Publications | Ritu Kundu

** The norm in my research-field is to order the names of the authors lexicographically based on their last names.

2024

Darian, J.C., Kundu, R., Rajaby, R. et al. "Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly” Nat Methods , 2024.
[Bibtex]

@article {Darian2024,
							author = { Casey, Joshua and Kundu, Ritu and Rajaby, Ramesh and Sung, Wing-Kin},
							title = {Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly},
							year = {2024},
							doi = {10.1038/s41592-023-02141-1},
							ISSN ={1548-7105},
							abstract = {Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers can enhance their quality, the error rate (including mismatches, indels and switching errors between paternal and maternal haplotypes) can be significant. Here, we develop two polishers, hypo-short and hypo-hybrid to address this issue. Hypo-short utilizes Illumina short reads to polish an ONT-based draft assembly, resulting in a high-quality assembly with low error rates and switching errors. Expanding on this, hypo-hybrid incorporates ONT long reads to further refine the assembly into a diploid representation. Leveraging on hypo-hybrid, we have created a diploid genome assembly pipeline called hypo-assembler. Hypo-assembler automates the generation of highly accurate, contiguous and nearly complete diploid assemblies using ONT long reads, Illumina short reads and optionally Hi-C reads. Notably, our solution even allows for the production of telomere-to-telomere diploid genomes with additional manual steps. As a proof of concept, we successfully assembled a fully phased telomere-to-telomere diploid genome of HG00733, achieving a quality value exceeding 50.},
							URL = {https://doi.org/10.1038/s41592-023-02141-1},
							journal = {Nature Methods}
							}

2019

R. Kundu, J. Casey, and W. Sung, “Hypo: super fast & accurate polisher for long read genome assemblies,” Biorxiv, 2019.
[Bibtex]

@article {Kundu2019.12.19.882506,
					author = {Kundu, Ritu and Casey, Joshua and Sung, Wing-Kin},
					title = {HyPo: Super Fast \& Accurate Polisher for Long Read Genome Assemblies},
					elocation-id = {2019.12.19.882506},
					year = {2019},
					doi = {10.1101/2019.12.19.882506},
					publisher = {Cold Spring Harbor Laboratory},
					abstract = {Efforts towards making population-scale long read genome assemblies (especially human genomes) viable have intensified recently with the emergence of many fast assemblers. The reliance of these fast assemblers on polishing for the accuracy of assemblies makes it crucial. We present HyPo--a Hybrid Polisher--that utilises short as well as long reads within a single run to polish a long read assembly of small and large genomes. It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments. As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assemblies in about one-third time with about half the memory requirements in comparison to Racon (the widely used polisher currently).},
					URL = {https://www.biorxiv.org/content/early/2019/12/20/2019.12.19.882506},
					eprint = {https://www.biorxiv.org/content/early/2019/12/20/2019.12.19.882506.full.pdf},
					journal = {bioRxiv}
					}

R. Kundu, “Algorithmic Advances in Handling Uncertainty and Regularity in Strings,” PhD Thesis, King’s College London, London WC2R 2LS, UK, 2019.
[Bibtex]

@PhDThesis{Kundu:Thesis:2019,
					author = {Ritu Kundu},
					title = {Algorithmic Advances in Handling Uncertainty and Regularity in Strings},
					school = {King's College London},
					address = {King's College London, London WC2R 2LS, UK},
					year = {2019},
					url = {https://kclpure.kcl.ac.uk/portal/en/persons/ritu-kundu(9e27ed7f-8132-4268-bd8e-e0a749554d39)/theses.html}
					}

2018

T. Kociumaka, R. Kundu, M. Mohamed, and S. P. Pissis, “Longest Unbordered Factor in Quasilinear Time,” in 29th international symposium on algorithms and computation (isaac 2018), Dagstuhl, Germany, 2018, p. 70:1–70:13.
[Bibtex]

@InProceedings{kociumaka_et_al:LIPIcs:2018:10018,
					author ={Tomasz Kociumaka and Ritu Kundu and Manal Mohamed and Solon P. Pissis},
					title ={Longest Unbordered Factor in Quasilinear Time},
					booktitle ={29th International Symposium on Algorithms and Computation (ISAAC 2018)},
					pages ={70:1--70:13},
					series ={Leibniz International Proceedings in Informatics (LIPIcs)},
					ISBN ={978-3-95977-094-1},
					ISSN ={1868-8969},
					year ={2018},
					volume ={123},
					editor ={Wen-Lian Hsu and Der-Tsai Lee and Chung-Shou Liao},
					publisher ={Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
					address ={Dagstuhl, Germany},
					URL ={http://drops.dagstuhl.de/opus/volltexte/2018/10018},
					URN ={urn:nbn:de:0030-drops-100184},
					doi ={10.4230/LIPIcs.ISAAC.2018.70},
					annote ={Keywords: longest unbordered factor, factorisation, period, border, strings}
					}

