Jeff Kinne
This page is maintained by me, Jeff Kinne. I am a professor of computer science at Indiana State University. I have taught just about every CS course that we offer at the BS and MS levels. I was trained in computational complexity (within theoretical computer science) during my PhD studies and continue to be interested in this area. Since maybe 2015 or so, most of my research work has been in bioinformatics. If you want a laundry list of things I have done, you can see my C.V. (aka resume).
Contents
Contact
I am currently in the midst of moving from Root Hall to Technology Center at ISU. My email address will not change, and I believe my phone number should stay the same as well.
Email: jkinne@indstate.edu (also jkinne@cs.indstate.edu and jeffrey.kinne@indstate.edu all go to the same place).
Phone: office phone - 812-237-3394.
Office: Myers Technology Center (TC), room 301D.
Virtual meetings: ISU uses Teams and Zoom. I am happy to meet on other platforms as well (Google meet, WebEx, Skype, etc.).
Schedule a meeting: https://cs.indstate.edu/jkinne-meeting
Note: I use a separate email account for things not related to ISU and research (e.g., things having to do with my kids' school, scouts, etc.). If you're not sure what email address to use for me, feel free to use any that you have.
Research
Author ordering In CS and mathematics, author ordering is normally alphabetical (so you cannot tell who is the primary author just by looking at the author list). In biology / bioinformatics, author ordering is normally in order of who contributed the most - normally the primary author is listed first, and the director of the laboratory that paid for the research is listed last. Many papers published recently have a statement on author contributions (who did what, etc.) at the end of the paper.
Current projects Projects that I am still actively working on from among those listed below include: differential gene expression analysis, transcription factor binding site analysis, and gene expression analysis in cichlids. For other completed projects, there is always the possibility to improve the results or apply techniques to a new setting.
Posters
Differential gene expression analysis - IAS 2024, 2022 BD4ISU/SURE, 2019 Indiana Academy of Sciences, 2019 ICIBM, 2019 BD4ISU/SURE, 2018 BD4ISU/SURE, 2018 SURF, 2018 SURE
Transcription factor binding site analysis - 2022 BD4ISU/SURE, 2019 BD4ISU/SURE
Transmembrane protein search in prokaryotes - 2021 BD4ISU/SURE
Predicting Drug-Gene Interactions - 2020 BD4ISU/SURE
Gene expression analysis in cichlids - 2021 BD4ISU/SURE, 2020 BD4ISU/SURE
3d printing - 2016 SURE
Large prime searches - 2014, 2013 SURE, 2013 CSUI
Publication list
Isaiah Bartlett, Jeff Kinne, Grace Martin, Kevin Coombes, and Kristopher R. Schwab. A high-throughput gene expression analysis software tool for developmental time series and gene signature analysis of human cardiomyocyte differentiation. F1000 Research, 2024. Under review. full text, software/code
Tara Hoffman, Jeff Kinne, Kyu Hong Cho. Pro-SMP finder-A systematic approach for discovering small membrane proteins in prokaryotes. PLoS One. 2024 Feb 29;19(2):e0299169. full text, pipeline.
Jeff Kinne, Akbar Rafiey, Arash Rafiey, Mohammad Sorkhpar. Vertex Ordering with Precedence Constraints. In: Fernau, H., Jansen, K. (eds) Fundamentals of Computation Theory. FCT 2023. Lecture Notes in Computer Science, vol 14292. Springer, Cham. DOI.
Nick Gabry, Jeff Kinne, and Rusty Gonser. MetaPlex: An Ion Torrent COI metabarcoding workflow and toolkit to increase experimental efficacy and efficiency. manuscript, source code.
Timothy J. Divoll, Veronica A. Brown, Jeff Kinne, Gary F. McCracken and Joy M. O'Keefe. Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows. Molecular Ecology Resources, 2018. abstract, source code.
Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan Rath, Aaron Cox, Siva Naidu and Youping Deng. Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly. BMC Bioinformatics, 18(Suppl 11):382, 2017. full text, presentation (for ugrad CS majors), source code, presented at ICIBM 2016.
Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin R. Hassler, and Randal J. Kaufman. Read-Split-Run: An improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data. BMC Genomics 17(Suppl 7):503, 2016. full text, source code, presented at ICIBM 2015.
