Google Scholar page HERE.

Journal

  • Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy.
    Chandak, S., Tatwawadi, K., Sridhar, S. & Weissman, T.
    Bioinformatics, Volume 36, Issue 22-23, 1 December 2020, Pages 5313–5321
    [Bioinformatics] [biorXiv] [GitHub]

  • SPRING: a next-generation compressor for FASTQ data.
    Chandak, S., Tatwawadi, K., Ochoa, I., Hernaez, M., & Weissman, T.
    Bioinformatics, Volume 35, Issue 15, 1 August 2019, Pages 2674–2676
    [Bioinformatics] [GitHub]

  • Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis.
    Chandak, S., Tatwawadi, K., & Weissman, T.
    Bioinformatics, Volume 34, Issue 4, 15 February 2018, Pages 558–567
    [Bioinformatics] [GitHub]

  • An Actively Detuned Wireless Power Receiver With Public Key Cryptographic Authentication and Dynamic Power Allocation.
    Desai, N.V., Juvekar, C., Chandak, S., & Chandrakasan, A.P.
    IEEE Journal of Solid-State Circuits, vol. 53, no. 1, pp. 236-246, Jan. 2018.
    [IEEE] [press]

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Conference

  • On Coding for an Abstracted Nanopore Channel for DNA Storage.
    Hulett, R., Chandak, S., & Wootters, M.
    2021 IEEE International Symposium on Information Theory (ISIT), 2021, pp. 2465-2470.
    [IEEE] [arXiv]

  • DZip: improved general-purpose lossless compression based on novel neural network modeling.
    Goyal, M., Tatwawadi, K., Chandak, S., & Ochoa, I.
    2021 Data Compression Conference (DCC), Snowbird, UT, USA, 2021, pp. 153-162.
    [IEEE] [arXiv] [GitHub] [SigPort]

  • Reducing latency and bandwidth for video streaming using keypoint extraction and digital puppetry.
    Prabhakar, R., Chandak, S., Chiu, C., Liang, R., Nguyen, H., Tatwawadi, K., & Weissman, T.
    2021 Data Compression Conference (DCC), Snowbird, UT, USA, 2021, pp. 360-360.
    [IEEE] [arXiv] [GitHub] [website] [slides] [video] [SigPort]

  • Overcoming high nanopore basecaller error rates for DNA storage via basecaller-decoder integration and convolutional codes.
    Chandak, S., Neu, J., Tatwawadi, K., Mardia, J., Lau, B., Kubit, M., Hulett, R., Griffin, P., Wootters, M., Weissman, T., & Ji, H.
    ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Barcelona, Spain, 2020, pp. 8822-8826.
    [IEEE] [bioRxiv] [GitHub] [slides] [video]

  • LFZip: Lossy compression of multivariate floating-point time series data via improved prediction.
    Chandak S., Tatwawadi K., Wen C., Wang L., Aparicio J., & Weissman T.
    2020 Data Compression Conference (DCC), Snowbird, UT, USA, 2020, pp. 342-351.
    [IEEE] [arXiv] [GitHub] [slides] [video]
    Awarded Siemens Inventors of the year 2020 [press]

  • DZip: improved general-purpose lossless compression based on novel neural network modeling.
    Goyal, M., Tatwawadi, K., Chandak, S., & Ochoa, I.
    2020 Data Compression Conference (DCC), Snowbird, UT, USA, 2020, pp. 372-372.
    [IEEE] [arXiv] [GitHub] [poster]

  • Genie: an MPEG-G Conformant Software to Compress Genomic Data.
    Bliss B., Allen J., Baheti S., Bockol M., Chandak S., Delgado J., Fostier J., Gelpi J., Hart S., Arrazola M., Hudson M., Kalmbach M., Klee E., Mainzer L., Müntefering F., Naro D., Ochoa-Alvarez I., Ostermann J., Paridaens T., Ross C., Voges J., Wieben E., Yang M., Weissman T. & Wiepert M.
    International Conference for High Performance Computing, Networking, Storage and Analysis (SC19), p. (poster), Denver, CO (US), November 2019.
    [SC19] [poster] [summary] [GitHub]

  • Improved read/write cost tradeoff in DNA-based data storage using LDPC codes.
    Chandak, S., Tatwawadi, K., Lau, B., Mardia, J., Kubit, M., Neu, J., Griffin, P., Wootters, M., Weissman, T., & Ji, H.
    2019 57th Annual Allerton Conference on Communication, Control, and Computing (Allerton), Monticello, IL, USA, 2019, pp. 147-156.
    [IEEE] [bioRxiv] [GitHub] [slides]

  • Towards improved lossy image compression: Human image reconstruction with public-domain images.
    Bhown, A., Mukherjee, S., Yang, S., Chandak, S., Fischer-Hwang, I., Tatwawadi, K., Fan, J., & Weissman, T.
    2019 Data Compression Conference (DCC), Snowbird, UT, USA, 2019, pp. 558-558.
    [IEEE] [arXiv] [website] [poster] [press]

