CS 399 and 699 and Jeff Kinne: Difference between pages

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CS 399 Cooperative Professional Experience and CS 699 Computer Science Internship are only offered on an arranged basis.  
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 [https://docs.google.com/document/d/1Z5ms6PFZH9H_dUcPF35VNS3u3IYnV2jlxagJVfJ9huE/edit#heading=h.h9dbt25tdl7r C.V.] (aka resume).


This page contains the model syllabus for for the course.
==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''': [http://mailto:jkinne@indstate.edu jkinne@indstate.edu] (also jkinne@cs.indstate.edu and jeffrey.kinne@indstate.edu all go to the same place).


=General Information=
'''Phone''': office phone - 812-237-3394.  
'''Course website''' - https://cs.indstate.edu/web/index.php/CS_399_and_699


'''Your Instructor'''
'''Office''': Myers Technology Center (TC), room 301D.


[https://kinnejeff.com Jeff Kinne], [http://mailto:jkinne@cs.indstate.edu jkinne@cs.indstate.edu] <br>
'''Virtual meetings''': ISU uses Teams and Zoom. I am happy to meet on other platforms as well (Google meet, WebEx, Skype, etc.).
''Office:'' Myers Technology Center, 301D and in Microsoft Teams, phone 812-237-3394 <br>
''Instructor Office Hours:'' by appointment for this course


'''Lecture'''
'''Schedule a meeting''': https://cs.indstate.edu/jkinne-meeting


''Lecture:'' meetings are arranged<br>
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.


'''Prerequisites''' - participation in Professional Practice Program and permission of supervising professor.
==Recommendations==
For those current and former CS students who ask me to write a letter of recommendation for you, please send me the following when you ask for this: course(s) that you took with me as instructor (including the term you took it and your final grade), your resume or cv being used to apply, your unofficial transcript(s), anything else you are submitting with your applications (e.g., cover letter), and anything else to jog my memory about you.


'''Required text'''
Also, if I ask you to schedule a short meeting with me, use my online scheduling link (above) to schedule a 15 minute online meeting. For this meeting I will do a short technical interview with you, so I have more to go on for writing the letter. For the technical interview you can expect questions about data structures and algorithms, programming, and courses you have taken.
None.


=Course Description and Content=
==Projects==
Other than ongoing research projects, a few things I have on my list to do (for courses, or other reasons).


'''Course Description'''
* [https://sycamoresindstate-my.sharepoint.com/:w:/r/personal/jeffrey_kinne_indstate_edu/_layouts/15/Doc.aspx?sourcedoc=%7B6F46EACC-CB89-4A9E-8BD5-823E7040E44E%7D&file=projects%20list.docx&action=default&mobileredirect=true project list] (must be logged in with ISU microsoft account).
* Past projects - put past small projects together onto github or gitlab.


The official description of this course from the catalog is
==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.


"Coordinated computer science work experience in business/industry. A comprehensive written report of the experience, including documented samples of software developed by the student, is required."
'''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.


Experience working on projects outside of the classroom can be a key step in a student’s development. The work of the student will be coordinated with their advisor, and a project report will be given at the conclusion of the experience. Students who do not arrange for outside experiences will be given the option to perform a project within the department to satisfy the requirement.
===Posters===
''Differential gene expression analysis'' - IAS 2024,
[https://cs.indstate.edu/info/posters/bd4isu2022-bartlett.pdf 2022 BD4ISU/SURE],
[https://cs.indstate.edu/info/posters/IAS_Poster-Schwab.pdf 2019 Indiana Academy of Sciences],
[https://cs.indstate.edu/info/posters/icibm2019-tally-.pdf 2019 ICIBM],
[https://cs.indstate.edu/info/posters/bd4isu2019-alvarezdubon-kaur.pdf 2019 BD4ISU/SURE],
[https://cs.indstate.edu/info/posters/bd4isu2018-tally-alvarez.pdf 2018 BD4ISU/SURE],
[https://cs.indstate.edu/info/posters/surf2018-revesz-knight.pdf 2018 SURF],  
[https://cs.indstate.edu/info/posters/sure2018-williamson.pdf 2018 SURE]


==Learning Outcomes==
''Transcription factor binding site analysis'' -
* Experience searching for jobs, preparing application materials, applying for jobs.
[https://cs.indstate.edu/info/posters/bd4isu2022-hoffman.pdf 2022 BD4ISU/SURE],  
* Experience working within a company and with others - being professional, having good communication.
[https://cs.indstate.edu/info/posters/bd4isu2019-bennet-bigler.pdf 2019 BD4ISU/SURE]
* Reflection on which course content and skills were most useful in the position.
* Presentation skills.


=Administrative Information=
''Transmembrane protein search in prokaryotes'' -
[https://cs.indstate.edu/info/posters/bd4isu2021-hoffman.pdf 2021 BD4ISU/SURE]


'''International Student Visa Requirements'''  International students have restrictions as to where and when an internship can be performed. The following restrictions apply.
''Predicting Drug-Gene Interactions'' -
* Must be registered full time (12 credits) unless it is a semester break (summer session).
[https://cs.indstate.edu/info/posters/bd4isu2020-bennett.pdf 2020 BD4ISU/SURE]
* Work 20 hours or less per week during the regular academic term (fall and spring). Can work more during the summer.
* In order to do an internship experience off campus, the following additional restrictions apply to international students.
** Must be registered for CS 399/699 for 3 credits.
** Have been a full-time student for at least one academic year.