R. Kundu and M. Mohamed, “Editorial,” Journal of discrete algorithms, vol. 50, p. 1, 2018.
[Bibtex]

@article{KUNDU20181,
					title = "Editorial",
					journal = "Journal of Discrete Algorithms",
					volume = "50",
					pages = "1",
					year = "2018",
					issn = "1570-8667",
					doi = "https://doi.org/10.1016/j.jda.2018.10.001",
					url = "http://www.sciencedirect.com/science/article/pii/S1570866718301369",
					author = "Ritu Kundu and Manal Mohamed"
					}

M. Alzamel, M. Crochemore, C. S. Iliopoulos, T. Kociumaka, R. Kundu, J. Radoszewski, W. Rytter, and T. Waleń, “How much different are two words with different shortest periods,” in Artificial intelligence applications and innovations, Cham, 2018, p. 168–178.
[Bibtex]

@InProceedings{10.1007/978-3-319-92016-0_16,
					author="Alzamel, Mai
					and Crochemore, Maxime
					and Iliopoulos, Costas S.
					and Kociumaka, Tomasz
					and Kundu, Ritu
					and Radoszewski, Jakub
					and Rytter, Wojciech
					and Wale{\'{n}}, Tomasz",
					editor="Iliadis, Lazaros
					and Maglogiannis, Ilias
					and Plagianakos, Vassilis",
					title="How Much Different Are Two Words with Different Shortest Periods",
					booktitle="Artificial Intelligence Applications and Innovations",
					year="2018",
					publisher="Springer International Publishing",
					address="Cham",
					pages="168--178",
					doi = "https://doi.org/10.1007/978-3-319-92016-0_16",
					abstract="Sometimes the difference between two distinct words of the same length cannot be smaller than a certain minimal amount. In particular if two distinct words of the same length are both periodic or quasiperiodic, then their Hamming distance is at least 2. We study here how the minimum Hamming distance {\$}{\$} dist (x,y){\$}{\$}dist(x,y)between two words x, y of the same length n depends on their periods. Similar problems were considered in [1] in the context of quasiperiodicities. We say that a period p of a word x is primitive if x does not have any smaller period {\$}{\$}p'{\$}{\$}p{\textasciiacutex}which divides p. For integers p, n ({\$}{\$}p{\backslash}le n{\$}{\$}p≤n) we define {\$}{\$}{\backslash}mathcal {\{}P{\}}{\_}{\{}p{\}}(n){\$}{\$}Pp(n)as the set of words of length n with primitive period p. We show several results related to the following functions introduced in this paper for {\$}{\$}p{\backslash}ne q{\$}{\$}p≠qand {\$}{\$}n {\backslash}ge {\backslash}max (p,q){\$}{\$}n≥max(p,q). {\$}{\$}{\backslash}begin{\{}aligned{\}} {\{}{\backslash}mathcal D{\}}{\_}{\{}p,q{\}}(n) = {\backslash}min {\backslash},{\backslash}{\{}{\backslash}, dist (x,y){\backslash},:{\backslash}; x{\backslash}in {\backslash}mathcal {\{}P{\}}{\_}{\{}p{\}}(n), {\backslash},y{\backslash}in {\backslash}mathcal {\{}P{\}}{\_}{\{}q{\}}(n){\backslash},{\backslash}{\}}, {\backslash}{\backslash} N{\_}{\{}p,q{\}}(h) = {\backslash}max {\backslash},{\backslash}{\{}{\backslash}, n {\backslash},:{\backslash}; {\{}{\backslash}mathcal D{\}}{\_}{\{}p,q{\}}(n){\backslash}le h{\backslash},{\backslash}{\}}. {\backslash}qquad {\backslash}qquad {\backslash}end{\{}aligned{\}}{\$}{\$}Dp,q(n)=min{\{}dist(x,y):x∈Pp(n),y∈Pq(n){\}},Np,q(h)=max{\{}n:Dp,q(n)≤h{\}}.",
					isbn="978-3-319-92016-0"
					}

2017

R. Kundu and T. Mahmoodi, “Mining acute stroke patients’ data using supervised machine learning,” in Mathematical aspects of computer and information sciences: 7th international conference, macis 2017, vienna, austria, november 15-17, 2017, proceedings, Cham, 2017, p. 364–377.
[Bibtex]

