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Avoiding Plagiarism: Dissertation / Thesis FAQ re: Copyright

• Dissertation / Thesis FAQ re: Copyright
• Copyright Vs. Plagiarism
• Avoiding Plagiarism
• More about Copyright This link opens in a new window

Copyright FAQ re Theses and Dissertations

• Who owns the copyright of my thesis or dissertation?
• The copyright to a thesis belongs to the student, according to the University's General Rules .
• As a condition of being awarded the degree, however, the student grants the University the non-exclusive right "to retain, use and distribute a limited number of copies of the thesis, together with the right to require its publication for archival use.“         http://www.uillinois.edu/trustees/ rules.cfm
•  Find out more about Author Rights  and Publishing, Scholarly Communication, and Open Access

What is INDIGO?  

• INDIGO is UIC's institutional repository for research & scholarship produced at UIC.  
• The electronic theses and dissertations (ETDs) produced by UIC's Master and PhD students are uploaded into INDIGO each semester, once final approval has been received for all submissions.
• Open Access: thesis is available immediately after date of degree conferral 
• Restricted Access: thesis is closed to the UIC community only, for a period of 2 years after which it becomes publicly available
• Closed Access: closed to all for a period of two years, after which it becomes publicly available. 

Can I use the copyrighted materials of others in my thesis or dissertation?

• The fair use section of copyright law allows for the limited use of copyright materials without the owner's permission.   If your use would not fall within fair use , then you need to seek permission from the copyright owner to use the material.   

How can I demonstrate I have permission to reuse already published materials in my thesis/dissertation?

• A reproduction of the publisher’s or journal’s webpage giving global  permission and outlining requirements for reuse (which you must follow) 
• A formal request to the journal or publisher with a written affirmative  response indicating their agreement for you to reuse the previously  published material for which they hold the copyright. (For more information see seek permission from the copyright owner .)

      Note: Videos or recordings included in your thesis/dissertation may require you to obtain permission from performers.

Can I include materials that I have already published in my thesis/dissertation?

• Check your departmental policies and thesis/  dissertation format and make sure your thesis/dissertation committee  agrees. 
• Next, you must determine whether the journal/publisher allows reuse  of these items in your thesis/dissertation.  If so, provide proof that this is  acceptable in an appendix to your thesis/dissertation.
• EXAMPLE: American Chemical Society Journals  (from the American Chemical Society Policy on Theses and Dissertations) “Copyright permission for published and submitted material from theses and dissertations ACS extends blanket permission to students to include in their theses and dissertations their own articles, or portions thereof, that have been published in ACS journals or submitted to ACS journals for publication, provided that the ACS copyright credit line is noted on the appropriate page(s).”

What if I cannot obtain permission to include materials that I have already published in my thesis/dissertation?

• Copyright law does not protect ideas but rather the expression of ideas (the word by word expression).   You can paraphrase the materials and express the content in a different way in order to avoid copyright infringement.

Can I later publish materials that I have included in my thesis/dissertation?  I that eventually my thesis/ dissertation will be available online. 

• Students in the humanities frequently rework their theses/dissertations into books that they publish early in their independent academic careers.
• Students in the sciences many times have figures/charts/images that have  been included in their theses/dissertations that are later published in  journal articles. 

“Publishing implications of electronic publication of theses and dissertation material:  Students and their mentors should be aware that posting of theses and dissertation material on the Web prior to submission of material from that thesis or dissertation to an ACS journal may affect publication in that journal. Whether Web posting is considered prior publication may be evaluated on a case-by-case basis by the journal’s editor. If an ACS journal editor considers Web posting to be “prior publication”, the paper will not be accepted for publication in that journal. If you intend to submit your unpublished paper to ACS for publication, check with the appropriate editor prior to posting your manuscript electronically.”

Some of the FAQ based on content from UIC Graduate College Guide on Copyright .

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• Last Updated: May 3, 2024 10:35 AM
• URL: https://researchguides.uic.edu/etds

UIC Library Digital Collections (Beta)

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Computer Science Research Resources: Dissertations & Theses

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As part of the requirements for graduate level degrees, students must complete a thesis for a Master's degree and/or dissertation for a Ph.D. Dissertations and theses are submitted to the academic department and the Graduate College and are made available through the University Library. Since 2010, all theses and dissertations are electronically deposited into IDEALS, the Illinois Digital Environment for Access to Learning and Scholarship, the University's open repository of scholarly content.

