Difference between revisions of "Papers, Presentations, Theses, Proposals, and Patents"

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m (Added website link to "The Role of Hydrophobicity in Peptide-MHC Binding" paper.)
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Here are links to our papers, theses, proposals, and presentations. When several version of a paper were published, for instance one in conference proceedings and another in a journal, these are grouped together and only the most significant version is linked. All materials are subject to copyrights.
Here are links to our papers, theses, proposals, and presentations. When several version of a paper were published, for instance one in conference proceedings and another in a journal, these are grouped together and only the most significant version is linked. All materials are subject to copyrights.


== Computing with Molecules ==
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//http://mriedel.ece.umn.edu/wiki/images/e/e0/DNA27_SIMD_DNA.pdf Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching]
|- valign="top"
| '''authors''':
| [[Tonglin Chen]], [[Arnav Solanki]] and [[Marc Riedel]]
|- valign="top"
| '''presented at''':
| [http://dna27.iopconfs.org/home International Conference on DNA Computing and Molecular Programming], 2021
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/e/e0/DNA27_SIMD_DNA.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/e/e0/DNA27_SIMD_DNA.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/d/d5/DNA27_Presentation.pdf http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/d/d5/DNA27_Presentation.pdf Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//http://mriedel.ece.umn.edu/wiki/images/5/58/VCIP2021_Blind.pdf Cascadable Stochastic Logic for DNA Storage]
|- valign="top"
| '''authors''':
| [[Arnav Solanki]], [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://www.vcip2021.org/ Visual Communications and Image Processing], 2021
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/5/58/VCIP2021_Blind.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/5/58/VCIP2021_Blind.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/8/81/FNANO20_Random_Cutting.pdf Stochastic Computation on DNA strands through Hydroxyl Nicking]
|- valign="top"
| '''authors''':
| [[Arnav Solanki]], [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://www2.cs.duke.edu/FNANO/ Foundations of Nanoscience: Self-Assembled Architectures and Devices], 2020
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/8/81/FNANO20_Random_Cutting.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/8/81/FNANO20_Random_Cutting.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/2/29/FNANO_poster2020.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/2/29/FNANO_poster2020.pdf Poster]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [http://mriedel.ece.umn.edu/wiki/images/3/38/Chen_Solanki_Riedel_Concentration-Based-Polynomial-Calculations-on-Nicked-DNA.pdf Concentration-Based-Polynomial-Calculations-on-Nicked-DNA]
|- valign="top"
| '''authors''':
| [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://rc.signalprocessingsociety.org/conferences/icassp-2020/SPSICASSP20VID1364.html IEEE International Conference on Acoustics, Speech, and Signal Processing], 2020
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/3/38/Chen_Solanki_Riedel_Concentration-Based-Polynomial-Calculations-on-Nicked-DNA.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/3/38/Chen_Solanki_Riedel_Concentration-Based-Polynomial-Calculations-on-Nicked-DNA.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/4/4c/Chen_Riedel_Parallel_Binary_Sorting_and_Shifting_with_DNA.pdf Parallel Binary Sorting and Shifting with DNA]
|- valign="top"
| '''authors''':
| [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://www.iwbdaconf.org/2019/ International Workshop on Bio-Design Automation], Cambridge, England, 2019.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/4/4c/Chen_Riedel_Parallel_Binary_Sorting_and_Shifting_with_DNA.pdf http://cctbio.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/4/4c/Chen_Riedel_Parallel_Binary_Sorting_and_Shifting_with_DNA.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/4/41/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding.pdf Computing Mathematical Functions using DNA via Fractional Coding]
|- valign="top"
| '''authors''':
| [https://www.engr.uky.edu/directory/salehi-sayed-ahmad Ahmad Salehi], Xingyi Liu, [[Marc Riedel]], and [http://people.ece.umn.edu/~parhi/ Keshab K. Parhi]
|- valign="top"
| '''appeared in''':
| [https://www.nature.com/articles/s41598-018-26709-6 Nature Scientific Reports], Vol. 8 No. 8312, 2018
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/4/41/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>
[//mriedel.ece.umn.edu/wiki/images/4/41/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/9/91/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding_Supplement.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>
[//mriedel.ece.umn.edu/wiki/images/9/91/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding_Supplement.pdf Supplement]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/d/d7/Salehi_Parhi_Riedel_Chemical_Reaction_Networks_for_Computing_Polynomials.pdf Chemical Reaction Networks for Computing Polynomials]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [http://www.ece.umn.edu/users/parhi Keshab Parhi] and  [[Marc Riedel]]
|- valign="top"
| '''appeared as''':
| [http://pubs.acs.org/journal/asbcd6 ACS Synthetic Biology],Vol. 6, No. 1, pp. 76–83, 2017
|- valign="top"
| '''presented at''':
| [http://globecom2016.ieee-globecom.org IEEE Globecom Symposium, 2016]
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/d/d7/Salehi_Parhi_Riedel_Chemical_Reaction_Networks_for_Computing_Polynomials.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/4/47/Salehi_Riedel_Parhi_Chemical_Reaction_Networks_for_Computing_Polynomials.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/2/25/Salehi_Riedel_Parhi_Molecular_Sensing_and_Computing_Systems.pdf Molecular Sensing and Computing Systems]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [[Marc Riedel]], [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''appeared as''':
| [http://mbmc.info IEEE Trans. on Molecular, Biological, and Multi-Scale Communications],<br>Vol. 1, No. 3, 2015
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/2/25/Salehi_Riedel_Parhi_Molecular_Sensing_and_Computing_Systems.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://cctbio.ece.umn.edu/wiki/images/2/25/Salehi_Riedel_Parhi_Molecular_Sensing_and_Computing_Systems.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/c/c0/Salehi_Riedel_Parhi_Markov_Chain_Computations_using_Molecular_Reactions.pdf Markov Chain Computations using Molecular Reactions]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [[Marc Riedel]], [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.dsp2015.org IEEE International Conference on Digital Signal Processing], 2015.
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/c/c0/Salehi_Riedel_Parhi_Markov_Chain_Computations_using_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/c/c0/Salehi_Riedel_Parhi_Markov_Chain_Computations_using_Molecular_Reactions.pdf Paper]
| width="70" align="center" |
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/b/b3/Salehi_Riedel_Parhi_Asynchronous_Discrete-Time_Signal_Processing_with_Molecular_Reactions.pdf Asynchronous Discrete-Time Signal Processing with Molecular Reactions]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [[Marc Riedel]], and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.asilomarsscconf.org/webpage/asil14/post_conf.htm Asilomar Conference on Signals, Systems, and Computers], 2014.
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/b/b3/Salehi_Riedel_Parhi_Asynchronous_Discrete-Time_Signal_Processing_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/b/b3/Salehi_Riedel_Parhi_Asynchronous_Discrete-Time_Signal_Processing_with_Molecular_Reactions.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/c/cf/Jiang_Riedel_Parhi_Digital_Logic_with_Molecular_Reactions.pdf Digital Logic with Molecular Reactions]
|- valign="top"
| '''authors''':
| [[Hua Jiang]], [[Marc Riedel]], [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iccad.com IEEE/ACM International Conference on Computer-Aided Design],<br>San Jose, CA, 2013.
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/c/cf/Jiang_Riedel_Parhi_Digital_Logic_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/c/cf/Jiang_Riedel_Parhi_Digital_Logic_with_Molecular_Reactions.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/3/36/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA.pdf Discrete-Time Signal Processing with DNA]
|- valign="top"
| '''authors''':
| [[Hua Jiang]], Ahmad Salehi, [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://pubs.acs.org/doi/abs/10.1021/sb300087n ACS Synthetic Biology], Vol. 2 no. 5, pp. 245&ndash;254, 2013.<br>[//mriedel.ece.umn.edu/wiki/images/4/40/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA_Appendix.pdf Supplementary Information: List of Reactions]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://www.computer.org/portal/web/dt IEEE Design & Test of Computers], Vol. 29, No. 3, pp. 21&ndash;31, 2012.
|- valign="top"
| '''presented at''':
| [http://www.iccad.com/ IEEE/ACM International Conference on Computer-Aided Design],<br> San Jose, CA, 2010.
|- valign="top"
| '''presented at''':
| [http://www.wikicfp.com/cfp/servlet/event.showcfp?eventid=7703&copyownerid=8242 IEEE Workshop on Signal Processing Systems], San Francisco, 2010
