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ORCIDBibTeX records: Murray Patterson
@article{DBLP:journals/cbm/TayebiAMKP24,
author = {Zahra Tayebi and
Sarwan Ali and
Taslim Murad and
Imdadullah Khan and
Murray Patterson},
title = {PseAAC2Vec protein encoding for {TCR} protein sequence classification},
journal = {Comput. Biol. Medicine},
volume = {170},
pages = {107956},
year = {2024},
url = {https://doi.org/10.1016/j.compbiomed.2024.107956},
doi = {10.1016/J.COMPBIOMED.2024.107956},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cbm/TayebiAMKP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isci/AliAMMP24,
author = {Sarwan Ali and
Tamkanat E. Ali and
Taslim Murad and
Haris Mansoor and
Murray Patterson},
title = {Molecular sequence classification using efficient kernel based embedding},
journal = {Inf. Sci.},
volume = {679},
pages = {121100},
year = {2024},
url = {https://doi.org/10.1016/j.ins.2024.121100},
doi = {10.1016/J.INS.2024.121100},
timestamp = {Fri, 02 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/isci/AliAMMP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Patterson24,
author = {Murray Patterson},
title = {\emph{Special Issue, Part I} 19th International Symposium on Bioinformatics
Research and Applications {(ISBRA} 2023)},
journal = {J. Comput. Biol.},
volume = {31},
number = {6},
pages = {473--474},
year = {2024},
url = {https://doi.org/10.1089/cmb.2024.0636},
doi = {10.1089/CMB.2024.0636},
timestamp = {Thu, 22 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Patterson24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/kbs/AliSMCP24,
author = {Sarwan Ali and
Madiha Shabbir and
Haris Mansoor and
Prakash Chourasia and
Murray Patterson},
title = {Elliptic geometry-based kernel matrix for improved biological sequence
classification},
journal = {Knowl. Based Syst.},
volume = {304},
pages = {112479},
year = {2024},
url = {https://doi.org/10.1016/j.knosys.2024.112479},
doi = {10.1016/J.KNOSYS.2024.112479},
timestamp = {Fri, 20 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/kbs/AliSMCP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mbec/AliCP24,
author = {Sarwan Ali and
Prakash Chourasia and
Murray Patterson},
title = {From {PDB} files to protein features: a comparative analysis of {PDB}
bind and {STCRDAB} datasets},
journal = {Medical Biol. Eng. Comput.},
volume = {62},
number = {8},
pages = {2449--2483},
year = {2024},
url = {https://doi.org/10.1007/s11517-024-03074-3},
doi = {10.1007/S11517-024-03074-3},
timestamp = {Thu, 22 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mbec/AliCP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AliMCAP24,
author = {Sarwan Ali and
Haris Mansoor and
Prakash Chourasia and
Yasir Ali and
Murray Patterson},
editor = {Wei Peng and
Zhipeng Cai and
Pavel Skums},
title = {Gaussian Beltrami-Klein Model for Protein Sequence Classification:
{A} Hyperbolic Approach},
booktitle = {Bioinformatics Research and Applications - 20th International Symposium,
{ISBRA} 2024, Kunming, China, July 19-21, 2024, Proceedings, Part
{I}},
series = {Lecture Notes in Computer Science},
volume = {14954},
pages = {52--62},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-981-97-5128-0\_5},
doi = {10.1007/978-981-97-5128-0\_5},
timestamp = {Tue, 23 Jul 2024 15:21:07 +0200},
biburl = {https://dblp.org/rec/conf/isbra/AliMCAP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pakdd/AliACP24,
author = {Sarwan Ali and
Tamkanat E. Ali and
Prakash Chourasia and
Murray Patterson},
editor = {De{-}Nian Yang and
Xing Xie and
Vincent S. Tseng and
Jian Pei and
Jen{-}Wei Huang and
Jerry Chun{-}Wei Lin},
title = {A Universal Non-parametric Approach for Improved Molecular Sequence
Analysis},
booktitle = {Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia
Conference on Knowledge Discovery and Data Mining, {PAKDD} 2024, Taipei,
Taiwan, May 7-10, 2024, Proceedings, Part {IV}},
series = {Lecture Notes in Computer Science},
volume = {14648},
pages = {194--206},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-981-97-2238-9\_15},
doi = {10.1007/978-981-97-2238-9\_15},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pakdd/AliACP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pakdd/MuradAP24,
author = {Taslim Murad and
Sarwan Ali and
Murray Patterson},
editor = {De{-}Nian Yang and
Xing Xie and
Vincent S. Tseng and
Jian Pei and
Jen{-}Wei Huang and
Jerry Chun{-}Wei Lin},
title = {Weighted Chaos Game Representation for Molecular Sequence Classification},
booktitle = {Advances in Knowledge Discovery and Data Mining - 28th Pacific-Asia
Conference on Knowledge Discovery and Data Mining, {PAKDD} 2024, Taipei,
Taiwan, May 7-10, 2024, Proceedings, Part {IV}},
series = {Lecture Notes in Computer Science},
volume = {14648},
pages = {234--245},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-981-97-2238-9\_18},
doi = {10.1007/978-981-97-2238-9\_18},
timestamp = {Fri, 03 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pakdd/MuradAP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-08117,
author = {Sarwan Ali and
Tamkanat E. Ali and
Prakash Chourasia and
Murray Patterson},
title = {A Universal Non-Parametric Approach For Improved Molecular Sequence
Analysis},
journal = {CoRR},