ProQuest Dissertations is a comprehensive collection of citations to dissertations and theses worldwide from 1861 to the present day. Full text PDFs are available for many Ph.D. dissertations added since 1997 and some older graduate works.

• IDEALS (UIUC Institutional Repository) Digital copies of theses, data sets, and publications by University of Illinois at Urbana-Champaign faculty and students.
• ProQuest Dissertations and Theses PDF copies of dissertations and theses from U.S. universities.

Computer Science Dissertations & Theses

• Computer Science Dissertations & Theses Search Interface

Print Dissertations & Theses

Prior to 2010, print format dissertations and theses were bound and cataloged separately for the Grainger Engineering Library. Prior to 1983, each thesis was shelved by a call number assigned by subject headings. To locate them, search the online catalog for the author’s last name, title word(s) if known, and “theses” and the year granted as subject term(s).

Computer Science dissertations and theses granted from 1985 to 1999 were assigned Q.629.1Ta, followed by the 2-number year, followed by starting letters from the author’s last name. (Example: A 1991 thesis by M. Doyle would be Q.629.1Ta91D). Dissertations and theses granted from 2000 to present were assigned Q.629.1Tb, followed by the 2-number year, followed by starting letters from the author’s last name. (Example: A 2006 thesis by H. Dewey would be Q.629.1Tb06De).

Computer Science - Q. 004T

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College of Pharmacy - Chicago | Rockford

Michael Federle

Professor , College of Pharmacy - Medicinal Chemistry and Pharmacognosy Director , Center for Biomolecular Sciences Affiliate , Center for Biomolecular Sciences

Office Phone:

(312) 413-0213 (work)

[email protected]

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About Heading link Copy link

Overview: I have spent over 25 years studying, researching, and mentoring in the field of molecular microbiology and bacterial pathogenesis. In 2008, I established an independent research laboratory at the University of Illinois at Chicago, focusing on chemical signaling in Gram-positive bacterial pathogens. My laboratory has helped to identify a widespread protein family characterized as cytoplasmic pheromone receptors. It is our mission to identify signaling pathways in Gram-positive pathogens (including Streptococcus pyogenes, S. pneumoniae, S. agalactiae, and S. mutans), characterize their benefits in bacterial survival or pathogenesis, and elucidate mechanisms of signaling interference as potential anti-virulence strategies. My training began at the University of Wisconsin, where I earned a bachelor’s degree in genetics. I spent three years working as a laboratory specialist in the labs of Dr. Frederick Blattner (Wisconsin, 2004-2005) and Dr. June R. Scott (Emory, 2005-2007). I completed my PhD in 2002 in the Microbiology and Molecular Genetics graduate program at Emory University under the mentorship of Dr. June Scott; my thesis was based on the characterization of the CovRS twocomponent signal transduction system in the human pathogen Streptococcus pyogenes. My postdoctoral training at Princeton University was under the mentorship of Dr. Bonnie Bassler. I helped to elucidate the molecular mechanism of autoinducer-2 sensory transduction through the LuxPQ receptor of Vibrio harveyi. Now, as a professor in the departments of Medicinal Chemistry and Pharmacognosy, and Microbiology and Immunology, I am the principle investigator of several research grants and lead a lab comprised of six graduate students and two postdoctoral scientists. I enjoy teaching to both graduate and professional students at UIC.

Teaching and Supervision Heading link Copy link

PhD Thesis Research (MIM 599), 1/8/2024 – 4/26/2024 PSCI Ph.D. Thesis Research (PSCI 599), 1/8/2024 – 4/26/2024 PhD Thesis Research (MIM 599), 8/21/2023 – 12/1/2023 PDAT 4: Immunology/Respiratory (PHAR 504), 8/21/2023 – 12/1/2023 Host Responses to Microbes (MIM 554), 8/21/2023 – 12/1/2023 PSCI Ph.D. Thesis Research (PSCI 599), 8/21/2023 – 12/1/2023 PDAT 4: Immunology/Respiratory (PHAR 504), 8/21/2023 – 12/1/2023 PSCI Ph.D. Thesis Research (PSCI 599), 6/12/2023 – 8/4/2023 PhD Thesis Research (MIM 599), 5/15/2023 – 8/4/2023

