博士研究生岗位（男女均可，F/M）：RobDNA——基于 DNA 的数据存储中的稳健数据检索

专注于开发基于DNA数据存储算法的博士研究生岗位。申请者应具备扎实的图像/信号处理及编程技能，且具备信息论知识将被视为加分项。

Assignment: Goal The goal of the project is to develop an algorithm to allow robust retrieval of data in the context of DNA-based data storage. Main activities: Challenges and envisaged approach Despite its potential, making DNA a practical and efficient storage medium requires overcoming several key challenges: (i) Data transformation: converting digital data into a quaternary alphabet (A, C, G, T). (ii) DNA synthesis: writing data through the physical synthesis of DNA strands. (iii) DNA sequencing: reading the stored data by sequencing DNA. (iv) Data retrieval: reconstructing the original digital data from the sequenced symbols. This PhD project focuses on the first and fourth challenges, by developing joint compression and error-correction algorithms that are robust to sequencing errors arising during step (iii). Efficient DNA storage critically depends on fast sequencing technologies, which often come at the cost of increased error rates. For example, nanopore sequencing, developed by Oxford Nanopore Technologies (ONT), enables real-time analysis but introduces relatively high error rates [4,5]. Unlike traditional sequencing technologies, nanopore sequencing produces not only substitution errors but also insertion and deletion errors. Deletions are particularly challenging, as they differ from erasure errors where the position of missing data is known e.g., packet losses in digital communications). In the case of deletions, neither the existence nor the location of the missing symbols is known, significantly complicating error correction. Two main approaches have been proposed in the literature to address these errors. The first consists of avoiding error-prone patterns by designing constrained DNA sequences, such as limiting homopolymers or enforcing balanced GC content [6]. The second approach embraces sequencing errors and focuses on correcting them using coding techniques [7]. These strategies are typically considered contradictory, as one seeks to prevent errors while the other assumes their presence [8]. In this project, we propose to explore an alternative route that combines both strategies: avoiding the majority of sequencing errors while correcting the remaining ones. This will be achieved by jointly structuring the compressed DNA stream and designing error-correction mechanisms tailored to nanopore sequencing. In particular, we will exploit the properties of the quaternary alphabet and the interaction between compression and error-correction algorithms. The work will build upon concepts from non-binary channel coding [10,11] and DNA-specific transcoding techniques [6], while also integrating efficient post-sequencing data retrieval methods such as those proposed in [9]. Bibliography [1] David Reinsel-John Gantz-John Rydning, John Reinsel, and John Gantz. “The digitization of the world from edge to core.Framingham: International Data Corporation”, 16:1–28, 2018. [2] Luis Ceze, Jeff Nivala, and Karin Strauss. “Molecular digital data storage using DNA”. NatureReviews Genetics, 20(8):456–466, 2019. [3] Victor Zhirnov, Reza M Zadegan, Gurtej S Sandhu, George M Church, and William L Hughes. “Nucleic acid memory”. Nature materials, 15(4):366–370, 2016. [4] Delahaye, Clara, and Jacques Nicolas. “Nanopore MinION Long Read Sequencer: An Overview of Its Error Landscape,” November 23, 2020. ［会员资料链接］. [5] ———. “Sequencing DNA with Nanopores: Troubles and Biases.” PLoS ONE, October 1, 202 [6] S. Al Sayyed and A. ［会员专属信息］ and T. Maugey. ``Efficient constraining of transcoding for DNA-based data storage'', IEEE International Conference on Image Processing (ICIP), 2025. [7] R. Khabbaz, M. Antonini, S. Kas Hanna, Marker Guess & Check Plus (MGC+): An Efficient Short Blocklength Code for Random Edit Errors, International Symposium on Topics in Coding (ISTC), 2025. [8] F. Weindel, A. L. Gimpel, R. N. Grass and R. Heckel, ”Embracing errors is more effective than avoiding them through constrained coding for DNA data storage,” Allerton Conference on Communication, Control, and Computing 2023. [9] F. De Moor, O. Boullé, D. Lavenier, De Bruijn Graph Partitioning for Scalable and Accurate DNA Storage Processing, BioRxiv, 2025. [10] M. C. Davey and D. J. C. Mackay, “Low density parity check codes over GF(q)”, Information Theory Workshop, 1998, pp. 70-71. [11] D. Declercq and M. Fossorier, “Decoding algorithms for nonbinary LDPC codes over GF(q)”, IEEE Trans. on Commun., vol. 55, pp. 633- 643, April 2007

成功的关键： 候选人简历 候选人应具备 在图像/信号处理、优化及编程方面的扎实背景 欢迎具备源编码及信息论相关概念的人才申请。

福利包： 补贴餐食 部分公共交通费用补贴 休假安排：7周的年假 + 因RTT（法定工时缩减）而额外获得10天假期 + 特殊休假的可能（适用于生病子女、迁居等情形）。 远程工作的可能性（在任职6个月后）及灵活的工作时间安排 提供专业设备（视频会议、计算机设备借用等） 社会、文化和体育活动及项目 职业培训机会 社会保障覆盖范围 薪酬： 每月 2,300 欧元 申请该职位

申请说明： 请在线提交简历、求职信及推荐信（如有）。 国防安全：本岗位可能位于受限区域（ZRR），此类区域依据保护国家科学技术潜力（PPST）的第2011-1425号法令界定。根据2012年7月3日关于PPST的法令，在主管部门作出批准决定后，由单位负责人授予区域准入许可。对于位于ZRR内的岗位，若主管部门作出不予批准的决定，将取消聘用。 招聘政策：作为多样性政策的一部分，法国国家信息与自动化研究所（Inria）的所有岗位均向残疾人士开放。