  • DeepZip: Lossless Data Compression using Recurrent Neural Networks.
    Goyal, M., Tatwawadi, K., Chandak, S., & Ochoa, I.
    2019 Data Compression Conference (DCC), Snowbird, UT, USA, 2019, pp. 575-575.
    [IEEE] [arXiv] [poster] [GitHub]

  • An Actively Detuned Wireless Power Receiver With Public Key Cryptographic Authentication and Dynamic Power Allocation.
    Desai, N.V., Juvekar, C., Chandak, S., & Chandrakasan, A.P.
    2017 IEEE International Solid-State Circuits Conference (ISSCC), San Francisco, CA, 2017, pp. 366-367.
    [IEEE] [press]

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Patents

  • Improved quality value compression framework in aligned sequencing data based on novel contexts.
    Chandak S., & Cheung Y.H.
    [patent application]

  • System and method for effective compression, representation and decompression of diverse tabulated data.
    Chandak S., & Cheung Y.H.
    [patent application]

  • Systems and Methods for Compressing Genetic Sequencing Data and Uses Thereof.
    Chandak, S., Tatwawadi, K., Ochoa, I., Hernaez, M., & Weissman, T.
    [patent application]

  • Embedded Deep Compression for Time Series Data.
    Wen, C., Wang, L., Aparicio, J., Chandak, S., Tatwawadi, K., & Weissman, T.
    [patent application]
    Awarded Siemens Inventors of the year 2020 [press]

  • Detuning for a resonant wireless power transfer system including cryptography.
    Chandrakasan, A.P., Desai, N.V., Juvekar, C., & Chandak, S.
    [patent] [tech brief]

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Preprints

  • Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing.
    Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S., Hernandez, A., Aksimentiev, A., Chen, M., Schroeder, C., & Milenkovic, O.
    [bioRxiv]

  • Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing.
    Lau, B., Chandak, S., Roy, S., Tatwawadi, K., Wootters, M., Weissman, T., & Ji, H.
    [bioRxiv] [GitHub]

  • Txt2Vid: Ultra-Low Bitrate Compression of Talking-Head Videos via Text.
    Tandon, P., Chandak, S., Pataranutaporn, P., Liu, Y., Mapuranga, A., Maes, P., Weissman, T., & Sra, M.
    [arXiv] [GitHub]

  • NanoSpring: reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach.
    Meng, Q., Chandak, S., Zhu, Y., & Weissman, T.
    [bioRxiv] [GitHub]

  • Tutorial on algebraic deletion correction codes.
    Tatwawadi, K., & Chandak, S.
    [arXiv] [GitHub]

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Thesis

  • Compression of raw genomic data.
    PhD thesis, May 2021
    Advisor: Prof. Tsachy Weissman, Stanford University
    [Stanford Libraries] [pdf]

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Magazine articles

  • Forget JPEG, How Would a Person Compress a Picture?
    Hwang, I., Chandak, S., Tatwawadi, K., & Weissman, T.
    IEEE Spectrum, October 2021.
    [article]

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Talks and Panels

  • Compression of raw genomic data.
    PhD defense, April 19, 2021.
    [slides] [video]

  • Moderator for panel on DNA-based data storage.
    Stanford Compression Workshop 2021, February 26, 2021.
    [video]

  • Genomic data compression. (Invited)
    Roche, November 13, 2020.
    [slides]

  • Error correcting codes for DNA based data storage.
    ISMB/ECCB 2019, Basel, July 21-25, 2019.
    [slides] [video]

  • SPRING: A next-generation compressor for FASTQ data. (Invited)
    ISMB/ECCB 2019, Basel, July 21-25, 2019.
    [slides] [video]

  • SPRING: A next-generation compressor for FASTQ data. (Invited)
    Stanford Compression Workshop 2019, Stanford, February 15, 2019.
    [slides] [video]

  • SPRING: A practical compressor for short-read FASTQ data. (Invited)
    56th Annual Allerton Conference on Communication, Control, and Computing, Urbana, IL, October 3-5, 2018.
    [slides]

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Posters

  • NanoSpring: reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach.
    ISMB/ECCB 2021, Virtual, July 25-30, 2021.
    Presented by Qingxi Meng.
    [poster] [video]

  • Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy.
    ISMB/ECCB 2021, Virtual, July 25-30, 2021.
    [poster] [video]

  • Utilizing a novel microfluidic technology to optimize enzymatic DNA synthesis for information storage applications.
    Advances in Genome Biology and Technology (AGBT) General Meeting 2020, Marco Island, FL, USA, February 23-26 2020.
    Presented by Mais Jebrail.
    [poster]

  • Error correcting codes for DNA based data storage.
    ISMB/ECCB 2019, Basel, July 21-25, 2019.
    [poster]

  • SPRING: A practical compressor for short-read FASTQ data.
    ISMB 2018, Chicago, IL, July 6-10, 2018.
    [poster]

  • Compression of genomic sequencing reads with and without preserving the order.
    2017 Biomedical Computation at Stanford Symposium, Stanford University, April 10th, 2017.

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