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/3/36/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/3/36/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/2/2a/Jiang_Kharam_Riedel_Parhi_Digital_Signal_Processing_with_Biomolecular_Reactions.pptx http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/2/2a/Jiang_Kharam_Riedel_Parhi_Digital_Signal_Processing_with_Biomolecular_Reactions.pptx Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/5/57/Kulkarni_Chanyaswad_Riedel_Kim_Robust_Tunable_In_Vitro_Transcriptional_Oscillator_Networks.pdf Robust Tunable ''In Vitro'' Transcriptional Oscillator Networks]
|- valign="top"
| '''authors''':
|  Vishwesh Kulkarni, [[Thee Chanyaswad]], [[Marc Riedel]] and Jongmin Kim
|- valign="top"
| '''presented at''':
| [http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6475439 Allerton Conference], Urbana-Champaign, IL, 2012.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/5/57/Kulkarni_Chanyaswad_Riedel_Kim_Robust_Tunable_In_Vitro_Transcriptional_Oscillator_Networks.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/5/57/Kulkarni_Chanyaswad_Riedel_Kim_Robust_Tunable_In_Vitro_Transcriptional_Oscillator_Networks.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/d/db/Senum_Riedel_Rate-Independent_Constructs_for_Chemical_Computation.pdf Rate-Independent Constructs for Chemical Computation]
|- valign="top"
| '''authors''':
| [[Phil Senum]] and [[Marc Riedel]]
|- valign="top"
| '''appeared in''':
| [http://dx.plos.org/10.1371/journal.pone.0021414 PLoS ONE], Vol. 6, No. 6, 2011.<br>[[Rate_Independent_Constructs_Supplementary_Information | Supplementary Information]]
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/d/db/Senum_Riedel_Rate-Independent_Constructs_for_Chemical_Computation.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/d/db/Senum_Riedel_Rate-Independent_Constructs_for_Chemical_Computation.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/d/d2/Senum_Riedel_Rate-Independent_Modules_for_Chemical_Computation.pptx http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/d/d2/Senum_Riedel_Rate-Independent_Modules_for_Chemical_Computation.pptx Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/0/07/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pdf Synchronous Sequential Computation with Molecular Reactions]
|- valign="top"
| '''authors''':
|  [[Hua Jiang]], [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented at''':
| [http://www.dac.com/dac+2011+conference+program.aspx ACM/EDAC/IEEE Design Automation Conference], San Diego, CA, 2011.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/0/07/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/0/07/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/9/9b/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pptx http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/9/9b/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pptx Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/a/ab/Jiang_Riedel_Parhi_Asynchronous_Computation_with_Molecular_Reactions.pdf Asynchronous Computation with Molecular Reactions]
|- valign="top"
| '''authors''':
|  [[Hua Jiang]], [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented at''':
| [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6190049&filter=AND(p_Publication_Number:6185739) Asilomar Conference on Signals, Systems, and Computers], Pacific Grove, CA, 2011.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://cctbio.ece.umn.edu/wiki/images/a/ab/Jiang_Riedel_Parhi_Asynchronous_Computation_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/a/ab/Jiang_Riedel_Parhi_Asynchronous_Computation_with_Molecular_Reactions.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/a/a7/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.pdf Binary Counting with Chemical Reactions]
|- valign="top"
| '''authors''':
| [[Aleksandra Kharam]], [[Hua Jiang]], [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented at''':
| [http://psb.stanford.edu/psb-online/proceedings/psb11 Pacific Symposium on Biocomputing], Hawaii, 2011.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://cadbio.com/wiki/images/a/a7/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://cadbio.com/wiki/images/a/a7/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/a/a6/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/a/a6/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/0/04/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.pdf Writing and Compiling Code into Biochemistry]
|- valign="top"
| '''authors''':
| [[Adam Shea]], [[Brian Fett]], [[Marc Riedel]], and [http://www.ece.umn.edu/~parhi/ Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iccad.com/events/eventdetails.aspx?id=106-2-C IEEE/ACM International Conference on Computer-Aided Design],<br>San Jose, CA, 2009; and at [http://psb.stanford.edu/psb-online/proceedings/psb10 Pacific Symposium on Biocomputing],<br> Kona, Hawaii, 2010 (see [http://friendfeed.com/pacific-symposium-for-bio/6476a568/marc-riedel-writing-and-compiling-code-into blog]).
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iwls.org/iwls2009/ IEEE/ACM International Workshop on Logic and Synthesis], Berkeley, 2009
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/0/04/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span><br>[//mriedel.ece.umn.edu/wiki/images/0/04/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/3/37/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.pdf Stochastic Transient Analysis of Biochemical Systems]
|- valign="top"
| '''authors''':
| [[Bin Cheng]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://psb.stanford.edu Pacific Symposium on Biocomputing], Hawaii, 2009.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/3/37/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/3/37/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/6/66/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.pdf Module Locking in Biochemical Systems]
|- valign="top"
| '''authors''':
| [[Brian Fett]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iccad.com/events/eventdetails.aspx?id=86-10-A IEEE/ACM International Conference on Computer-Aided Design],<br>San Jose, CA, 2008; and at [http://sb4.biobricks.org Synthetic Biology 4.0], Hong Kong, 2008.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/6/66/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/6/66/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/e/e6/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.pdf Synthesizing Stochasticity in Biochemical Systems]
|- valign="top"
| '''authors''':
| [[Brian Fett]], [http://paradise.caltech.edu/bruck.html Shuki Bruck], and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.dac.com/45th/index.aspx ACM/EDAC/IEEE Design Automation Conference], San Diego, 2007; and at<br>[http://www.syntheticbiology3.ethz.ch/monday.htm Synthetic Biology 3.0], Z&uuml;rich, 2007.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/e/e6/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/e/e6/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.ppt Slides]
|}
== Computing about Molecules ==
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//http://mriedel.ece.umn.edu/wiki/images/e/e6/ISMCO_netMHC.pdf The Role of Hydrophobicity in Peptide-MHC Binding]
|- valign="top"
| '''authors''':
| [[Arnav Solanki]], [[Marc Riedel]], [https://orion.math.iastate.edu/cornette/ James Cornette], [[Julia Udell]], Ishaan Koratkar, and [https://www.mayo.edu/research/faculty/vasmatzis-george-ph-d/bio-00027811 George Vasmatzis]
|- valign="top"
| '''presented&nbsp;at''':
| [http://ismco.net/ 3rd International Symposium on Mathematical and Computational Oncology], 2021
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/e/e6/ISMCO_netMHC.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>
[//http://mriedel.ece.umn.edu/wiki/images/e/e6/ISMCO_netMHC.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/8/8b/ISMCO2021.pdf http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br>
[http://mriedel.ece.umn.edu/wiki/images/8/8b/ISMCO2021.pdf Slides]
|}
View an interactive version of the data for this paper [https://hydrophobicitydata.ishaankoratkar.repl.co here].
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/8/86/Kulkarni_Arastoo_Bhat_Subramanian_Kothare_Riedel_Gene_Regulatory_Network_Modeling_Using_Literature_Curated_and_High_Throughput_Data.pdf Gene Regulatory Network Modeling Using Literature Curated and High Throughput Data]
|- valign="top"
| '''authors''':
| [http://www2.warwick.ac.uk/fac/sci/eng/people/bio/?tag=vk Vishwesh Kulkarni], Reza Arastoo, Anupama Bhat,<br>Kalyansundaram Subramanian, Mayuresh Kothare, Marc Riedel and [[Marc Riedel]]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://www.springer.com/biomed/journal/11693 Systems and Synthetic Biology], Vol. 6, No. 3&ndash;4, pp. 69--77, 2012
|}
| width="70" align="center" |
<span class="plainlinks">
[http://cctbio.ece.umn.edu/wiki/images/8/86/Kulkarni_Arastoo_Bhat_Subramanian_Kothare_Riedel_Gene_Regulatory_Network_Modeling_Using_Literature_Curated_and_High_Throughput_Data.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/8/86/Kulkarni_Arastoo_Bhat_Subramanian_Kothare_Riedel_Gene_Regulatory_Network_Modeling_Using_Literature_Curated_and_High_Throughput_Data.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/2/2b/Kulkarni_Kareenhalli_Viswananthan_Riedel_Characterizing_the_Memory_of_the_GAL_Regulatory_Network_in_Saccharomyces_cerevisiae.pdf Characterizing the Memory of the GAL Regulatory Network in<br> ''Saccharomyces cerevisiae'']
|- valign="top"
| '''authors''':
| Vishwesh Kulkarni, [http://www.che.iitb.ac.in/online/node/63 Venkatesh Kareenhalli], Ganesh Viswananthan, and [[Marc Riedel]]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://www.springer.com/biomed/journal/11693 Systems and Synthetic Biology], Vol. 5, No. 3&ndash;4, pp. 97--104, 2011
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/2/2b/Kulkarni_Kareenhalli_Viswananthan_Riedel_Characterizing_the_Memory_of_the_GAL_Regulatory_Network_in_Saccharomyces_cerevisiae.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/2/2b/Kulkarni_Kareenhalli_Viswananthan_Riedel_Characterizing_the_Memory_of_the_GAL_Regulatory_Network_in_Saccharomyces_cerevisiae.pdf Paper]
|}