@inproceedings{Kundu2017,
					author="Kundu, Ritu
					and Mahmoodi, Toktam",
					editor="Bl{\"o}mer, Johannes
					and Kotsireas, Ilias S.
					and Kutsia, Temur
					and Simos, Dimitris E.",
					title="Mining Acute Stroke Patients' Data Using Supervised Machine Learning",
					bookTitle="Mathematical Aspects of Computer and Information Sciences: 7th International Conference, MACIS 2017, Vienna, Austria, November 15-17, 2017, Proceedings",
					year="2017",
					publisher="Springer International Publishing",
					address="Cham",
					pages="364--377",
					abstract="Analysis of data for identifying patterns and building models has been used as a strong tool in different domains, including medical domains. In this paper, we analyse the registry of brain stroke patients collected over fifteen years in south London hospitals, known as South London Stroke Register. Our attempt is to identify the similar patterns between patients' background and living conditions, their cognitive ability, the treatments they received, and the speed of their cognitive recovery; based on which most effective treatment can be predicted for new admitted patients. We designed a novel strategy which takes into account two different approaches. First is to predict, for each of the potential intervention treatments, whether that particular treatment would lead to recovery of a new patient or not. Second is to suggest a treatment (treatments) for the patient based on those that were given to the patients who have recovered and are most similar to the new patient. We built different classifiers using various state of the art machine learning algorithms. These algorithms were evaluated and compared based on three performance metrics, defined in this paper. Given that time is very crucial for stroke patients, main motivation of this research work is identifying the most effective treatment immediately for a new patient, and potentially increase the probability of their cognitive recovery.",
					isbn="978-3-319-72453-9",
					doi="10.1007/978-3-319-72453-9_30",
					url="https://doi.org/10.1007/978-3-319-72453-9_30"
					}

A. Bhardwaj, B. Cizmeci, E. Steinbach, Q. Liu, M. Eid, J. AraUjo, A. E. Saddik, R. Kundu, X. Liu, O. Holland, M. A. Luden, S. Oteafy, and V. Prasad, “A candidate hardware and software reference setup for kinesthetic codec standardization,” in 2017 ieee international symposium on haptic, audio and visual environments and games (have), 2017, pp. 1-6.
[Bibtex]

@INPROCEEDINGS{8240353,
					author={A. Bhardwaj and B. Cizmeci and E. Steinbach and Q. Liu and M. Eid and J. AraUjo and A. E. Saddik and R. Kundu and X. Liu and O. Holland and M. A. Luden and S. Oteafy and V. Prasad},
					booktitle={2017 IEEE International Symposium on Haptic, Audio and Visual Environments and Games (HAVE)},
					title={A candidate hardware and software reference setup for kinesthetic codec standardization},
					year={2017},
					volume={},
					number={},
					pages={1-6},
					keywords={Internet;closed loop systems;codecs;control engineering computing;haptic interfaces;telecontrol;virtual reality;Haptic Codecs;IEEE P1918.1 standardization activity;Tactile Internet;candidate hardware;closed-loop kinesthetic interactions;dynamic kinesthetic interactions;kinesthetic codec standardization;kinesthetic codecs;kinesthetic information exchange;reference hardware;software reference setup;software setup;static interactions;tactile information exchange;task group;Codecs;Delays;Electronic mail;Force feedback;Hardware;Virtual environments},
					doi={10.1109/HAVE.2017.8240353},
					ISSN={},
					month={Oct},}

I. Fontana, G. Giacalone, A. Bonanno, S. Mazzola, G. Basilone, S. Genovese, S. Aronica, S. Pissis, C. S. Iliopoulos, R. Kundu, A. Fiannaca, A. Langiu, G. L. Bosco, M. L. Rosa, and R. Rizzo, “Pelagic species identification by using a probabilistic neural network and echo-sounder data,” in Artificial neural networks and machine learning – icann 2017: 26th international conference on artificial neural networks, alghero, italy, september 11-14, 2017, proceedings, Cham, 2017, p. 454–455.
[Bibtex]