'''Credit Hours'''  To be counted as an internship for X credit hours, students should work at least 30*X hours in the internship. For a 3 credit hour internship, the student should normally work at least 90 hours. The type of work must be approved by the student’s advisor ahead of time.
''Gene expression analysis in cichlids'' -
[https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf 2021 BD4ISU/SURE],  
[https://cs.indstate.edu/info/posters/bd4isu2020-gosnell-sagarsee.pdf 2020 BD4ISU/SURE]


'''Final Report and Presentation'''  Students who complete CS 399/699 are required to submit a report at the conclusion of the internship experience, and are required to offer to give a short presentation to the department about their experience (especially in relation to computer science skills used or developed during the experience).
''3d printing'' -
[https://cs.indstate.edu/info/posters/sure2016-golish-watts.pdf 2016 SURE]


'''Nature of Work'''  For an internship experience to be approved, the work must be directly related to computer science. Positions that entail programming are normally approved. Positions that do not entail programming but instead involve systems administration are considered on a case by case basis.
''Large prime searches'' -
[https://cs.indstate.edu/info/posters/sure2014-xiang.pdf 2014],
[https://cs.indstate.edu/info/posters/sure2013-salman-toure.pdf 2013 SURE],  
[https://cs.indstate.edu/info/posters/csui2013-salman-toure.pdf 2013 CSUI]


=Presentation=
===Publication list===
For the presentation to the department after your internship is complete, you should include the following information.
* Position information - company, job title, job description. 
** If possible, include a link to the job posting online. You should save the job posting when you are applying so that you will be able to share it even it is no longer available online.
* Applying for the position - information about the steps in securing the position - what types of interviews, calls, etc.
** Include some details about interview questions at each stage.  If possible, give specific examples; if not, at least give a sense for the types of questions and how you prepared.
** How did you find the position, what was your job search like?
* Job/experience summary - what was your daily experience like, did you work in a team (and if so how was that), what main project did you work on, what tools/languages did you use, what skills/knowledge did you gain on the job, anything you wish you had experience with more before starting
** If possible give a demo of your work environment (what the tools/languages look like when open, etc.).
* Advice to other students based on your experience - in terms of finding positions and in terms of preparing for them.
You should plan on your presentation being 20 minutes or so, and be ready to answer any questions.


=Grading and Assignments=
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. [https://f1000research.com/articles/13-1097 full text], [https://gitlab.com/jkinne/devgea software/code]
<div class="mw-collapsible mw-collapsed" style="overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Summary:</div>
<div class="mw-collapsible-content">
Gene expression analysis has become a standard tool used to determine important genes in biological and biomedical studies. Biologists and medical researchers often work together with programmers, data scientists, or statisticians to complete the analysis after sequencing is performed. I have worked with the lab of biologist Dr. Kris Schwab at Indiana State University and Dr. Kevin Coombes of the Augusta University Medical College of Georgia to develop a software tool, the Developmental Gene Expression Analysis (devGEA), that encapsulates our analysis pipeline and can be used by biologists. The tool is written in the R programming language, uses the R shiny UI, and is available as both a stand-alone program and as a web tool. The Schwab lab and other labs at Indiana State University are now using devGEA to help streamline the analysis of gene expression experiments. devGEA performs the main steps of gene expression analysis: data import, filtering, normalization, scaling, statistical modeling and p value computation, clustering, and visualization. devGEA introduces a correlation-based clustering method that is conceptually simpler than other clustering methods and yields results that are easier to interpret. I was the lead programmer for the tool (together with Isaiah Bartlett and other student researchers) and shared with Drs. Schwab and Coombes in the design and analysis.
</div></div>


The students of this course have the following responsibilities: coordinate with advisor and project supervisor, maintain communication with advisor during the experience, and submit a report to the advisor at the conclusion of the experience.
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. [https://dx.plos.org/10.1371/journal.pone.0299169. full text], [https://cs.indstate.edu/pro-smp-finder pipeline].
<div class="mw-collapsible mw-collapsed" style="overflow:auto;">
<div style="font-weight:bold;line-height:1.6;">Summary:</div>
<div class="mw-collapsible-content">
Prokaryotic chromosomes contain numerous small open reading frames (ORFs) of less than 200 bases. Since high-throughput proteomics methods often miss proteins containing fewer than 60 amino acids, it is difficult to discern if they encode proteins. Recent studies have revealed that many small proteins are membrane proteins with a single membrane-anchoring α-helix. As membrane anchoring or transmembrane motifs are accurately identifiable with high confidence using computational algorithms like Phobius and TMHMM, small membrane proteins (SMPS) can be predicted with high accuracy. I worked with Dr. Kyu Hong Cho at Indiana State University to create a software pipeline to systematically search for novel putative small membrane proteins in prokaryotic genomes. The pipeline is written in Python and uses previous work (Orfipy, Phobius, and Blast) for key steps in the pipeline. The pipeline is available as a web service and can be downloaded and run locally. Numerous parameters can be chosen depending on the needs of the researcher. This resource aims to assist researchers in identifying new SMPs encoded in microbial genomes of interest. We utilized the pipeline on numerous prokaryotic genomes to survey potential novel small membrane proteins across various species. Our findings indicate that each prokaryote possesses many SMPs, with some identified in the intergenic regions of currently annotated chromosomes. More extensively studied microorganisms, such as Escherichia coli and Bacillus subtilis, have more SMPs identified in their genomes compared to less studied microorganisms, suggesting the possibility of undiscovered SMPs in less studied microorganisms. I oversaw the programming and software development, sharing coding duties with student researcher Tara Hoffman. I shared with Dr. Cho in the overall design.
</div></div>


'''The course is graded pass/fail.'''
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. [https://doi.org/10.1007/978-3-031-43587-4_22 DOI].


