Computing (BPC) committee, chairing the BPC committee's subcomittee on data, and as a Director of Academic Data Analysis. Luther is active in family history data standards where he is the chair of the board for FHISO, a managing editor of GEDCOM, and the technical lead for FHMWG; he also serves on the program committee for various conferences in CS education and as a Broadening Participation in Computing consultant for BPCnet.org, an NSF-funded service of the CRA. While at UVA he served as the chair of the Undergraduate Curriculum Committee and a member of the Diversty, Ops, Advisory, BA CS program committees, BS CS program committee, and the steering committee of the Center for Innovation in Computing Education and Outreach. He also serves on the program committee for various conferences in CS education.
Luther earned his Ph.D. degree in computer science from the University of Virginia, M.S. and B.S. degrees in computer science from Brigham Young University, and A.A. and A.S. degrees from Lakeland Community College. As a community college alumnus, he is an advocate for community colleges generally and the community college to univeristy pipeline.
Tandy Warnow
Grainger Distinguished Chair in Engineering
Professional development: Warnow received her PhD in Mathematics at UC Berkeley (1991) under the direction of Gene Lawler, and did postdoctoral training with Simon Tavare and Michael Waterman at the University of Southern California (1991-1992). After positions at Sandia National Laboratories (1992-1993), University of Pennsylvania (1993-1998), and the University of Texas (1998-2014), she joined the University of Illinois at Urbana-Champaign as a Founder Professor of Engineering. She is now Associate Head for Computer Science, and has affiliate faculty appointments in Bioengineering, Electrical and Computer Engineering, Mathematics, Statistics, and several biology departments.
Awards: She received the National Science Foundation Young Investigator Award in 1994, the David and Lucile Packard Foundation Award in Science and Engineering in 1996, a Radcliffe Institute Fellowship in 2006, and a Guggenheim Foundation Fellowship for 2011. She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the International Society for Computational Biology (ISCB) in 2017.
Teaching: At the undergraduate level, Warnow teaches courses in discrete mathematics and algorithm design and analysis, and use problems from computational biology to demonstrate the applications of these skills and techniques to real world problems. At the graduate level, Warnow teaches CS 581: Algorithmic Computational Genomics. The main focus of CS 581 is on phylogeny (evolutionary tree) estimation, but the course also covers the related problems of computing multiple sequence alignments, genome assembly, and analyzing microbiomes. Students will learn the mathematical and computational foundations in these areas, read the current literature, and do a team research project. The techniques involved include discrete algorithms, graph theory, simulations, and probabilistic analysis of algorithms. Course website: http://tandy.cs.illinois.edu/581-2018.html.
Leadership roles: Warnow has had several leadership roles in international consortia, including Genome 10K, the Avian Phylogenomics Project and the Thousand Plant Transcriptome Initiative. She was also the Director of the CIPRES (Cyber-Infrastructure for Phylogenetics Research) project (funded by a large ITR grant from NSF), which had more than 10 universities around the country, trained more than 50 PhD students (including many of the computer scientists now working in computational biology), and led to the establishment of the CIPRES Gateway. She also chaired the NIH study section for Biodata Management and Analysis (BDMA), and was the main program officer at NSF for the BIg Data solicitation.
Research contributions: Warnow's main research is in algorithms for statistical estimation problems in computational biology and historical linguistics. Among her major contributions are advances in mathematical foundations in phylogenetics and methods for multiple sequence alignment, for species tree estimation from multi-gene datasets, and for metagenomic taxon identification. Warnow's collaboration with linguist Don Ringe (Univ of Pennsylvania) led to a rigorous approach to inferring evolutionary histories (both trees and networks) for natural languages, and settled several outstanding conjectures for Indo-European.
Charith Mendis
Assistant Professor
I am an Assistant Professor in the Department of Computer Science at the University of Illinois at Urbana-Champaign. Prior to that, I was a visiting faculty researcher at Google Brain. My broad interests are at the intersection of compilers, program optimization and machine learning. I lead the ADAPT lab. Our current work is focused on two main fronts.
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