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Chandra, G and Gibney, D and Jain, C (2024) Haplotype-Aware Sequence Alignment to Pangenome Graphs. In: 28th International Conference on Research in Computational Molecular Biology., 29 April 2024 through 2 May 2024, Cambridge, pp. 381-384.
Mahajan, D and Jain, C and Kashyap, N (2024) On the Coverage Required for Diploid Genome Assembly. In: 2024 IEEE International Symposium on Information Theory, ISIT 2024, 7 July 2024through 12 July 2024, Athens, pp. 3636-3641.
Rajput, J and Chandra, G and Jain, C (2023) Co-Linear Chaining on Pangenome Graphs. In: 23rd International Workshop on Algorithms in Bioinformatics, WABI 2023, 4-6 September 2023, Bangalore, India.
Chandra, G and Jain, C (2023) Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining. In: 27th International Conference on Research in Computational Molecular Biology, RECOMB 2023, 16 - 19 April 2023, Istanbul, pp. 58-73.
Jain, C and Gibney, D and Thankachan, SV (2022) Co-linear Chaining with Overlaps and Gap Costs. In: 26th International Conference on Research in Computational Molecular Biology, RECOMB 2022, 22 - 25 May 2022, San Diego, pp. 246-262.
Rajput, J and Chandra, G and Jain, C (2024) Co-linear chaining on pangenome graphs. In: Algorithms for Molecular Biology, 19 (1).
Jain, C (2023) Coverage-preserving sparsification of overlap graphs for long-read assembly. In: Bioinformatics (Oxford, England), 39 (3).
Chandra, G and Jain, C (2023) Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs. In: Journal of Computational Biology .
Jain, C and Gibney, D and Thankachan, SV (2022) Algorithms for Colinear Chaining with Overlaps and Gap Costs. In: Journal of computational biology : a journal of computational molecular cell biology, 29 (11). pp. 1237-1251.
Mc Cartney, AM and Shafin, K and Alonge, M and Bzikadze, AV and Formenti, G and Fungtammasan, A and Howe, K and Jain, C and Koren, S and Logsdon, GA and Miga, KH and Mikheenko, A and Paten, B and Shumate, A and Soto, DC and Sovic, I and Wood, JMD and Zook, JM and Phillippy, AM and Rhie, A (2022) Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. In: Nature Methods .
Jain, C and Rhie, A and Hansen, NF and Koren, S and Phillippy, AM (2022) Long-read mapping to repetitive reference sequences using Winnowmap2. In: Nature Methods .
Nurk, S and Koren, S and Rhie, A and Rautiainen, M and Bzikadze, AV and Mikheenko, A and Vollger, MR and Altemose, N and Uralsky, L and Gershman, A and Aganezov, S and Hoyt, SJ and Diekhans, M and Logsdon, GA and Alonge, M and Antonarakis, SE and Borchers, M and Bouffard, GG and Brooks, SY and Caldas, GV and Chen, N-C and Cheng, H and Chin, C-S and Chow, W and de Lima, LG and Dishuck, PC and Durbin, R and Dvorkina, T and Fiddes, IT and Formenti, G and Fulton, RS and Fungtammasan, A and Garrison, E and Grady, PGS and Graves-Lindsay, TA and Hall, IM and Hansen, NF and Hartley, GA and Haukness, M and Howe, K and Hunkapiller, MW and Jain, C and Jain, M and Jarvis, ED and Kerpedjiev, P and Kirsche, M and Kolmogorov, M and Korlach, J and Kremitzki, M and Li, H and Maduro, VV and Marschall, T and McCartney, AM and McDaniel, J and Miller, DE and Mullikin, JC and Myers, EW and Olson, ND and Paten, B and Peluso, P and Pevzner, PA and Porubsky, D and Potapova, T and Rogaev, EI and Rosenfeld, JA and Salzberg, SL and Schneider, VA and Sedlazeck, FJ and Shafin, K and Shew, CJ and Shumate, A and Sims, Y and Smit, AFA and Soto, DC and Sovi, I and Storer, JM and Streets, A and Sullivan, BA and Thibaud-Nissen, F and Torrance, J and Wagner, J and Walenz, BP and Wenger, A and Wood, JMD and Xiao, C and Yan, SM and Young, AC and Zarate, S and Surti, U and McCoy, RC and Dennis, MY and Alexandrov, IA and Gerton, JL and O'Neill, RJ and Timp, W and Zook, JM and Schatz, MC and Eichler, EE and Miga, KH and Phillippy, AM (2022) The complete sequence of a human genome. In: Science, 376 (6588). pp. 44-53.
Kalikar, S and Jain, C and Vasimuddin, M and Misra, S (2022) Accelerating minimap2 for long-read sequencing applications on modern CPUs. In: Nature Computational Science, 2 (2). pp. 78-83.
Rodriguez-R, LM and Jain, C and Conrad, RE and Aluru, S and Konstantinidis, KT (2021) Reply to: �Re-evaluating the evidence for a universal genetic boundary among microbial species�. In: Nature Communications, 12 (1).
Zhang, H and Li, H and Jain, C and Cheng, H and Au, KF and Li, H and Aluru, S (2021) Real-time mapping of nanopore raw signals. In: Bioinformatics, 37 . I477-I483.
Jain, C and Tavakoli, N and Aluru, S (2021) A variant selection framework for genome graphs. In: Bioinformatics, 37 . I460-I467.
Rodriguez-R, LM and Jain, C and Conrad, RE and Aluru, S and Konstantinidis, KT (2021) Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”. In: Nature Communications, 12 (1).