As part of the experience, the student should develop a resume and apply for a job. Students performing an internship experience within the department will apply to work on an area they are interested in. As part of the internal application process, students will be interviewed and evaluated by the course instructor.
Nick Gabry, Jeff Kinne, and Rusty Gonser. MetaPlex: An Ion Torrent COI metabarcoding workflow and toolkit to increase experimental efficacy and efficiency. [https://doi.org/10.22541/au.166322714.48673632/v1 manuscript], [https://github.com/NGabry/MetaPlex source code].


Students are required to give a presentation to the department on their internship experience. The presentation should include at least the following elements. For each of these, you should include any advice you have to other students as they apply for or start internships/jobs.  
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. [https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12770 abstract], [https://github.com/tdivoll/Bat-Diet-Metabarcoding source code].
* About the position
* Company, job description
* Applying for the position
* How did you find the position?
* Job posting - keep a copy to save and show during the presentation.
* Interview process - how many interviews, what were they like?
* Starting the position
* Was there training? What was it like getting started? Did you have a mentor?
* Job/experience summary
* Summarize what kind of work you did by the end.  
* If allowed by the employer, include screenshot(s) of your development environment(s), list of software used for development, screenshot(s) of demo(s) of your work.
* Your background - skills/knowledge that you feel you were well prepared.
* Your background - skills/knowledge you were not well prepared for.
* Improvement - skills/knowledge you improved through the experience.
* Follow up - has the company asked you to continue in the future or apply for a full time position when you graduate?
* Closing / additional thoughts


You should share your presentation with your supervisor at the company and ask whether they would want any of the slides/information to be redacted (a) when presenting to the department, (b) when posting the presentation internally, (c) for posting the presentation if publicly available.
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.  [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1801-y full text], [https://docs.google.com/presentation/d/1KtcMnQgTUsoFvKGxOGlOLtWa8Dypkyd7LhuF1K0z4Y0/edit?usp=sharing presentation (for ugrad CS majors)], [https://github.com/kinnejeff/read-split-fly source code], presented at ICIBM 2016.


=CS-Specific Items=
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. [https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2896-7 full text],  [https://github.com/xuric/read-split-run source code], presented at ICIBM 2015.
This section contains items that are generally the same for all CS courses (and in particular those taught by this instructor).


==CS Course Policies==
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.  [http://cs.indstate.edu/~jkinne/research/CKK.pdf draft PDF], [http://eccc.hpi-web.de/report/2012/007/#revision1 ECCC report].
Note that this course follows all standard CS course policies.  See http://cs.indstate.edu/info/policies.html for details.


==Lab Help==
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.  [http://cs.indstate.edu/~jkinne/research/perm-tc0.pdf draft PDF], [http://cs.indstate.edu/~jkinne/talks/COCOON2012.pdf presentation].
Please see https://cs.indstate.edu/web/index.php/Unix_Lab_and_Help for information about lab help.


==Course Announcements==
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. [http://cs.indstate.edu/~jkinne/research/mon.pdf draft PDF]
Announcements regarding the course will be made both during class and via email to your @sycamores.indstate.edu email address. You should regularly check this email account or have it forwarded to an account that you check regularly. You can set the account to forward by logging into your indstate.edu email online (if you aren't able to find the option, try a different browser or search online for things like - outlook online forward email setting).


==Classroom conduct==
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.  [http://cs.indstate.edu/~jkinne/research/KvMS.pdf draft PDF], [http://eccc.uni-trier.de/report/2010/129/ ECCC report].
You may not use cell phones, iPods/music players, etc. during class. You should be civil and respectful to both the instructor and your classmates, and you should arrive to class a few minutes before the scheduled lecture so you are ready for lecture to begin on time. You may use your computer during class if you are using it to follow along with the examples that are being discussed. You should avoid spending time on email, Facebook, work on other courses, etc. during the lecture for this class (be fully present wherever you are, make the most of each experience).


==Academic Integrity==
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. [http://cs.indstate.edu/~jkinne/research/Jeff-Kinne-thesis.pdf PDF], [http://cs.indstate.edu/~jkinne/talks/Jeff-Kinne-defense.pdf presentation].
Please follow these guidelines to avoid problems with academic misconduct in this course:


''Homework:'' You may discuss the homework assignments, but should solve and finish them on your own. To make sure you are not violating this, if you discuss with someone, you should DESTROY any work or evidence of the discussion, go your separate ways, SPEND at least an hour doing something completely unrelated to the assignment, and then you should be able to RECREATE the program/solution on your own, then turn that in. If you cannot recreate the solution on your own, then it is not your work, and you should not turn it in.
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.  [http://cs.indstate.edu/~jkinne/research/KM-space-hierarchies-CC.pdf draft PDF], [http://eccc.hpi-web.de/eccc-reports/2007/TR07-134/index.html ECCC report].