== Computing with Random Bit Streams  ==
== Computing with Random Bit Streams  ==
Line 646: Line 1,136:
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Qian_Riedel_The_Synthesis_of_Robust_Polynomial_Arithmetic_with_Stochastic_Logic.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Qian_Riedel_The_Synthesis_of_Robust_Polynomial_Arithmetic_with_Stochastic_Logic.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Qian_Riedel_The_Synthesis_of_Robust_Polynomial_Arithmetic_with_Stochastic_Logic.ppt Slides]
<br> [http://mriedel.ece.umn.edu/files/Qian_Riedel_The_Synthesis_of_Robust_Polynomial_Arithmetic_with_Stochastic_Logic.ppt Slides]
|}
== Computing with Molecules ==
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//http://mriedel.ece.umn.edu/wiki/images/e/e0/DNA27_SIMD_DNA.pdf Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching]
|- valign="top"
| '''authors''':
| [[Tonglin Chen]], [[Arnav Solanki]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://dna27.iopconfs.org/home International Conference on DNA Computing and Molecular Programming], 2021
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/e/e0/DNA27_SIMD_DNA.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/e/e0/DNA27_SIMD_DNA.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/d/d5/DNA27_Presentation.pdf http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/d/d5/DNA27_Presentation.pdf Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//http://mriedel.ece.umn.edu/wiki/images/5/58/VCIP2021_Blind.pdf Cascadable Stochastic Logic for DNA Storage]
|- valign="top"
| '''authors''':
| [[Arnav Solanki]], [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://www.vcip2021.org/ Visual Communications and Image Processing], 2021
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/5/58/VCIP2021_Blind.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/5/58/VCIP2021_Blind.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/8/81/FNANO20_Random_Cutting.pdf Stochastic Computation on DNA strands through Hydroxyl Nicking]
|- valign="top"
| '''authors''':
| [[Arnav Solanki]], [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://www2.cs.duke.edu/FNANO/ Foundations of Nanoscience: Self-Assembled Architectures and Devices], 2020
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/8/81/FNANO20_Random_Cutting.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/8/81/FNANO20_Random_Cutting.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/2/29/FNANO_poster2020.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/2/29/FNANO_poster2020.pdf Poster]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [http://mriedel.ece.umn.edu/wiki/images/3/38/Chen_Solanki_Riedel_Concentration-Based-Polynomial-Calculations-on-Nicked-DNA.pdf Concentration-Based-Polynomial-Calculations-on-Nicked-DNA]
|- valign="top"
| '''authors''':
| [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://rc.signalprocessingsociety.org/conferences/icassp-2020/SPSICASSP20VID1364.html IEEE International Conference on Acoustics, Speech, and Signal Processing], 2020
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/3/38/Chen_Solanki_Riedel_Concentration-Based-Polynomial-Calculations-on-Nicked-DNA.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[http://mriedel.ece.umn.edu/wiki/images/3/38/Chen_Solanki_Riedel_Concentration-Based-Polynomial-Calculations-on-Nicked-DNA.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/4/4c/Chen_Riedel_Parallel_Binary_Sorting_and_Shifting_with_DNA.pdf Parallel Binary Sorting and Shifting with DNA]
|- valign="top"
| '''authors''':
| [[Tonglin Chen]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [https://www.iwbdaconf.org/2019/ International Workshop on Bio-Design Automation], Cambridge, England, 2019.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/4/4c/Chen_Riedel_Parallel_Binary_Sorting_and_Shifting_with_DNA.pdf http://cctbio.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/4/4c/Chen_Riedel_Parallel_Binary_Sorting_and_Shifting_with_DNA.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/4/41/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding.pdf Computing Mathematical Functions using DNA via Fractional Coding]
|- valign="top"
| '''authors''':
| [https://www.engr.uky.edu/directory/salehi-sayed-ahmad Ahmad Salehi], Xingyi Liu, [[Marc Riedel]], and [http://people.ece.umn.edu/~parhi/ Keshab K. Parhi]
|- valign="top"
| '''appeared in''':
| [https://www.nature.com/articles/s41598-018-26709-6 Nature Scientific Reports], Vol. 8 No. 8312, 2018
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/4/41/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>
[//mriedel.ece.umn.edu/wiki/images/4/41/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/9/91/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding_Supplement.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>
[//mriedel.ece.umn.edu/wiki/images/9/91/Salehi_Liu_Riedel_Parhi_Computation_of_Mathematical_Functions_using_DNA_via_Fractional_Coding_Supplement.pdf Supplement]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/d/d7/Salehi_Parhi_Riedel_Chemical_Reaction_Networks_for_Computing_Polynomials.pdf Chemical Reaction Networks for Computing Polynomials]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [http://www.ece.umn.edu/users/parhi Keshab Parhi] and  [[Marc Riedel]]
|- valign="top"
| '''appeared as''':
| [http://pubs.acs.org/journal/asbcd6 ACS Synthetic Biology],Vol. 6, No. 1, pp. 76–83, 2017
|- valign="top"
| '''presented at''':
| [http://globecom2016.ieee-globecom.org IEEE Globecom Symposium, 2016]
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/d/d7/Salehi_Parhi_Riedel_Chemical_Reaction_Networks_for_Computing_Polynomials.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/4/47/Salehi_Riedel_Parhi_Chemical_Reaction_Networks_for_Computing_Polynomials.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/2/25/Salehi_Riedel_Parhi_Molecular_Sensing_and_Computing_Systems.pdf Molecular Sensing and Computing Systems]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [[Marc Riedel]], [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''appeared as''':
| [http://mbmc.info IEEE Trans. on Molecular, Biological, and Multi-Scale Communications],<br>Vol. 1, No. 3, 2015
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/2/25/Salehi_Riedel_Parhi_Molecular_Sensing_and_Computing_Systems.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://cctbio.ece.umn.edu/wiki/images/2/25/Salehi_Riedel_Parhi_Molecular_Sensing_and_Computing_Systems.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/c/c0/Salehi_Riedel_Parhi_Markov_Chain_Computations_using_Molecular_Reactions.pdf Markov Chain Computations using Molecular Reactions]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [[Marc Riedel]], [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.dsp2015.org IEEE International Conference on Digital Signal Processing], 2015.
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/c/c0/Salehi_Riedel_Parhi_Markov_Chain_Computations_using_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/c/c0/Salehi_Riedel_Parhi_Markov_Chain_Computations_using_Molecular_Reactions.pdf Paper]
| width="70" align="center" |
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/b/b3/Salehi_Riedel_Parhi_Asynchronous_Discrete-Time_Signal_Processing_with_Molecular_Reactions.pdf Asynchronous Discrete-Time Signal Processing with Molecular Reactions]
|- valign="top"
| '''authors''':
| [[Ahmad Salehi]], [[Marc Riedel]], and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.asilomarsscconf.org/webpage/asil14/post_conf.htm Asilomar Conference on Signals, Systems, and Computers], 2014.
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/b/b3/Salehi_Riedel_Parhi_Asynchronous_Discrete-Time_Signal_Processing_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/b/b3/Salehi_Riedel_Parhi_Asynchronous_Discrete-Time_Signal_Processing_with_Molecular_Reactions.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/c/cf/Jiang_Riedel_Parhi_Digital_Logic_with_Molecular_Reactions.pdf Digital Logic with Molecular Reactions]
|- valign="top"
| '''authors''':
| [[Hua Jiang]], [[Marc Riedel]], [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iccad.com IEEE/ACM International Conference on Computer-Aided Design],<br>San Jose, CA, 2013.
|}
| width="70" align="center" |
<span class="plainlinks">[http://cctbio.ece.umn.edu/wiki/images/c/cf/Jiang_Riedel_Parhi_Digital_Logic_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>[//mriedel.ece.umn.edu/wiki/images/c/cf/Jiang_Riedel_Parhi_Digital_Logic_with_Molecular_Reactions.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/3/36/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA.pdf Discrete-Time Signal Processing with DNA]
|- valign="top"
| '''authors''':
| [[Hua Jiang]], Ahmad Salehi, [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://pubs.acs.org/doi/abs/10.1021/sb300087n ACS Synthetic Biology], Vol. 2 no. 5, pp. 245&ndash;254, 2013.<br>[//mriedel.ece.umn.edu/wiki/images/4/40/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA_Appendix.pdf Supplementary Information: List of Reactions]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://www.computer.org/portal/web/dt IEEE Design & Test of Computers], Vol. 29, No. 3, pp. 21&ndash;31, 2012.
|- valign="top"
| '''presented at''':
| [http://www.iccad.com/ IEEE/ACM International Conference on Computer-Aided Design],<br> San Jose, CA, 2010.
|- valign="top"
| '''presented at''':
| [http://www.wikicfp.com/cfp/servlet/event.showcfp?eventid=7703&copyownerid=8242 IEEE Workshop on Signal Processing Systems], San Francisco, 2010
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/3/36/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/3/36/Jiang_Salehi_Riedel_Parhi_Discrete-Time_Signal_Processing_with_DNA.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/2/2a/Jiang_Kharam_Riedel_Parhi_Digital_Signal_Processing_with_Biomolecular_Reactions.pptx http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/2/2a/Jiang_Kharam_Riedel_Parhi_Digital_Signal_Processing_with_Biomolecular_Reactions.pptx Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/5/57/Kulkarni_Chanyaswad_Riedel_Kim_Robust_Tunable_In_Vitro_Transcriptional_Oscillator_Networks.pdf Robust Tunable ''In Vitro'' Transcriptional Oscillator Networks]
|- valign="top"
| '''authors''':
|  Vishwesh Kulkarni, [[Thee Chanyaswad]], [[Marc Riedel]] and Jongmin Kim
|- valign="top"
| '''presented at''':