Ruiwen Chen, Valentine Kabanets, and Jeff Kinne. Lower Bounds against Weakly-Uniform Threshold Circuits. In special issue of Algorithmica for invited papers from the the 18th International Computing and Combinatorics Conference (COCOON), Volume 17, issue 1, pages 47-75, 2014, doi:10.1007/s00453-013-9823-y. draft PDF, ECCC report.
Jeff Kinne. On TC0 Lower Bounds for the Permanent. In Proceedings of the 18th International Computing and Combinatorics Conference (COCOON), LNCS 7434, pages 420-432, 2012. draft PDF, presentation.
George Karakostas, Jeff Kinne, Dieter van Melkebeek. On Derandomization and Average-Case Complexity of Monotone Functions. In Theoretical Computer Science, volume 434, pages 35-44, 2012. draft PDF
Jeff Kinne, Dieter van Melkebeek, and Ronen Shaltiel. Pseudorandom Generators, Typically-Correct Derandomization, and Circuit Lower Bounds. In the special issue of Computational Complexity for selected papers from The 13th International Workshop on Randomization and Computation (RANDOM), Volume 21, number 1, pages 3-61, 2012. draft PDF, ECCC report.
Jeff Kinne. Deterministic Simulations and Hierarchy Theorems for Randomized Algorithms. Ph.D. dissertation from the Computer Sciences department at the University of Wisconsin-Madison, 2010. PDF, presentation.
Jeff Kinne and Dieter van Melkebeek. Space Hierarchy Results for Randomized and Other Semantic Models. In Computational Complexity volume 19, number 3, 2010, pages 423-475. draft PDF, ECCC report.
Jeff Kinne, Dieter van Melkebeek, and Ronen Shaltiel. Pseudorandom Generators and Typically-Correct Derandomization. In Proceedings of the 13th International Workshop on Randomization and Computation (RANDOM), LNCS 5687, pages 574-587, 2009. PDF, presentation.
Jeff Kinne and Dieter van Melkebeek. Space Hierarchy Results for Randomized Models. In Proceedings of the 25th International Symposium on Theoretical Aspects of Computer Science (STACS), pages 433-444, 2008. PDF, presentation.
Teaching
For some of my recent thoughts on teaching, see teaching thoughts. I tend to update that once a year or few.
And here is the laundry list of links to course websites...
Indiana State University
Summer Honors (high school) - Arificial Intelligence (2017)
GH 101 Computing and Data Science - fall 2021, fall 2018
CS 151 Introduction to Programming - spring 2024, fall 2023, summer 2020, spring 2020, fall 2019, summer 2017 fall 2014, spring 2014, fall 2013, spring 2013 sections 001 and 003, fall 2012 section 001, spring 2012 sections 001 and 003, fall 2011 sections 001 and 002, spring 2011 section 003, fall 2010 section 003
CS 170 Web Programming I - Summer 2016
CS 201 Computer Science I - Summer 2016, spring 2015, spring 2014
CS 203 (formerly 303) Discrete Structures and Computing Theory - spring 2024, fall 2023, spring 2023, fall 2022,
CS 220 Java Programming - spring 2015
CS 302 (formerly 202) Computer Science II - fall 2020, fall 2019, fall 2017, spring 2017, spring 2016
CS 420/520 Theory of Computation - spring 2019, fall 2016, fall 2015
CS 440/540 Graphics Programming - fall 2012
CS 457/557 Database Processing - fall 2012
CS 458/558 Algorithms - fall 2020, fall 2013
CS 459/559 Topics in Computer Science - BD4ISU Summer 2019, BD4ISU Bioinformatics Programming, Spring 2019, Computational Software Packages and Tools, Summer I 2014
CS 469/569 Unix/Linux Administration and Networking - spring 2022
CS 471/571 Operating Systems - Fall 2018
CS 473/573 Computer Networks - fall 2021, spring 2021, spring 2020, spring 2015
CS 475/575 Artificial Intelligence - fall 2011
CS 499 Senior Seminar - fall 2020, fall 2019, information
CS 500 Programming Fundamentals - spring 2024, fall 2023, spring 2023, fall 2022
CS 510 Fast Track Introduction to Programming - spring 2023, fall 2022
CS 559 Topics in Computer Science - fall 2013
CS 609 Web Programming and Applications - fall 2015 (as CS 650-003)
CS 603 Networking and Security - fall 2016
CS 617 Databases, Data Mining, and Big Data - fall 2017
CS 618 Computational Biology - summer 2024, spring 2022
CS 620 Theory of Computation II - spring 2016, spring 2011, fall 2010
CS 658 Algorithms II - spring 2014, spring 2012
CS 670 Concurrent Programming - spring 2021, spring 2013
CS 671 Operating Systems II - spring 2017
CS 695 Computer Science Research - fall 2014, spring 2011
CS 399/699 Computer Science Internship - information
Wisconsin-Madison
CS/Math 240 Discrete Mathematics - summer 2007
CS 810/710 Theory of Computation - spring 2007
CS 310 Problem Solving with Computers - fall 2003 - spring 2005
Other presentations
Other presentations I have given that I have saved...