''Note on sources:'' if you use some other source, the web or whatever, you better cite it! Not doing so is plagiarism.
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. [http://cs.indstate.edu/~jkinne/research/KvMS_derand_RANDOM09.pdf PDF], [http://cs.indstate.edu/~jkinne/talks/typ-correct-derand.ppt presentation].


''Exams:'' This should be clear no cheating during exams. Each instructor has different rules for what is allowed on exams in terms of notes, etc. If not noted otherwise, you should assume that a quiz or exam is closed notes, no computer, no calculator.
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.  [http://cs.indstate.edu/~jkinne/research/space-hierarchies-STACS2008.pdf PDF], [http://cs.indstate.edu/~jkinne/talks/jkinne-STACS2008-presentation-web.pps presentation].


''Projects:'' You should not copy from the Internet or anywhere else. The project should be your own work. It will be fairly obvious to me if you do copy code from the Internet, and the consequences will be at the least a 0 on the project.
==Teaching==
If cheating is observed, you will at the least receive a 0 for the assignment (and may receive an F for the course), and I will file a Notification of Academic Integrity Violation Report with Student Judicial Programs, as required by the university's policy on Academic Integrity. A student who is caught cheating twice (whether in a single course or different courses) is likely to be brought before the All University Court hearing panel, which can impose sanctions up to and including suspension/expulsion. See http://www.indstate.edu/sjp/docs/code.pdf and http://www.indstate.edu/academicintegrity/ for more information.
For some of my recent thoughts on teaching, see [https://docs.google.com/document/d/1fnNjQ6comNXZ8c_UwsDVLN2TUcp9tJovfF0tqyAdFe8/edit?usp=sharing teaching thoughts]. I tend to update that once a year or few.


Please ask the instructor if you have doubts about what is considered cheating in this course.
And here is the laundry list of links to course websites...


==Office hours (using Teams)==
===Indiana State University===
Office hours will be through Microsoft Teams by default. If you would like to meet in person you should reserve an appointment using http://cs.indstate.edu/jkinne-meeting to reserve an in person meeting with Jeff Kinne. I am normally in my office during my listed office hours, but by making an appointment you can be more certain. For meeting through Teams, you should start Teams in your browser or start the application. You should be logged in using your ISU credentials. Once you have Teams open you can message me to ask me questions or to ask to talk. We can use Teams to message (better than emailing back and forth repeatedly if you have questions about something that you just want to write about) or to talk and share screens (e.g., to take a look at your code). I normally have Teams open on my computer all of the time, including during my office hours. During my office hours I will normally reply right away; at other times I will reply when I get a chance.


==Canvas==
'''Summer Honors (high school)''' -
The course has a canvas site. Click https://indstate.instructure.com/ to go to canvas. You should see this course listed under your courses for the current term. If you don't you may need to click on the Courses icon and then click the "All courses" link. The canvas site is used for giving you your grades, for quizzes/exams, and for getting to online lectures (which are done using Zoom). Announcements will be sent through canvas and to your university email. Links and such will be kept on this website.
[https://docs.google.com/document/d/13_NUmSFZ09gXjRUmwAmL-HWUgTFz6Hmo1KxbU7YZRtY/edit?usp=sharing Arificial Intelligence (2017)]


=ISU Required Syllabus Items=
'''GH 101 Computing and Data Science''' -
The items in this section are required and are the same for every ISU course.
[https://cs.indstate.edu/~jkinne/cs101-f2021 fall 2021],
[https://docs.google.com/document/d/1BbmHvR47jKPkmNzi8J6EYxis0zKYlmLx5GK_2umti3E/edit?usp=sharing fall 2018]


==COVID-19 Information==
'''CS 151 Introduction to Programming''' -
Information specific to CS courses - [[Start of Term Announcements]]
[https://cs.indstate.edu/web/index.php/CS_151 fall 2025], [https://cs.indstate.edu/web/index.php/CS_151_Spring_2025 spring 2025], [https://cs.indstate.edu/web/index.php/CS_151_Fall_2024 fall 2024], [https://cs.indstate.edu/web/index.php/CS_151_Spring_2024 spring 2024], [https://cs.indstate.edu/web/index.php/CS_151_Fall_2023 fall 2023], [http://cs.indstate.edu/~jkinne/cs151-su2020 summer 2020], [http://cs.indstate.edu/~jkinne/cs151-s2020 spring 2020], [http://cs.indstate.edu/~jkinne/cs151-f2019 fall 2019], [https://docs.google.com/document/d/1VEWRjgIMCfVNs_j4RvBGbLcERl7Q02zP_235LFm5DJE/edit?usp=sharing summer 2017] [https://docs.google.com/document/d/1i5BpZicaiHu2Zlaqalkc5_wLuxvoVI-OFzAW2KdIxz8/edit?usp=sharing fall 2014], [http://cs.indstate.edu/~jkinne/cs151-s2014 spring 2014], [http://cs.indstate.edu/~jkinne/cs151-f2013 fall 2013],
[http://cs.indstate.edu/~jkinne/cs151-s2013 spring 2013 sections 001 and 003], [http://cs.indstate.edu/~jkinne/cs151-f2012 fall 2012 section 001], [http://cs.indstate.edu/~jkinne/cs151-s2012 spring 2012 sections 001 and 003], [http://cs.indstate.edu/~jkinne/cs151-f2011 fall 2011 sections 001 and 002],
[http://cs.indstate.edu/~jkinne/cs151-s2011 spring 2011 section 003], [http://cs.indstate.edu/~jkinne/cs151-f2010 fall 2010 section 003]