| [http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6475439 Allerton Conference], Urbana-Champaign, IL, 2012.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/5/57/Kulkarni_Chanyaswad_Riedel_Kim_Robust_Tunable_In_Vitro_Transcriptional_Oscillator_Networks.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/5/57/Kulkarni_Chanyaswad_Riedel_Kim_Robust_Tunable_In_Vitro_Transcriptional_Oscillator_Networks.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/d/db/Senum_Riedel_Rate-Independent_Constructs_for_Chemical_Computation.pdf Rate-Independent Constructs for Chemical Computation]
|- valign="top"
| '''authors''':
| [[Phil Senum]] and [[Marc Riedel]]
|- valign="top"
| '''appeared in''':
| [http://dx.plos.org/10.1371/journal.pone.0021414 PLoS ONE], Vol. 6, No. 6, 2011.<br>[[Rate_Independent_Constructs_Supplementary_Information | Supplementary Information]]
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/d/db/Senum_Riedel_Rate-Independent_Constructs_for_Chemical_Computation.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/d/db/Senum_Riedel_Rate-Independent_Constructs_for_Chemical_Computation.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/d/d2/Senum_Riedel_Rate-Independent_Modules_for_Chemical_Computation.pptx http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/d/d2/Senum_Riedel_Rate-Independent_Modules_for_Chemical_Computation.pptx Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/0/07/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pdf Synchronous Sequential Computation with Molecular Reactions]
|- valign="top"
| '''authors''':
|  [[Hua Jiang]], [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented at''':
| [http://www.dac.com/dac+2011+conference+program.aspx ACM/EDAC/IEEE Design Automation Conference], San Diego, CA, 2011.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/0/07/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/0/07/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/9/9b/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pptx http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/9/9b/Jiang_Riedel_Parhi_Synchronous_Sequential_Computation_with_Molecular_Reactions.pptx Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/a/ab/Jiang_Riedel_Parhi_Asynchronous_Computation_with_Molecular_Reactions.pdf Asynchronous Computation with Molecular Reactions]
|- valign="top"
| '''authors''':
|  [[Hua Jiang]], [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented at''':
| [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6190049&filter=AND(p_Publication_Number:6185739) Asilomar Conference on Signals, Systems, and Computers], Pacific Grove, CA, 2011.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://cctbio.ece.umn.edu/wiki/images/a/ab/Jiang_Riedel_Parhi_Asynchronous_Computation_with_Molecular_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/a/ab/Jiang_Riedel_Parhi_Asynchronous_Computation_with_Molecular_Reactions.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/a/a7/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.pdf Binary Counting with Chemical Reactions]
|- valign="top"
| '''authors''':
| [[Aleksandra Kharam]], [[Hua Jiang]], [[Marc Riedel]] and [http://www.ece.umn.edu/users/parhi Keshab Parhi]
|- valign="top"
| '''presented at''':
| [http://psb.stanford.edu/psb-online/proceedings/psb11 Pacific Symposium on Biocomputing], Hawaii, 2011.
|}
| width="70" align="center" |
<span class="plainlinks">
[http://cadbio.com/wiki/images/a/a7/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://cadbio.com/wiki/images/a/a7/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/a/a6/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/a/a6/Kharam_Jiang_Riedel_Parhi_Binary_Counting_with_Chemical_Reactions.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/0/04/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.pdf Writing and Compiling Code into Biochemistry]
|- valign="top"
| '''authors''':
| [[Adam Shea]], [[Brian Fett]], [[Marc Riedel]], and [http://www.ece.umn.edu/~parhi/ Keshab Parhi]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iccad.com/events/eventdetails.aspx?id=106-2-C IEEE/ACM International Conference on Computer-Aided Design],<br>San Jose, CA, 2009; and at [http://psb.stanford.edu/psb-online/proceedings/psb10 Pacific Symposium on Biocomputing],<br> Kona, Hawaii, 2010 (see [http://friendfeed.com/pacific-symposium-for-bio/6476a568/marc-riedel-writing-and-compiling-code-into blog]).
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iwls.org/iwls2009/ IEEE/ACM International Workshop on Logic and Synthesis], Berkeley, 2009
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/0/04/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span><br>[//mriedel.ece.umn.edu/wiki/images/0/04/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Shea_Fett_Riedel_Parhi_Writing_and_Compiling_code_into_Biochemistry.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/3/37/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.pdf Stochastic Transient Analysis of Biochemical Systems]
|- valign="top"
| '''authors''':
| [[Bin Cheng]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://psb.stanford.edu Pacific Symposium on Biocomputing], Hawaii, 2009.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/3/37/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/3/37/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Cheng_Riedel_Stochastic_Transient_Analysis_of_Biochemical_Systems.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/6/66/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.pdf Module Locking in Biochemical Systems]
|- valign="top"
| '''authors''':
| [[Brian Fett]] and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.iccad.com/events/eventdetails.aspx?id=86-10-A IEEE/ACM International Conference on Computer-Aided Design],<br>San Jose, CA, 2008; and at [http://sb4.biobricks.org Synthetic Biology 4.0], Hong Kong, 2008.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/6/66/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/6/66/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Fett_Riedel_Module_Locking_in_Biochemical_Synthesis.ppt Slides]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/e/e6/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.pdf Synthesizing Stochasticity in Biochemical Systems]
|- valign="top"
| '''authors''':
| [[Brian Fett]], [http://paradise.caltech.edu/bruck.html Shuki Bruck], and [[Marc Riedel]]
|- valign="top"
| '''presented&nbsp;at''':
| [http://www.dac.com/45th/index.aspx ACM/EDAC/IEEE Design Automation Conference], San Diego, 2007; and at<br>[http://www.syntheticbiology3.ethz.ch/monday.htm Synthetic Biology 3.0], Z&uuml;rich, 2007.
|}
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/wiki/images/e/e6/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/e/e6/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">[http://mriedel.ece.umn.edu/files/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.ppt http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br> [http://mriedel.ece.umn.edu/files/Fett_Bruck_Riedel_Synthesizing_Stochasticity_in_Biochemical_Systems.ppt Slides]
|}
== Computing about Molecules ==
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//http://mriedel.ece.umn.edu/wiki/images/e/e6/ISMCO_netMHC.pdf The Role of Hydrophobicity in Peptide-MHC Binding]
|- valign="top"
| '''authors''':
| [[Arnav Solanki]], [[Marc Riedel]], [https://orion.math.iastate.edu/cornette/ James Cornette], [[Julia Udell]], Ishaan Koratkar, and [https://www.mayo.edu/research/faculty/vasmatzis-george-ph-d/bio-00027811 George Vasmatzis]
|- valign="top"
| '''presented&nbsp;at''':
| [http://ismco.net/ 3rd International Symposium on Mathematical and Computational Oncology], 2021
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/e/e6/ISMCO_netMHC.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br>
[//http://mriedel.ece.umn.edu/wiki/images/e/e6/ISMCO_netMHC.pdf Paper]
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/8/8b/ISMCO2021.pdf http://mriedel.ece.umn.edu/wiki/images/3/36/Ppt.jpg]</span>
<br>
[http://mriedel.ece.umn.edu/wiki/images/8/8b/ISMCO2021.pdf Slides]
|}
View an interactive version of the data for this paper [https://hydrophobicitydata.ishaankoratkar.repl.co here].
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/8/86/Kulkarni_Arastoo_Bhat_Subramanian_Kothare_Riedel_Gene_Regulatory_Network_Modeling_Using_Literature_Curated_and_High_Throughput_Data.pdf Gene Regulatory Network Modeling Using Literature Curated and High Throughput Data]
|- valign="top"
| '''authors''':
| [http://www2.warwick.ac.uk/fac/sci/eng/people/bio/?tag=vk Vishwesh Kulkarni], Reza Arastoo, Anupama Bhat,<br>Kalyansundaram Subramanian, Mayuresh Kothare, Marc Riedel and [[Marc Riedel]]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://www.springer.com/biomed/journal/11693 Systems and Synthetic Biology], Vol. 6, No. 3&ndash;4, pp. 69--77, 2012
|}
| width="70" align="center" |
<span class="plainlinks">
[http://cctbio.ece.umn.edu/wiki/images/8/86/Kulkarni_Arastoo_Bhat_Subramanian_Kothare_Riedel_Gene_Regulatory_Network_Modeling_Using_Literature_Curated_and_High_Throughput_Data.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [//mriedel.ece.umn.edu/wiki/images/8/86/Kulkarni_Arastoo_Bhat_Subramanian_Kothare_Riedel_Gene_Regulatory_Network_Modeling_Using_Literature_Curated_and_High_Throughput_Data.pdf Paper]
|}
{|
|
{| style="background:#F0E68C"
|- valign="top"
| width="100" | '''title''':
| width="500" | [//mriedel.ece.umn.edu/wiki/images/2/2b/Kulkarni_Kareenhalli_Viswananthan_Riedel_Characterizing_the_Memory_of_the_GAL_Regulatory_Network_in_Saccharomyces_cerevisiae.pdf Characterizing the Memory of the GAL Regulatory Network in<br> ''Saccharomyces cerevisiae'']
|- valign="top"
| '''authors''':
| Vishwesh Kulkarni, [http://www.che.iitb.ac.in/online/node/63 Venkatesh Kareenhalli], Ganesh Viswananthan, and [[Marc Riedel]]
|- valign="top"
| '''appeared&nbsp;in''':
| [http://www.springer.com/biomed/journal/11693 Systems and Synthetic Biology], Vol. 5, No. 3&ndash;4, pp. 97--104, 2011
|}
| width="70" align="center" |
<span class="plainlinks">
[http://mriedel.ece.umn.edu/wiki/images/2/2b/Kulkarni_Kareenhalli_Viswananthan_Riedel_Characterizing_the_Memory_of_the_GAL_Regulatory_Network_in_Saccharomyces_cerevisiae.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
<br> [http://mriedel.ece.umn.edu/wiki/images/2/2b/Kulkarni_Kareenhalli_Viswananthan_Riedel_Characterizing_the_Memory_of_the_GAL_Regulatory_Network_in_Saccharomyces_cerevisiae.pdf Paper]
|}
|}