Biology journal club at ISU on Oct 2, 2019. The intended audience are biology graduate students and faculty. The main goal of the talk is to do a detailed demo of the different tools used to process and analyze RNA sequence data, with a focus on performing differential gene expression analysis. google slides.
CCSC Midwest (Consortium for Computing Sciences in Colleges) on Sept 29, 2018 at the 2018 . The talk gives the current status of K-12 CS education in the state of Indiana. There were new state standards and resources available. It is a good time to be involved in CS Education in Indiana. google slides.
Terre Haute Children's Museum K-4 Coding Camp on Jul 26, 2018. The basic format could work for any age K-8. google slides.
Indiana Academy of Sciences on Mar 15, 2014. The goal of the talk was to give an overview of the records for largest known primes, and a touch of the computation that goes into these computer searches. The intended audience is people who are interested in the topic (fairly broad). PDF.
Midwest Theory Day on Nov 23, 2013. The goal of the talk was to give an overview of the techniques and theorems used in computational searches for the largest (provably) known prime numbers. The intended audience is math and CS graduate students and faculty. PDF.
Capital University on Feb 4, 2013, Ohio Northern University on Feb 14, 2013, and Indiana State University on April 17. The goal of the talk was to introduce some research topics in the area of randomized algorithms and derandomization through some examples and considering the best algorithms known for primality testing. The intended audience was math and CS students. PPTx.
Panel discussion on undergraduate research at ISU on October 3, 2012 and October 9, 2012. The goal of the talk is to share my experiences with undergraduate research - as it applies to Math and CS students at ISU. The audience was an interdisciplinary group of faculty. PDF.
Math and CS Department Seminar on March 21, 2012. The goal of the talk was to give an overview of some of the important results in lower bounds in theory of computing. For many problems, we think they are intractable (require exponential time to solve), but this has not been proved yet. This talk looks at some things that are known. At the end is a mention of my own work in this area, but that is not the focus of the talk. PDF.
Rose Hulman Institute of Technology Mathematics Seminar on April 27, 2011. The goal with the talk was to give a flavor of the problems looked at within computational complexity, how the problems are posed, some interesting results and open questions, ... The talk is aimed at a general audience with some knowledge of math and computer science. google doc.
ISU Math and CS department seminar on February 11 and 25, 2011. A series of two talks on (1) an algebraic version of the P versus NP problem and (2) connections between obtaining algorithms for polynomial identity testing and lower bounds against algebraic P. The talk is aimed at a general audience who has some knowledge of math and computer science. [PPTx].
Wabash College Math and CS department colloquium on November 16, 2010, on the P versus NP problem. The talk is aimed at a general audience who has some knowledge of computer science. PPT.
My "job talk" that I gave at Indiana State when I was applying for the job. This describes my research within the context of some of the major open questions in computer science. The intended audience is people with some knowledge of computer science. PDF.
Hot topics on theory of computing. This talk, given in March of 2009 at UW-Madison, was given to a group of graduate students at UW-Madison who were on the job market. The idea was to give some flavor about what some of the topics are that theory researchers currently work on. PDF.
Links
These are for my personal use, but I like to have them somewhere I can get to from anywhere.
News/Info: Terre Haute (tribune star | mywabashvalley), Indianapolis | Cincinnati | Google News (es) | Wikipedia (es) | BBC Mundo
Terre Haute/Indiana: weather (NWS | windy.com) (es) | ISU library | Public Library
Non-public: Home repairs and bills | Google Calendar
Astronomy: Sky and Telescope | Heavens Above Terre Haute | Terre Haute Clear Sky Chart | light pollution map | World Wide Telescope | 111 treasures for light-polluted skies (PDF) | Space Time Capsule | Stellarium (web) | SpaceWeatherLive
