Difference between revisions of "Papers, Presentations, Theses, Proposals, and Patents"
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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 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 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 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 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 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 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 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 in''': | |||
| [http://pubs.acs.org/doi/abs/10.1021/sb300087n ACS Synthetic Biology], Vol. 2 no. 5, pp. 245–254, 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 in''': | |||
| [http://www.computer.org/portal/web/dt IEEE Design & Test of Computers], Vol. 29, No. 3, pp. 21–31, 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©ownerid=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 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 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 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 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 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], Zürich, 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 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 in''': | |||
| [http://www.springer.com/biomed/journal/11693 Systems and Synthetic Biology], Vol. 6, No. 3–4, 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 in''': | |||
| [http://www.springer.com/biomed/journal/11693 Systems and Synthetic Biology], Vol. 5, No. 3–4, 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] | ||
|} | |} | ||
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
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Computing about Molecules
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Computing with Random Bit Streams
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Computing with Nanoscale Lattices
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Computing with Feedback
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Algorithms and Data Structures
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Mathematics
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Theses
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Funding Proposals
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