Selected Grants

UIC Portal to Biomedical Research Careers (UIC PBRC) PREP, National Institutes of Health (National Institute of General Medical Sciences)., 2/1/2024 - 1/31/2029, Obligated Amount: $415994; Anticipated Amount: $2079970

Determining the mechanism and impact of streptococcal RaS-RiPPs on the human oral microbiome, National Institutes of Health (National Institute of Dental and Craniofacial Research)., 8/1/2023 - 7/31/2025, Obligated Amount: $111701; Anticipated Amount: $223402

Discovery of a pigment produced by Streptococcus pyogenes, National Institutes of Health (National Institute of Allergy and Infectious Diseases)., 3/1/2023 - 2/28/2025, Obligated Amount: $193496; Anticipated Amount: $423776

Macrophage Immunosuppression by Quorum-Induced Streptococcus pyogenes, National Institutes of Health (National Institute of Allergy and Infectious Diseases)., 7/1/2022 - 6/30/2026, Obligated Amount: $1311528; Anticipated Amount: $2362683

Antipsychotic Associated Acquisition of Antimicrobial Resistance Mechanisms in Gut Microbiota, Hans W. Vahlteich Research Award., 2/28/2022 - 2/28/2023, Obligated Amount: $50000; No Anticipated Amount Set

Norway-India-Brazil-Canada-USA: Partnership for excellence in education, research and innovation in biofilm and antibiotic resistance, Univ of Oslo., 1/1/2021 - 12/31/2026, Obligated Amount: $33480; Anticipated Amount: $33480

Chemical profiling of bacterial-fungal interactions to elucidate mechanisms of growth and survival in multi-domain microbial communities, National Institutes of Health (National Center for Complementary and Integrative Health)., 1/1/2020 - 12/31/2020, Obligated Amount: $46016; Anticipated Amount: $46016

Transcriptomic and Genomic Differences of Group A Streptococcus in Humans: Acute Infection Versus Carriage, State University of New York - Binghampton., 7/10/2019 - 6/30/2023, Obligated Amount: $45843; Anticipated Amount: $45843

Novel Biofilm Inhibitors of Oral Streptococci, National Institutes of Health (National Institute of Dental and Craniofacial Research)., 7/1/2019 - 6/30/2024, Obligated Amount: $691270; Anticipated Amount: $691270

Selected Publications

Wilkening, Reid V, Langouët-Astrié, Christophe, Severn, Morgan M, Federle, Michael J, Horswill, Alexander R. (2023). Identifying genetic determinants of Streptococcus pyogenes-host interactions in a murine intact skin infection model. Cell Reports , 42 , (11), 113332. doi: 10.1016/j.celrep.2023.113332 .

Nepomuceno, Vanessa M, Tylor, Kaitlyn M, Carlson, Skylar, Federle, Michael J, Murphy, Brian T, Morales, Tiara Perez. (2023). A Streptomyces tendae Specialized Metabolite Inhibits Quorum Sensing in Group A Streptococcus. Microbiology Spectrum , 11 , (4), e05279-e05222. doi: 10.1128/spectrum.05279-22 .

Hu, Duoyi, Laczkovich, Irina, Federle, Michael J, Morrison, Donald A. (2023). Identification and Characterization of Negative Regulators of Rgg1518 Quorum Sensing in Streptococcus pneumoniae. Journal of Bacteriology , 205 , (7), e00087-e00023. doi: 10.1128/jb.00087-23 .

Rued, Britta E, Federle, Michael J. (2023). The ComRS-SigX Pathway Regulates Natural Transformation in Streptococcus ferus. Journal of Bacteriology , 205 , (6), e00089-e00023. doi: 10.1128/jb.00089-23 .

Resko, Zachary J, Anderson, Caleb M, Federle, Michael J, Alonzo, Francis. (2023). A Staphylococcal Glucosaminidase Drives Inflammatory Responses by Processing Peptidoglycan Chains to Physiological Lengths. Infection and Immunity , 91 , (2), e00500-e00522. doi: 10.1128/iai.00500-22 .

Rued, Britta E, Anderson, Caleb M, Federle, Michael J. (2022). The Proteomic and Transcriptomic Landscapes Altered by Rgg2/3 Activity in Streptococcus pyogenes. Journal of Bacteriology , 204 , (11), e00175-e00122. doi: 10.1128/jb.00175-22 .