''Standard ISU language required in all syllabi (read this all once, then skim for your other courses)...''
'''CS 170 Web Programming I''' -
[https://docs.google.com/document/d/1LpYfGDfj5UAGdRDBuIkqJRx0v9GDvkzmfQSxjto5ez8/edit?usp=sharing Summer 2016]


'''CS 201 Computer Science I''' -
[https://docs.google.com/document/d/10N9tS-9aKqBMfd46XjtdUbS0UxXP6x4B9LNpP68rRtg/edit?usp=sharing Summer 2016],
[https://docs.google.com/document/d/1RqUrbIYWtuBRgnNlf1RQNrhttuKZTYjT_q5hBxlScCk/edit?usp=sharing spring 2015],
[http://cs.indstate.edu/~jkinne/cs201-s2014 spring 2014]


Students are expected to adhere to course attendance policies, as stated in the course syllabus. Documented COVID-related absences will be treated like any other serious medical issue. Following University policy, students with a documented, serious medical issue must contact the Office of the Dean of Students for assistance. The Office of the Dean of Students will supply documentation for faculty. Students with a documented serious medical issue should not be penalized and will be given a reasonable chance to complete exams or assignments. Once notification is made, faculty will make reasonable efforts to accommodate the student’s absence and will communicate that accommodation directly to the student. Please note that faculty are not required to accommodate a serious medical issue with virtual content options, like streaming or recorded lectures. To avoid the potential of missing significant class time, students are strongly encouraged to receive the COVID vaccination that has been made available on campus. For more information about the vaccines or to find a vaccination site, go to: https://ourshot.in.gov. The ISU Health Center also administers COVID-19 vaccines by appointment.
'''CS 203 (formerly 303) Discrete Structures and Computing Theory''' -
[https://cs.indstate.edu/web/index.php/CS_203_Spring_2025 spring 2025],
[https://cs.indstate.edu/web/index.php/CS_203_Fall_2024 fall 2024],
[https://cs.indstate.edu/web/index.php/CS_203_Spring_2024 spring 2024],
[https://cs.indstate.edu/web/index.php/CS_203_Fall_2024 fall 2023], [https://cs.indstate.edu/web/index.php/CS_303_Spring_2023 spring 2023], [https://cs.indstate.edu/web/index.php/CS_303_Fall_2022 fall 2022],


Students should contact the Office of the Dean of Students with questions by calling 812-237-3829.
'''CS 220 Java Programming''' -  
[https://docs.google.com/document/d/11WUUvp8mwWOL0i8Et5t-Glsyu61iJAZz0njo78ZAzpg/edit?usp=sharing spring 2015]


The information provided in this section of the syllabus is subject to modification based on guidance by public health authorities. Changes to Covid-related policies or updated information will, as always, be posted on the ISU website and communicated in multiple ways.
'''CS 302 (formerly 202) Computer Science II''' -
[http://cs.indstate.edu/~jkinne/cs202-f2020 fall 2020],
[http://cs.indstate.edu/~jkinne/cs202-f2019/ fall 2019],
[https://docs.google.com/document/d/1z5FkzB_ttV0K1gfqZM194wHEDZ-wx5I_ovBiI4etJp8/edit?usp=sharing fall 2017],  
[https://docs.google.com/document/d/1cAYqtdLtO5fCmiore0utezzpTRsxddfDWLcXi2yhmn0/edit?usp=sharing spring 2017],  
[https://docs.google.com/document/d/1QadsJAAQgscX6I13gDF6HloHY3-hX2AX_6oa0TwSs3E/edit?usp=sharing spring 2016]


==Special Needs / Disability Services==
'''CS 420/520 Theory of Computation''' -
''Standard ISU language required in all syllabi...''
[http://cs.indstate.edu/~jkinne/cs420-s2019/index.html spring 2019],
[https://docs.google.com/document/d/1JzBW5D2nuXiPNLAvvr2UNaYJvkV9vvn6241MmbqLNl8/edit?usp=sharing fall 2016],
[https://docs.google.com/document/d/1qxGwx9a_5BZyTt5eJeSxutCYUZ-tbvvWW2FLB1yVdTM/edit?usp=sharing fall 2015]


Indiana State University recognizes that students with disabilities may have special needs that must be met to give them equal access to college programs and facilities. If you need course adaptations or accommodations because of a disability, please contact us as soon as possible in a confidential setting either after class or in my office. All conversations regarding your disability will be kept in strict confidence. Indiana State University's Student Support Services (SSS) office coordinates services for students with disabilities: documentation of a disability needs to be on file in that office before any accommodations can be provided. Student Support Services is located on the lower level of Normal Hall in the Center for Student Success and can be contacted at 812-237-2700, or you can visit the ISU website under A-Z, Disability Student Services and submit a Contact Form. Appointments to discuss accommodations with SSS staff members are encouraged.
'''CS 440/540 Graphics Programming''' -
[http://cs.indstate.edu/~jkinne/cs440-f2012 fall 2012]