Revision as of 16:10, 2 July 2023

Here are links to our papers, theses, proposals, and presentations. When several version of a paper were published, for instance one in conference proceedings and another in a journal, these are grouped together and only the most significant version is linked. All materials are subject to copyrights.

Computing with Molecules

title: Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching
authors: Tonglin Chen, Arnav Solanki and Marc Riedel
presented at: International Conference on DNA Computing and Molecular Programming, 2021

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Paper

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Slides

title: Cascadable Stochastic Logic for DNA Storage
authors: Arnav Solanki, Tonglin Chen and Marc Riedel
presented at: Visual Communications and Image Processing, 2021

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Paper

title: Stochastic Computation on DNA strands through Hydroxyl Nicking
authors: Arnav Solanki, Tonglin Chen and Marc Riedel
presented at: Foundations of Nanoscience: Self-Assembled Architectures and Devices, 2020

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Paper

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Poster

title: Concentration-Based-Polynomial-Calculations-on-Nicked-DNA
authors: Tonglin Chen and Marc Riedel
presented at: IEEE International Conference on Acoustics, Speech, and Signal Processing, 2020

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Paper

title: Parallel Binary Sorting and Shifting with DNA
authors: Tonglin Chen and Marc Riedel
presented at: International Workshop on Bio-Design Automation, Cambridge, England, 2019.