@inproceedings{fontana2017pelagic,
					author = "Ignazio Fontana and Giovanni Giacalone and Angelo Bonanno and Salvatore Mazzola and Gualtiero Basilone and Simona Genovese and Salvatore Aronica and Solon Pissis and Costas S. Iliopoulos and Ritu Kundu and Antonino Fiannaca and Alessio Langiu and Giosue’ Lo Bosco and Massimo La Rosa and Riccardo Rizzo",
					title = "Pelagic Species Identification by using a
					Probabilistic Neural Network and Echo-sounder
					Data",
					year = "2017",
					booktitle = "ICANN (accepted)",
					editor="Lintas, Alessandra
					and Rovetta, Stefano
					and Verschure, Paul F.M.J.
					and Villa, Alessandro E.P.",
					bookTitle={Artificial Neural Networks and Machine Learning -- ICANN 2017: 26th International Conference on Artificial Neural Networks, Alghero, Italy, September 11-14, 2017, Proceedings},
					number={pt. 1},
					isbn={9783319686004},
					series={Lecture Notes in Computer Science},
					year={2017},
					publisher={Springer International Publishing},
					volume = "10613 LNCS",
					address="Cham",
					pages="454--455",
					doi="10.1007/978-3-319-68600-4",
					url={https://link.springer.com/content/pdf/bbm%3A978-3-319-68600-4%2F1.pdf}
					}

C. S. Iliopoulos, R. Kundu, and S. P. Pissis, “Efficient pattern matching in elastic-degenerate texts,” in Language and automata theory and applications: 11th international conference, lata 2017, umeå, sweden, march 6-9, 2017, proceedings, Cham, 2017, p. 131–142.
[Bibtex]

@inproceedings{Iliopoulos2017,
					author="Iliopoulos, Costas S.
					and Kundu, Ritu
					and Pissis, Solon P.",
					editor="Drewes, Frank
					and Mart{\'i}n-Vide, Carlos
					and Truthe, Bianca",
					title="Efficient Pattern Matching in Elastic-Degenerate Texts",
					bookTitle="Language and Automata Theory and Applications: 11th International Conference, LATA 2017, Ume{\aa}, Sweden, March 6-9, 2017, Proceedings",
					year="2017",
					publisher="Springer International Publishing",
					address="Cham",
					pages="131--142",
					isbn="978-3-319-53733-7",
					doi="10.1007/978-3-319-53733-7_9",
					url="http://dx.doi.org/10.1007/978-3-319-53733-7_9"
					}

2016

M. Crochemore, C. S. Iliopoulos, T. Kociumaka, R. Kundu, S. P. Pissis, J. Radoszewski, W. Rytter, and T. Waleń, “Near-optimal computation of runs over general alphabet via non-crossing lce queries,” in String processing and information retrieval: 23rd international symposium, spire 2016, beppu, japan, october 18-20, 2016, proceedings, Cham, 2016, p. 22–34.
[Bibtex]

@inproceedings{Crochemore2016,
					author="Crochemore, Maxime
					and Iliopoulos, Costas S.
					and Kociumaka, Tomasz
					and Kundu, Ritu
					and Pissis, Solon P.
					and Radoszewski, Jakub
					and Rytter, Wojciech
					and Wale{\'{n}}, Tomasz",
					editor="Inenaga, Shunsuke
					and Sadakane, Kunihiko
					and Sakai, Tetsuya",
					title="Near-Optimal Computation of Runs over General Alphabet via Non-Crossing LCE Queries",
					bookTitle="String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings",
					year="2016",
					publisher="Springer International Publishing",
					address="Cham",
					pages="22--34",
					isbn="978-3-319-46049-9",
					doi="10.1007/978-3-319-46049-9_3",
					url="http://dx.doi.org/10.1007/978-3-319-46049-9_3"
					}

C. S. Iliopoulos, R. Kundu, and M. Mohamed, “Efficient computation of clustered-clumps in degenerate strings,” in Artificial intelligence applications and innovations: 12th ifip wg 12.5 international conference and workshops, aiai 2016, thessaloniki, greece, september 16-18, 2016, proceedings, Cham, 2016, p. 510–519.
[Bibtex]

@inproceedings{Kundu2016,
					author="Iliopoulos, Costas S.
					and Kundu, Ritu
					and Mohamed, Manal",
					editor="Iliadis, Lazaros
					and Maglogiannis, Ilias",
					title="Efficient Computation of Clustered-Clumps in Degenerate Strings",
					bookTitle="Artificial Intelligence Applications and Innovations: 12th IFIP WG 12.5 International Conference and Workshops, AIAI 2016, Thessaloniki, Greece, September 16-18, 2016, Proceedings",
					year="2016",
					publisher="Springer International Publishing",
					address="Cham",
					pages="510--519",
					isbn="978-3-319-44944-9",
					doi="10.1007/978-3-319-44944-9_45",
					url="http://dx.doi.org/10.1007/978-3-319-44944-9_45"
					}