Once a faculty member is notified by Student Support Services that a student is qualified to receive academic accommodations, a faculty member is obligated to provide or allow a reasonable classroom accommodation under ADA.
'''CS 457/557 Database Processing''' -
[http://cs.indstate.edu/~jkinne/cs457-f2012 fall 2012]


==Disclosures Regarding Sexual Misconduct==
'''CS 458/558 Algorithms''' -
''Standard ISU language required in all syllabi...''
[http://cs.indstate.edu/~jkinne/cs458-f2020 fall 2020],
[http://cs.indstate.edu/~jkinne/cs458-f2013/ fall 2013]


Indiana State University Policy 923 strictly prohibits discrimination on the basis of: age, disability, genetic information, national origin, pregnancy, race/color, religion, sex, gender identity or expression, sexual orientation, veteran status, or any other class protected by federal and state statutes in ISU programs and activities or that interferes with the educational or workplace environment.
'''CS 459/559 Topics in Computer Science''' -
[http://cs.indstate.edu/~jkinne/bd4isu-summer-2019/ BD4ISU Summer 2019],
[http://cs.indstate.edu/~jkinne/cs459-bd4isu-s2019/ BD4ISU Bioinformatics Programming, Spring 2019],
[https://docs.google.com/document/d/1mzYcEOwY0_FPybYhXVZwszgHYRXK6k8yrQAqgEhjaBg/edit?usp=sharing Computational Software Packages and Tools, Summer I 2014]


Title IX of the Educational Amendments of 1972 prohibits discrimination based on sex, including sexual harassment. Sexual harassment includes quid pro quo harassment, unwelcome verbal or physical conduct, sexual assault, dating violence, domestic violence, and stalking.
'''CS 469/569 Unix/Linux Administration and Networking''' -
[https://cs.indstate.edu/~jkinne/cs469-s2022 spring 2022]


If you witness or experience any forms of the above discrimination, you may report to:
'''CS 471/571 Operating Systems''' -
[https://docs.google.com/document/d/1w2bGyWU5YWTlb4hvEJlIa5cAlKsbaOcKoACBGC8F-Is/edit?usp=sharing Fall 2018]


''Office:'' Equal Opportunity & Title IX; (812) 237-8954; Rankin Hall, Room 426 <br>
'''CS 473/573 Computer Networks''' -  
''Email:'' ISU-equalopportunity-titleix@mail.indstate.edu <br>
[http://cs.indstate.edu/~jkinne/cs473-f2021 fall 2021],
''Online:'' https://cm.maxient.com/reportingform.php?IndianaStateUniv&layout_id=10
[http://cs.indstate.edu/~jkinne/cs473-s2021 spring 2021],
[http://cs.indstate.edu/~jkinne/cs473-s2020 spring 2020],
[https://docs.google.com/document/d/1ObUd5k_iIVWf28LeZYUfBlNjzCLA87zBbM0US5aa5pY/edit?usp=sharing spring 2015]


Disclosures made to the following confidential campus resources will not be reported to the Office of Equal Opportunity and Title IX:<br>
'''CS 475/575 Artificial Intelligence''' -
''ISU Student Counseling Center:'' (812) 237-3939; Gillum Hall, 2nd Floor <br>
[http://cs.indstate.edu/~jkinne/cs475-f2011/ fall 2011]
''Victim Advocate:'' (812) 237-3829; HMSU 7th Floor <br>  
 
''UAP Clinic/ISU Health Center:'' (812) 237-3883; 567 N. 5th Street
'''CS 499 Senior Seminar''' -
[http://cs.indstate.edu/~jkinne/cs499-f2020 fall 2020],
[http://cs.indstate.edu/~jkinne/cs499-f2019 fall 2019],
[https://docs.google.com/document/d/1p-v_b9Nr4bxCXGVX4rk4TJbdaMgFa9qkLutopfKcfmE/edit?usp=sharing information]
 
'''CS 500 Programming Fundamentals''' -
[https://cs.indstate.edu/web/index.php/CS_500_Spring_2024 spring 2024],
[https://cs.indstate.edu/web/index.php/CS_500_Fall_2023 fall 2023], [https://cs.indstate.edu/web/index.php/CS_500_Spring_2023 spring 2023], [https://cs.indstate.edu/web/index.php/CS_500_Fall_2022 fall 2022]
 
'''CS 510 Fast Track Introduction to Programming''' -
[https://cs.indstate.edu/web/index.php/CS_510_Spring_2023 spring 2023], [https://cs.indstate.edu/web/index.php/CS_510_Fall_2022 fall 2022]
 
'''CS 559 Topics in Computer Science''' -
[http://cs.indstate.edu/~jkinne/cs559-f2013/ fall 2013]
 
'''CS 609 Web Programming and Applications''' -
[https://docs.google.com/document/d/1SSEoV9GVN2bufYw4Bf9cXnmwbMeq5IFqF6jX7SNH3vI/edit?usp=sharing fall 2015 (as CS 650-003)]
 
'''CS 603 Networking and Security''' -
[https://docs.google.com/document/d/1NAauNCjScp25i3Es0XUiKJRO38TdAEWeQ_m4D5N5LHs/edit?usp=sharing fall 2016]
 