Chang, Jennifer C, Wilkening, Reid V, Rahbari, Kate M, Federle, Michael J. (2022). Quorum Sensing Regulation of a Major Facilitator Superfamily Transporter Affects Multiple Streptococcal Virulence Factors. Journal of Bacteriology , 204 , (9), e00176-e00122. doi: 10.1128/jb.00176-22 .

Laczkovich, Irina, Mangano, Kyle, Shao, Xinhao, Hockenberry, Adam J, Gao, Yu, Mankin, Alexander, Vázquez-Laslop, Nora, Federle, Michael J. (2022). Discovery of Unannotated Small Open Reading Frames in Streptococcus pneumoniae D39 Involved in Quorum Sensing and Virulence Using Ribosome Profiling. mBio , 13 , (4), e01247-e01222. doi: 10.1128/mbio.01247-22 .

Kyono, Yasuhiro, Ellezian, Lori, Hu, YueYue, Eliadis, Kanella, Moy, Junlone, Hirsch, Elizabeth B, Federle, Michael J, Flowers, Stephanie A. (2022). The Atypical Antipsychotic Quetiapine Promotes Multiple Antibiotic Resistance in Escherichia coli. Journal of Bacteriology , 204 , (5), e00102-e00122. doi: 10.1128/jb.00102-22 .

Professional Leadership

Ad Hoc Reviewer, American Society for Microbiology, 3/31/2021 - Present

Special Emphasis Panel, National Institutes of Health, 7/2019 - 7/2019

NIH F13 Infectious Diseases and Microbiology Fellowship Panel, National Institutes of Health, 7/2018 - 7/2018

NIH ZRG1 IDM-B 80 Special Emphasis Panel, National Institutes of Health, 3/2018 - 3/2018

NIH Bacterial Pathogenesis Study Section, National Institutes of Health, 10/2016 - 10/2016

NIH ZRG1 IDM-B 80 Special Emphasis Panel, National Institutes of Health, 3/2016 - 3/2016

NIH ZRG1 IDM-B 80 Special Emphasis Panel, National Institutes of Health, 3/2015 - 3/2015

Planning Committee, American Society for Microbiology, 10/2014 - 10/2014

NIH, ZRG1 IDM-B 80 Special Emphasis Panel, National Institutes of Health, 7/2013 - 7/2013

Notable Honors

2020, ASM American Academy of Microbiology Fellow, American Society of Microbiology

2014, Rising Star Researcher, University of Illinois at Chicago

2014, ASM Distinguished Lecturer,

Degrees: Ph.D., Emory University, United States, 2002 B.S., University of Wisconsin–Madison, United States, 1994

Postgraduate Training: Postdoctoral Research Fellow and Research Associate, Howard Hughes Medical Institute, United States, 2008

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Chemical Engineering

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Graduate College

Recipients of spring 2024 awards and retention fellowships.

The Graduate College is pleased to announce the recipients of several internal competitions:

• Graduate Mentoring Award
• Award for Graduate Research
• Provost’s Graduate Internship Award
• Access to Excellence Fellowship
• Dean’s Scholar Fellowship

Recipients have been notified. Please note that the Graduate College reserves the authority to announce additional winners if funding can be secured.

The Graduate College wishes to thank the applicants for preparing their materials on top of their other responsibilities as well as the members of our awards committees for their indefatigable service this academic year. While we cannot fund all of the worthy individuals, we hope that students learn from the process and that our faculty appreciate the excellence in their midst.

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The Mohr Group at UIC

Target directed synthesis enabled by new synthetic methods.

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From Left to Right: Rida, Fatima, Sara, Sebastian, Corey, Justin, Gena, Mihir, Anh, Daria, Sruthi

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Department of Biochemistry and Molecular Genetics

“multiscale modeling and topological data analysis in artificial intelligence-driven biology” by dr. yuchi qiu (uc irvine).

May 8, 2024

Herman Auditorium, MBRB

Host: Dr. Merrill

Date posted

May 2, 2024

Date updated

Dr. Yuchi Qiu | “Multiscale modeling and topological data analysis in artificial intelligence-driven biology” | University of California, Irvine