M. Crochemore, C. S. Iliopoulos, R. Kundu, M. Mohamed, and F. Vayani, “Linear algorithm for conservative degenerate pattern matching,” Engineering applications of artificial intelligence, vol. 51, pp. 109-114, 2016.
[Bibtex]

@article{Crochemore2016109,
					title = "Linear algorithm for conservative degenerate pattern matching ",
					journal = "Engineering Applications of Artificial Intelligence ",
					volume = "51",
					number = "",
					pages = "109 - 114",
					year = "2016",
					note = "Mining the Humanities: Technologies and Applications ",
					issn = "0952-1976",
					doi = "http://www.sciencedirect.com/science/article/pii/S0952197616000130",
					url = "http://www.sciencedirect.com/science/article/pii/S0952197616000130",
					author = "Maxime Crochemore and Costas S. Iliopoulos and Ritu Kundu and Manal Mohamed and Fatima Vayani",
					keywords = "Degenerate string",
					keywords = "Pattern matching",
					keywords = "Algorithm "
					}

C. S. Iliopoulos, R. Kundu, M. Mohamed, and F. Vayani, “Popping superbubbles and discovering clumps: recent developments in biological sequence analysis,” in Walcom: algorithms and computation: 10th international workshop, walcom 2016, kathmandu, nepal, march 29–31, 2016, proceedings, Cham, 2016, p. 3–14.
[Bibtex]

@inproceedings{Iliopoulos2016,
					author="Iliopoulos, Costas S.
					and Kundu, Ritu
					and Mohamed, Manal
					and Vayani, Fatima",
					editor="Kaykobad, Mohammad
					and Petreschi, Rossella",
					title="Popping Superbubbles and Discovering Clumps: Recent Developments in Biological Sequence Analysis",
					bookTitle="WALCOM: Algorithms and Computation: 10th International Workshop, WALCOM 2016, Kathmandu, Nepal, March 29--31, 2016, Proceedings",
					year="2016",
					publisher="Springer International Publishing",
					address="Cham",
					pages="3--14",
					isbn="978-3-319-30139-6",
					doi="10.1007/978-3-319-30139-6_1",
					url="http://dx.doi.org/10.1007/978-3-319-30139-6_1"
					}

L. Brankovic, C. S. Iliopoulos, R. Kundu, M. Mohamed, S. P. Pissis, and F. Vayani, “Linear-time superbubble identification algorithm for genome assembly,” Theoretical computer science, vol. 609, Part 2, pp. 374-383, 2016.
[Bibtex]

@article{Brankovic2016374,
					title = "Linear-time superbubble identification algorithm for genome assembly ",
					journal = "Theoretical Computer Science ",
					volume = "609, Part 2",
					number = "",
					pages = "374 - 383",
					year = "2016",
					note = "",
					issn = "0304-3975",
					doi = "http://dx.doi.org/10.1016/j.tcs.2015.10.021",
					url = "http://www.sciencedirect.com/science/article/pii/S0304397515009147",
					author = "Ljiljana Brankovic and Costas S. Iliopoulos and Ritu Kundu and Manal Mohamed and Solon P. Pissis and Fatima Vayani",
					keywords = "Genome assembly",
					keywords = "de Bruijn graphs",
					keywords = "Superbubble "
					}

2015

C. Barton, C. S. Iliopoulos, R. Kundu, S. P. Pissis, A. Retha, and F. Vayani, “Accurate and efficient methods to improve multiple circular sequence alignment,” in Experimental algorithms: 14th international symposium, sea 2015, paris, france, june 29 – july 1, 2015, proceedings, Cham, 2015, p. 247–258.
[Bibtex]

@inproceedings{Barton2015,
					author="Barton, Carl
					and Iliopoulos, Costas S.
					and Kundu, Ritu
					and Pissis, Solon P.
					and Retha, Ahmad
					and Vayani, Fatima",
					editor="Bampis, Evripidis",
					title="Accurate and Efficient Methods to Improve Multiple Circular Sequence Alignment",
					bookTitle="Experimental Algorithms: 14th International Symposium, SEA 2015, Paris, France, June 29 -- July 1, 2015, Proceedings",
					year="2015",
					publisher="Springer International Publishing",
					address="Cham",
					pages="247--258",
					isbn="978-3-319-20086-6",
					doi="10.1007/978-3-319-20086-6_19",
					url="http://dx.doi.org/10.1007/978-3-319-20086-6_19"
					}

** The norm in my research-field is to order the names of the authors lexicographically based on their last names.