'''CS 617 Databases, Data Mining, and Big Data''' -
[https://docs.google.com/document/d/1G_gtgO0f3fgNcV8qcQ_BOtrwQKMZ3uhCFO3psd6OusI/edit?usp=sharing fall 2017]
 
'''CS 618 Computational Biology''' -
[https://cs.indstate.edu/web/index.php/CS_618 summer 2024], [https://cs.indstate.edu/~jkinne/cs618-s2022 spring 2022]
 
'''CS 620 Theory of Computation II''' -
[https://docs.google.com/document/d/1ivvIzcExIW3rvdnxiL95cNwd0YHOhcFhhCwciCnHHA4/edit?usp=sharing  spring 2016],
[http://cs.indstate.edu/~jkinne/cs620-s2011 spring 2011], [http://cs.indstate.edu/~jkinne/cs620-f2010 fall 2010]
 
'''CS 658 Algorithms II''' -
[http://cs.indstate.edu/~jkinne/cs658-s2014 spring 2014], [http://cs.indstate.edu/~jkinne/cs658-s2012 spring 2012]
 
'''CS 670 Concurrent Programming''' -
[http://cs.indstate.edu/~jkinne/cs670-s2021 spring 2021], [http://cs.indstate.edu/~jkinne/cs670-s2012 spring 2013]
 
'''CS 671 Operating Systems II''' -
[https://docs.google.com/document/d/1kJVEYJYOo7mZyz5GcasP890V3K6mLji6naDUFa4m4UQ/edit?usp=sharing spring 2017]
 
'''CS 695 Computer Science Research''' -
[https://docs.google.com/document/d/1L8doHFFBIgnNuZ38X-uOq2OnU8vWJTBeGUC2jXj0yzc/edit?usp=sharing fall 2014],
[http://cs.indstate.edu/~jkinne/cs695-s2011 spring 2011]
 
'''CS 399/699 Computer Science Internship''' -
[https://docs.google.com/document/d/19IBirbzutL4ldaXIvKvzZHOMa9JULalt7clvvy0SDBk/edit?usp=sharing information]
 
[http://cs.indstate.edu/~jkinne/bio491-f2014/ old bioinformatics stuff]
 
===Wisconsin-Madison===
'''CS/Math 240 Discrete Mathematics''' -  [http://pages.cs.wisc.edu/~jkinne/CS240-sum2007/ summer 2007]
 
'''CS 810/710 Theory of Computation''' - [http://pages.cs.wisc.edu/~dieter/Courses/2007s-CS810 spring 2007]
 
'''CS 310 Problem Solving with Computers''' - [http://pages.cs.wisc.edu/~hasti/cs310/ 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. [https://docs.google.com/presentation/d/1oNM-eA0NlzaFhY5s5nDZqmyk3SVkhI2N3uUF8_DpOtg/edit?usp=sharing 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. [https://docs.google.com/presentation/d/1NVjVeq91qJ3UpeAlYrKmyVGtx2yIQPjA3A9lt2Nv8mE/edit#slide=id.p 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. [https://docs.google.com/presentation/d/1KtcMnQgTUsoFvKGxOGlOLtWa8Dypkyd7LhuF1K0z4Y0/edit?usp=sharing 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). [http://cs.indstate.edu/~jkinne/talks/IAS-jkinne-2014.pdf 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. [http://cs.indstate.edu/~jkinne/talks/MTD-jkinne-2013.pdf 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. [http://cs.indstate.edu/~jkinne/talks/randAndDerand.pptx 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. [http://cs.indstate.edu/~jkinne/talks/undergradResearch.pdf 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. [http://cs.indstate.edu/~jkinne/talks/lower-bounds-in-theory.pdf 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. [https://docs.google.com/present/edit?id=0AbxM6icc2fOUZGhmM3FndzVfOTVnNmZubnBkMw&hl=en 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. [http://cs.indstate.edu/~jkinne/talks/p-versus-np.ppt 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. [http://cs.indstate.edu/~jkinne/talks/isu-job-talk.pdf 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. [http://cs.indstate.edu/~jkinne/talks/theory-hot-topics.pdf 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 ([http://tribstar.com/ tribune star] | [http://www.mywabashvalley.com mywabashvalley]), [http://www.indystar.com Indianapolis] | [http://www.cincinnati.com Cincinnati] |
[http://news.google.com Google News] ([https://news.google.com/home?hl=es-419&gl=US&ceid=US:es-419 es]) | [https://en.wikipedia.org/wiki/Main_Page Wikipedia] ([https://es.wikipedia.org/wiki/Wikipedia:Portada es]) | [https://www.bbc.com/mundo BBC Mundo]
 
'''Terre Haute/Indiana:''' weather ([http://forecast.weather.gov/MapClick.php?CityName=Terre+Haute&state=IN&site=IND&textField1=39.4704&textField2=-87.3835&e=0 NWS] | [https://www.wunderground.com/dashboard/pws/KINTERRE188 121 Jackson Blvd] | [https://www.windy.com/39.467/-87.414?38.988,-87.414,8 windy.com]) ([https://www.nws.noaa.gov/wtf/MapClick.php?CityName=Terre+Haute&state=IN&site=IND&textField1=39.4704&textField2=-87.3835&e=0&lg=sp es]) |
[http://library.indstate.edu ISU library] | [http://www.vigo.lib.in.us/ Public Library]
</p>
 