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Paper

title: Computing Mathematical Functions using DNA via Fractional Coding
authors: Ahmad Salehi, Xingyi Liu, Marc Riedel, and Keshab K. Parhi
appeared in: Nature Scientific Reports, Vol. 8 No. 8312, 2018

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Paper

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Supplement

title: Chemical Reaction Networks for Computing Polynomials
authors: Ahmad Salehi, Keshab Parhi and Marc Riedel
appeared as: ACS Synthetic Biology,Vol. 6, No. 1, pp. 76–83, 2017
presented at: IEEE Globecom Symposium, 2016

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Paper

title: Molecular Sensing and Computing Systems
authors: Ahmad Salehi, Marc Riedel, Keshab Parhi
appeared as: IEEE Trans. on Molecular, Biological, and Multi-Scale Communications,
Vol. 1, No. 3, 2015

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Paper

title: Markov Chain Computations using Molecular Reactions
authors: Ahmad Salehi, Marc Riedel, Keshab Parhi
presented at: IEEE International Conference on Digital Signal Processing, 2015.

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Paper

title: Asynchronous Discrete-Time Signal Processing with Molecular Reactions
authors: Ahmad Salehi, Marc Riedel, and Keshab Parhi
presented at: Asilomar Conference on Signals, Systems, and Computers, 2014.

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Paper

title: Digital Logic with Molecular Reactions
authors: Hua Jiang, Marc Riedel, Keshab Parhi
presented at: IEEE/ACM International Conference on Computer-Aided Design,
San Jose, CA, 2013.

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Paper

title: Discrete-Time Signal Processing with DNA
authors: Hua Jiang, Ahmad Salehi, Marc Riedel and Keshab Parhi
appeared in: ACS Synthetic Biology, Vol. 2 no. 5, pp. 245–254, 2013.
Supplementary Information: List of Reactions
appeared in: IEEE Design & Test of Computers, Vol. 29, No. 3, pp. 21–31, 2012.
presented at: IEEE/ACM International Conference on Computer-Aided Design,
San Jose, CA, 2010.
presented at: IEEE Workshop on Signal Processing Systems, San Francisco, 2010

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Paper

Ppt.jpg
Slides

title: Robust Tunable In Vitro Transcriptional Oscillator Networks
authors: Vishwesh Kulkarni, Thee Chanyaswad, Marc Riedel and Jongmin Kim
presented at: Allerton Conference, Urbana-Champaign, IL, 2012.

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Paper

title: Rate-Independent Constructs for Chemical Computation
authors: Phil Senum and Marc Riedel
appeared in: PLoS ONE, Vol. 6, No. 6, 2011.
Supplementary Information

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Paper

Ppt.jpg
Slides

title: Synchronous Sequential Computation with Molecular Reactions
authors: Hua Jiang, Marc Riedel and Keshab Parhi
presented at: ACM/EDAC/IEEE Design Automation Conference, San Diego, CA, 2011.

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Paper

Ppt.jpg
Slides

title: Asynchronous Computation with Molecular Reactions
authors: Hua Jiang, Marc Riedel and Keshab Parhi
presented at: Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, 2011.

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Paper

title: Binary Counting with Chemical Reactions
authors: Aleksandra Kharam, Hua Jiang, Marc Riedel and Keshab Parhi
presented at: Pacific Symposium on Biocomputing, Hawaii, 2011.

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Paper

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Slides

title: Writing and Compiling Code into Biochemistry
authors: Adam Shea, Brian Fett, Marc Riedel, and Keshab Parhi
presented at: IEEE/ACM International Conference on Computer-Aided Design,
San Jose, CA, 2009; and at Pacific Symposium on Biocomputing,
Kona, Hawaii, 2010 (see blog).
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, 2009

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Paper

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Slides

title: Stochastic Transient Analysis of Biochemical Systems
authors: Bin Cheng and Marc Riedel
presented at: Pacific Symposium on Biocomputing, Hawaii, 2009.

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Paper

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title: Module Locking in Biochemical Systems
authors: Brian Fett and Marc Riedel
presented at: IEEE/ACM International Conference on Computer-Aided Design,
San Jose, CA, 2008; and at Synthetic Biology 4.0, Hong Kong, 2008.

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Paper

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title: Synthesizing Stochasticity in Biochemical Systems
authors: Brian Fett, Shuki Bruck, and Marc Riedel
presented at: ACM/EDAC/IEEE Design Automation Conference, San Diego, 2007; and at
Synthetic Biology 3.0, Zürich, 2007.

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Paper

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Computing about Molecules

title: The Role of Hydrophobicity in Peptide-MHC Binding
authors: Arnav Solanki, Marc Riedel, James Cornette, Julia Udell, Ishaan Koratkar, and George Vasmatzis
presented at: 3rd International Symposium on Mathematical and Computational Oncology, 2021

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Paper

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Slides

View an interactive version of the data for this paper here.

title: Gene Regulatory Network Modeling Using Literature Curated and High Throughput Data
authors: Vishwesh Kulkarni, Reza Arastoo, Anupama Bhat,
Kalyansundaram Subramanian, Mayuresh Kothare, Marc Riedel and Marc Riedel
appeared in: Systems and Synthetic Biology, Vol. 6, No. 3–4, pp. 69--77, 2012

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Paper

title: Characterizing the Memory of the GAL Regulatory Network in
Saccharomyces cerevisiae
authors: Vishwesh Kulkarni, Venkatesh Kareenhalli, Ganesh Viswananthan, and Marc Riedel
appeared in: Systems and Synthetic Biology, Vol. 5, No. 3–4, pp. 97--104, 2011

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Paper

Computing with Random Bit Streams

title: A Scalable Deterministic Approach to Stochastic Computing
authors: Yadu Kiran and Marc Riedel
appeared in: Great Lakes Symposium on VLSI (GLSVLSI), 2022

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Paper

title: Performing Stochastic Computation Deterministically
authors: M. Hassan Najafi, Devon Jenson, David Lilja, and Marc Riedel
appeared in: IEEE Transactions on Very Large Scale Integration (VLSI) Systems,
Vol. 27, No. 29, pp. 2925–2938, 2019
presented at: IEEE International Symposium of Circuits and Systems, 2020
presented at: IEEE/ACM International Conference on Computer-Aided Design, 2016

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Paper

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title: Synthesis of Polynomial Functions
authors: Weikang Qian and Marc Riedel
appeared in: Chapter 4, Stochastic Computing: Techniques and Applications,
Springer, W.J Gross and V. C. Gaudet, Editors, pp. pp. 103–120, 2019

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Paper

title: Deterministic Approaches to Bitstream Computing
authors: Marc Riedel
appeared in: Chapter 5, Stochastic Computing: Techniques and Applications,
Springer, W.J Gross and V. C. Gaudet, Editors, pp. pp. 121–136, 2019

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Paper

title: A Survey of Computation-Driven Data Encodings
authors: Weikang Qian, Runsheng Wang, Yuan Wang, Marc Riedel and Ru Huang
presented at: IEEE Workshop on Signal Processing Systems, 2019

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Paper

title: Deterministic Methods for Stochastic Computing using Low-Discrepancy Sequences
authors: M. Hassan Najafi, David Lilja, and Marc Riedel
presented at: IEEE/ACM International Conference on Computer-Aided Design, 2018

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Paper

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title: Low Cost Sorting Network Circuits using Unary Processing
authors: M. Hassan Najafi, David Lilja, Marc Riedel, and Kia Bazargan
appeared in: IEEE Trans. on Very Large Scale Integration Sytems,
Vol. 26, No. 8, pp. 1471–1480, 2018
presented at: IEEE International Conference on Computer Design, 2017

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Paper

title: An Overview of Time-Based Computing with Stochastic Constructs
authors: M. Hassan Najafi, S. Jamali-Zavareh, David Lilja, Marc Riedel, Kia Bazargan and
Ramesh Harjani
appeared in: IEEE Micro, Vol. 37, No. 6, pp. 62--71, 2017 

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Paper

title: Time-Encoded Values for Highly Efficient Stochastic Circuits
authors: M. Hassan Najafi, S. Jamali-Zavareh, David Lilja, Marc Riedel, Kia Bazargan and
Ramesh Harjani
appeared in: IEEE Transactions on VLSI, Vol. 25, No. 5, pp. 1644–1657, 2017
presented at: IEEE International Symposium on Circuits and Systems, 2017

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Paper

title: Unary Positional Computing
authors: McKenzie van der Hagen and Marc Riedel
presented at: IEEE Global Conference on Signal and Information Processing, 2017

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Paper

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Poster

title: Computing Polynomials with Positive Coefficients using Stochastic Logic by Double NAND Expansion
authors: Ahmad Salehi, Yin Liu, Marc Riedel, and Keshab Parhi
presented at: ACM Great Lakes Symposium on VLSI, 2017

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Paper

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title: Polysynchronous Clocking: Exploiting the Skew Tolerance of Stochastic Circuits
authors: M. Hassan Najafi, David Lilja, Marc Riedel, and Kia Bazargan
appeared in: IEEE Transactions on Computers, Vol. 66, No. 10, pp. 1734–1746, 2017
Feature Paper of the Month
presented at: Work-in-Progress Session, IEEE/ACM Design Automation Conference, 2016
presented at: IEEE/ACM Asia and South Pacific Design Automation Conference, 2016

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Paper

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title: A Reconfigurable Architecture with Sequential Logic-based Stochastic Computing
authors: M. Hassan Najafi, Peng Li, David J. Lilja, Weikang Qian and Marc Riedel
appeared in: ACM Journal on Emerging Technologies in Computing Systems,
Vol. 13, No. 4, pp. 1–28, 2017

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Paper

title: Synthesis of Correlated Bit Streams for Stochastic Computing
authors: Yin Liu, Megha Parhi, Marc Riedel and Keshab Parhi
presented at: Asilomar Conference on Signals, Systems, and Computers, 2016

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Paper

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Slides

title: Effect of Bit-Level Correlation in Stochastic Computing
authors: Megha Parhi, Marc Riedel, and Keshab Parhi
presented at: IEEE International Conference on Digital Signal Processing, Singapore, 2015.

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Paper

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title: Computation on Stochastic Bit Streams: Digital Image Processing Case Studies
authors: Peng Li, David Lilja, Weikang Qian, Kia Bazargan and Marc Riedel
appeared in: IEEE Transactions on VLSI Sytems, Vol. 22, No. 3, pp. 449–462, 2014
appeared in: Lecture Notes in Computer Science
Power and Timing Modeling, Optimization and Simulation Workshop
G. Goos, J. Hartmanis, and J. V. Leeuwen Editors, Springer, pp. 235–244, 2012

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Paper

title: Logical Computation on Stochastic Bit Streams with Linear Finite State Machines
authors: Peng Li, David Lilja, Weikang Qian,Kia Bazargan and Marc Riedel
appeared in: IEEE Transactions on Computers, Vol. 63, No. 6., pp. 1474–1486, 2014
presented at: IEEE/ACM Asia and South Pacific Design Automation Conference,
Sydney, Australia, 2012

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Paper

title: IIR Filters Using Stochastic Arithmetic
authors: Naman Saraf, Kia Bazargan, David Lilja, and Marc Riedel
appeared in: IEEE/ACM Design, Automation, and Test in Europe, 2014

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Paper

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Slides

title: Stochastic Functions Using Sequential Logic
authors: Naman Saraf, Kia Bazargan, David Lilja, and Marc Riedel
appeared in: IEEE International Conference on Computer Design, Asheville, NC, 2013

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Paper

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Slides

title: An Efficient Implementation of Numerical Integration Using Logical Computation
on Stochastic Bit Streams
authors: Weikang Qian, Cheng Wang, Peng Li, David Lilja,
Kia Bazargan and Marc Riedel
appeared in: IEEE/ACM Int'l Conference on Computer-Aided Design, San Jose, CA 2012

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Paper

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Slides

title: The Synthesis of Complex Arithmetic Computation on Stochastic Bit Streams Using Sequential Logic
authors: Peng Li, David Lilja, Weikang Qian, Kia Bazargan and Marc Riedel
presented at: IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA 2012
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA 2012

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Paper

title: Transforming Probabilities with Combinational Logic
authors: Weikang Qian, Marc Riedel, Hongchao Zhou, and Jehoshua Bruck
appeared in: IEEE Trans. on Computer-Aided Design of Integrated Circuits and Systems,
Vol. 30, No. 9, pp. 1279–1292, 2011
appeared in: Advanced Techniques in Logic Synthesis, Optimizations and Applications
Sunil Khatri and Kanupriya Gulati editors, Springer Publishing, 2011
presented at: IEEE/ACM International Conference on Computer-Aided Design, San Jose, 2009
(nominated for IEEE/ACM William J. McCalla ICCAD Best Paper Award).
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA, 2009

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title: An Architecture for Fault-Tolerant Computation with Stochastic Logic
authors: Weikang Qian, Xin Li, Marc Riedel, Kia Bazargan, and David Lilja
appeared in: IEEE Transactions on Computers, Vol. 60, No. 1, pp. 93–105, 2011

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Paper

title: The Synthesis of Stochastic Circuits for Nanoscale Computation
authors: Weikang Qian, John Backes, and Marc Riedel
appeared in: International Journal of Nanotechnology and Molecular Computation,
Vol. 1, No. 4, pp. 39–57, 2010
presented at: IEEE/ACM International Workshop on Logic and Synthesis, San Diego, CA, 2007

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Paper

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title: Two-Level Logic Synthesis for Probabilistic Computation
authors: Weikang Qian and Marc Riedel
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Irvine, CA, 2010

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Paper

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title: A Reconfigurable Stochastic Architecture for Highly Reliable Computing
authors: Xin Li, Weikang Qian, Marc Riedel, Kia Bazargan, and David Lilja
presented at: Great Lakes Symposium on VLSI, Boston, MA, 2009

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Paper

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title: Estimation and Optimization of Reliability of Noisy Digital Circuits
authors: Satish Sivaswamy, Kia Bazargan and Marc Riedel
presented at: IEEE International Symposium on Quality Electronic Design, San Jose, CA, 2009.

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Paper

title: The Synthesis of Stochastic Logic to Perform Multivariate Polynomial Arithmetic
authors: Weikang Qian and Marc Riedel
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Lake Tahoe, CA, 2008

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Paper

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Poster

title: The Synthesis of Robust Polynomial Arithmetic with Stochastic Logic
authors: Weikang Qian and Marc Riedel
presented at: ACM/EDAC/IEEE Design Automation Conference, Anaheim, CA, 2008

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Paper

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Computing with Nanoscale Lattices

title: Logic Synthesis for Switching Lattices
authors: Mustafa Altun and Marc Riedel
appear in: IEEE Transactions on Computers, Vol. 61, No. 11, pp. 1588–1600, 2012.
presented at: ACM/EDAC/IEEE Design Automation Conference, Anaheim, CA, 2010.

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Paper

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title: Synthesizing Logic with Percolation in Nanoscale Lattices
authors: Mustafa Altun and Marc Riedel
appeared in: International Journal of Nanotechnology and Molecular Computation,
Vol. 3, No. 2, pp. 12–30, 2011.
presented at: ACM/EDAC/IEEE Design Automation Conference, San Francisco, CA, 2009.