''Non-public:''
[https://docs.google.com/spreadsheets/d/198I0idSJptzUU5wjQxrUIWQBgOYMgw_CrBvTDyrZY54/edit?usp=sharing Home repairs and bills] | [https://calendar.google.com Google Calendar]
 
''German:''    [https://en.wikibooks.org/wiki/German Wikibook] | [https://docs.google.com/document/d/1kFzWpnl4kiEYwYbFJs3MsqyRyDkIMEBosDMm7g3P9Dg/edit?usp=sharing notes]
 
''Astronomy:'' [http://www.skyandtelescope.com Sky and Telescope] | [http://www.heavens-above.com/?Loc=Terre+Haute&Lat=39.467&Lng=-87.414&Alt=138&TZ=EST Heavens Above Terre Haute] |
[http://www.cleardarksky.com/c/TrrHtINkey.html?1 Terre Haute Clear Sky Chart] | [https://www.lightpollutionmap.info/ light pollution map] | [http://worldwidetelescope.org World Wide Telescope] | [http://media.skyandtelescope.com/documents/MullaneyDeepSky111.pdf 111 treasures for light-polluted skies (PDF)] | [http://www.keo.org/uk/pages/introuk.html Space Time Capsule] | [https://stellarium.org/ Stellarium] ([https://stellarium-web.org/ web]) | [https://www.spaceweatherlive.com/ SpaceWeatherLive]

Revision as of 11:35, 3 September 2025

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).

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.

Recommendations

For those current and former CS students who ask me to write a letter of recommendation for you, please send me the following when you ask for this: course(s) that you took with me as instructor (including the term you took it and your final grade), your resume or cv being used to apply, your unofficial transcript(s), anything else you are submitting with your applications (e.g., cover letter), and anything else to jog my memory about you.

Also, if I ask you to schedule a short meeting with me, use my online scheduling link (above) to schedule a 15 minute online meeting. For this meeting I will do a short technical interview with you, so I have more to go on for writing the letter. For the technical interview you can expect questions about data structures and algorithms, programming, and courses you have taken.

Projects

Other than ongoing research projects, a few things I have on my list to do (for courses, or other reasons).

  • project list (must be logged in with ISU microsoft account).
  • Past projects - put past small projects together onto github or gitlab.

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

Summary:

Gene expression analysis has become a standard tool used to determine important genes in biological and biomedical studies. Biologists and medical researchers often work together with programmers, data scientists, or statisticians to complete the analysis after sequencing is performed. I have worked with the lab of biologist Dr. Kris Schwab at Indiana State University and Dr. Kevin Coombes of the Augusta University Medical College of Georgia to develop a software tool, the Developmental Gene Expression Analysis (devGEA), that encapsulates our analysis pipeline and can be used by biologists. The tool is written in the R programming language, uses the R shiny UI, and is available as both a stand-alone program and as a web tool. The Schwab lab and other labs at Indiana State University are now using devGEA to help streamline the analysis of gene expression experiments. devGEA performs the main steps of gene expression analysis: data import, filtering, normalization, scaling, statistical modeling and p value computation, clustering, and visualization. devGEA introduces a correlation-based clustering method that is conceptually simpler than other clustering methods and yields results that are easier to interpret. I was the lead programmer for the tool (together with Isaiah Bartlett and other student researchers) and shared with Drs. Schwab and Coombes in the design and analysis.

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.

Summary:

Prokaryotic chromosomes contain numerous small open reading frames (ORFs) of less than 200 bases. Since high-throughput proteomics methods often miss proteins containing fewer than 60 amino acids, it is difficult to discern if they encode proteins. Recent studies have revealed that many small proteins are membrane proteins with a single membrane-anchoring α-helix. As membrane anchoring or transmembrane motifs are accurately identifiable with high confidence using computational algorithms like Phobius and TMHMM, small membrane proteins (SMPS) can be predicted with high accuracy. I worked with Dr. Kyu Hong Cho at Indiana State University to create a software pipeline to systematically search for novel putative small membrane proteins in prokaryotic genomes. The pipeline is written in Python and uses previous work (Orfipy, Phobius, and Blast) for key steps in the pipeline. The pipeline is available as a web service and can be downloaded and run locally. Numerous parameters can be chosen depending on the needs of the researcher. This resource aims to assist researchers in identifying new SMPs encoded in microbial genomes of interest. We utilized the pipeline on numerous prokaryotic genomes to survey potential novel small membrane proteins across various species. Our findings indicate that each prokaryote possesses many SMPs, with some identified in the intergenic regions of currently annotated chromosomes. More extensively studied microorganisms, such as Escherichia coli and Bacillus subtilis, have more SMPs identified in their genomes compared to less studied microorganisms, suggesting the possibility of undiscovered SMPs in less studied microorganisms. I oversaw the programming and software development, sharing coding duties with student researcher Tara Hoffman. I shared with Dr. Cho in the overall design.

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 - fall 2025, spring 2025, fall 2024, 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 2025, fall 2024, 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

old bioinformatics stuff

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 | 121 Jackson Blvd | windy.com) (es) | ISU library | Public Library

Non-public: Home repairs and bills | Google Calendar

German: Wikibook | notes

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

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