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Computing with Feedback

title: Cyclic Boolean Circuits
authors: Marc Riedel and Shuki Bruck
appeared  in: Discrete Applied Mathematics, Vol. 160, No. 13–14, pp. 1877–1900, 2012

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Paper

title: The Synthesis of Cyclic Dependencies with Boolean Satisfiability
authors: John Backes and Marc Riedel
appeared in: ACM Transactions on Design Automation of Electronic Systems
Vol. 17, No. 4, pp. 1–24, 2012

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Paper

title: The Analysis and Mapping of Cyclic Circuits with Boolean Satisfiability
authors: John Backes, Brian Fett, and Marc Riedel
appeared as: Technical Report, UMN
presented at: IEEE/ACM Int'l Conference on Computer-Aided Design, San Jose, CA, 2008

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Paper

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title: The Synthesis of Cyclic Dependencies with Craig Interpolation
authors: John Backes and Marc Riedel
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA, 2009

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Paper

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Slides

title: Timing Analysis of Cyclic Combinational Circuits
authors: Marc Riedel and Shuki Bruck
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Temecula, CA, 2004

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Paper

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Slides

title: Cyclic Combinational Circuits: Analysis for Synthesis
authors: Marc Riedel and Shuki Bruck
presented at: IEEE/ACM Int'l Workshop on Logic and Synthesis, Orange County, CA, 2003

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Paper

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Slides

title: The Synthesis of Cyclic Combinational Circuits
authors: Marc Riedel and Shuki Bruck
presented at: ACM/EDAC/IEEE Design Automation Conference, Anahiem, CA, 2003
(winner of DAC Best Paper Award).

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Paper

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Algorithms and Data Structures

title: Using Cubes of Non-state Variables With Property Directed Reachability
authors: John Backes and Marc Riedel
presented at: IEEE/ACM Design Automation & Test in Europe, Grenoble, France, 2013

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Paper

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Poster

title: Resolution Proofs as a Data Structure For Logic Synthesis
authors: John Backes and Marc Riedel
presented at: IEEE/ACM International Workshop on Logic Synthesis, La Jolla, CA, 2011

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Paper

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Slides

title: Reduction of Interpolants For Logic Synthesis
authors: John Backes and Marc Riedel
presented at: IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA, 2010
presented at: IEEE/ACM International Workshop on Logic Synthesis, Irvine, CA, 2010

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Paper

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Mathematics

title: A Study on Monotone Self-Dual Boolean Functions
authors: Mustafa Altun and Marc Riedel
appeared in: Acta Mathematicae Applicatae Sinica, Vol. 33, No. 1, pp. 43–52, 2017

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Paper

title: Synthesizing Cubes to Satisfy a Given Intersection Pattern
authors: Weikang Qian, Marc Riedel, and Ivo Rosenberg
appeared in: Journal of Discrete Applied Mathematics, Vol. 193, pp. 11–38, 2015
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Irvine, CA, 2010

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title: Networks of Passive Oscillators
authors: Vishwesh V. Kulkarni, Marc Riedel, and Guy-Bart Stan
presented at: Allerton Conference, Urbana-Champaign, Illinois, 2011

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title: Uniform Approximation and Bernstein Polynomials with Coefficients in the Unit Interval
authors: Weikang Qian, Marc Riedel, and Ivo Rosenberg
appeared in: European Journal of Combinatorics, Vol. 32, No. 3, pp. 448–463, 2011

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Theses

title: Simulating Chemical Reaction Networks for Computing with Naturally-Occurring DNA
author: Owen Hoffend
degree: B.S., Computer Engineering, University of Minnesota
year: 2020.

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Senior Honors Thesis

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title: Algorithms and Data Structures For Logic Synthesis And Verification
Using Boolean Satisfiability
(received the University of Minnesota Doctoral Dissertation Fellowship)
author: John Backes
degree: Ph.D., Electrical and Computer Engineering, University of Minnesota
year: 2013.

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Ph.D. Dissertation

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Slides

title: Digital Logic and Signal Processing Computations with Molecular Reactions
author: Hua Jiang
degree: Ph.D., Electrical Engineering, University of Minnesota
year: 2012.

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Ph.D. Dissertation

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Slides

title: Logic Synthesis for Networks of Four-Terminal Switches
author: Mustafa Altun
degree: Ph.D., Electrical Engineering, University of Minnesota
year: 2012.

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Ph.D. Dissertation

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Slides

title: Digital Yet Deliberately Random:
Synthesizing Logical Computation on.Stochastic Bit Streams
(received the University of Minnesota Doctoral Dissertation Fellowship)
author: Weikang Qian
degree: Ph.D., Electrical Engineering, University of Minnesota
year: 2011.

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Ph.D. Dissertation

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Slides

title: Synthesizing Stochasticity in Biochemical Systems
author: Brian Fett
degree: M.S., Biomedical Informatics and Computational Biology,
University of Minnesota
year: 2010.

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M.S. Thesis

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title: Stochastic Transient Analysis of Biochemical Systems
author: Bin Cheng
degree: M.S., Electrical Engineering, University of Minnesota
year: 2010.

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M.S. Thesis

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title: Cyclic Combinational Circuits
author: Marc Riedel
degree: Ph.D., Electrical Engineering, Caltech, 2004
(winner of Charles H. Wilts Prize for the Best Ph.D. Dissertation in EE at Caltech)
year: 2004.

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Ph.D. Dissertation

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Funding Proposals

title: Back to the Future with Printed, Flexible Electronics:
Design in a Post-CMOS Era when Transistor Counts Matter Again
Investigators: Kia Bazargan, Daniel Frisbie, Ramesh Harjani, David Lilja and Marc Riedel.
Agency: National Science Foundation
Program: Software and Hardware Foundations
Award: $800,000
Duration: 2014 – 2017

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Proposal

title: Advanced Signal Processing with DNA
Investigators: Keshab Parhi and Marc Riedel
Agency: National Science Foundation
Program: Computing and Communications Foundations.
Amount: $300,000
Duration: 2014 – 2017

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Proposal

title: Digital Yet Deliberately Random:
Synthesizing Logical Computation on Stochastic Bit Streams
Investigators: Marc Riedel, Kia Bazargan, Ramesh Harjani, and David Lilja.
Agency: National Science Foundation
Program: Software and Hardware Foundations
Award: $300,000
Duration: 2012 – 2014

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Proposal

title: Digital Signal Processing with Biomolecular Reactions
Investigators: Keshab Parhi and Marc Riedel
Agency: National Science Foundation
Program: Computing and Communications Foundations
Amount: $400,000
Duration: 2011 – 2014

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Proposal

title: Synthesizing Signal Processing Functions with Biochemical Reactions
Investigators: Yiannis Kaznessis, Claudia Dannert Schmidt and Marc Riedel
Agency: University of Minnesota
Program: Digital Technology Center Seed Grant.
Amount: $100,000
Duration: 2011 – 2012

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Proposal

title: Computing with Things Small, Wet, and Random – Design Automation for Digital Computation with Nanoscale Technologies and Biological Processes
Investigator: Marc Riedel
Agency: National Science Foundation
Program: NSF CAREER Award
Amount: $500,000
Duration: 2009 – 2014

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Proposal

title: Synthesizing Signal Processing Functions with Biochemical Reactions
Investigators: Keshab Parhi and Marc Riedel
Agency: National Science Foundation
Program: Computing and Communications Foundations.
Amount: $200,000
Duration: 2009 – 2011

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Proposal

title: Tackling the Stochastic Simulation of Biochemical_Networks with Real Computing Power
Investigators: Marc Riedel and Tim Mullins (IBM)
Agency: University of Minnesota
Program: Biomedical Informatics and Computational Biology Traineeships
Amount: $78,000
Duration: 2007 – 2009

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Proposal

title: Concurrent Logical and Physical Design of Digital Nanoscale Circuits
Investigator: Marc Riedel
Agency: SRC Focus Center Research Program (FCRP)
Program: Functional Engineered Nano-Architectonics (FENA)
Amount: $325,000
Duration: 2006 – 2009

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Proposal



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