volume = {abs/2402.08117},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.08117},
doi = {10.48550/ARXIV.2402.08117},
eprinttype = {arXiv},
eprint = {2402.08117},
timestamp = {Mon, 19 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-08117.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2403-19844,
author = {Sarwan Ali and
Prakash Chourasia and
Murray Patterson},
title = {Expanding Chemical Representation with k-mers and Fragment-based Fingerprints
for Molecular Fingerprinting},
journal = {CoRR},
volume = {abs/2403.19844},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2403.19844},
doi = {10.48550/ARXIV.2403.19844},
eprinttype = {arXiv},
eprint = {2403.19844},
timestamp = {Thu, 11 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2403-19844.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BansalMMPRSZ23,
author = {Mukul S. Bansal and
Ion I. Mandoiu and
Marmar Moussa and
Murray Patterson and
Sanguthevar Rajasekaran and
Pavel Skums and
Alexander Zelikovsky},
title = {Special Issue: 11th International Computational Advances in Bio and
Medical Sciences {(ICCABS} 2021)},
journal = {J. Comput. Biol.},
volume = {30},
number = {4},
pages = {363--365},
year = {2023},
url = {https://doi.org/10.1089/cmb.2023.29085.msb},
doi = {10.1089/CMB.2023.29085.MSB},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BansalMMPRSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AliBTP23,
author = {Sarwan Ali and
Babatunde Bello and
Zahra Tayebi and
Murray Patterson},
title = {Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location},
journal = {J. Comput. Biol.},
volume = {30},
number = {4},
pages = {432--445},
year = {2023},
url = {https://doi.org/10.1089/cmb.2022.0391},
doi = {10.1089/CMB.2022.0391},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/AliBTP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ChourasiaACVP23,
author = {Prakash Chourasia and
Sarwan Ali and
Simone Ciccolella and
Gianluca Della Vedova and
Murray Patterson},
title = {Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads
Data},
journal = {J. Comput. Biol.},
volume = {30},
number = {4},
pages = {469--491},
year = {2023},
url = {https://doi.org/10.1089/cmb.2022.0424},
doi = {10.1089/CMB.2022.0424},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ChourasiaACVP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mbec/AliCTBP23,
author = {Sarwan Ali and
Prakash Chourasia and
Zahra Tayebi and
Babatunde Bello and
Murray Patterson},
title = {ViralVectors: compact and scalable alignment-free virome feature generation},
journal = {Medical Biol. Eng. Comput.},
volume = {61},
number = {10},
pages = {2607--2626},
year = {2023},
url = {https://doi.org/10.1007/s11517-023-02837-8},
doi = {10.1007/S11517-023-02837-8},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mbec/AliCTBP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ml/MuradAKP23,
author = {Taslim Murad and
Sarwan Ali and
Imdadullah Khan and
Murray Patterson},
title = {Spike2CGR: an efficient method for spike sequence classification using
chaos game representation},
journal = {Mach. Learn.},
volume = {112},
number = {10},
pages = {3633--3658},
year = {2023},
url = {https://doi.org/10.1007/s10994-023-06371-4},
doi = {10.1007/S10994-023-06371-4},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ml/MuradAKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/AliSKZKP23,
author = {Sarwan Ali and
Bikram Sahoo and
Muhammad Asad Khan and
Alexander Zelikovsky and
Imdadullah Khan and
Murray Patterson},
title = {Efficient Approximate Kernel Based Spike Sequence Classification},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {20},
number = {6},
pages = {3376--3388},
year = {2023},
url = {https://doi.org/10.1109/TCBB.2022.3206284},
doi = {10.1109/TCBB.2022.3206284},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/AliSKZKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bigdataconf/MuradACMP23,
author = {Taslim Murad and
Sarwan Ali and
Prakash Chourasia and
Haris Mansoor and
Murray Patterson},
editor = {Jingrui He and
Themis Palpanas and
Xiaohua Hu and
Alfredo Cuzzocrea and
Dejing Dou and
Dominik Slezak and
Wei Wang and
Aleksandra Gruca and
Jerry Chun{-}Wei Lin and
Rakesh Agrawal},
title = {Circular Arc Length-Based Kernel Matrix For Protein Sequence Classification},
booktitle = {{IEEE} International Conference on Big Data, BigData 2023, Sorrento,
Italy, December 15-18, 2023},
pages = {1429--1437},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/BigData59044.2023.10386477},
doi = {10.1109/BIGDATA59044.2023.10386477},
timestamp = {Tue, 20 Aug 2024 07:54:43 +0200},
biburl = {https://dblp.org/rec/conf/bigdataconf/MuradACMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/chil/AliBCPCKP23,
author = {Sarwan Ali and
Babatunde Bello and
Prakash Chourasia and
Ria Thazhe Punathil and
Pin{-}Yu Chen and
Imdadullah Khan and
Murray Patterson},
editor = {Bobak J. Mortazavi and
Tasmie Sarker and
Andrew Beam and
Joyce C. Ho},
title = {Counterfactually Guided Policy Transfer in Clinical Settings},
booktitle = {Conference on Health, Inference, and Learning, {CHIL} 2023, Broad
Institute of {MIT} and Harvard (Merkin Building), 415 Main Street,
Cambridge, MA, {USA}},
series = {Proceedings of Machine Learning Research},
volume = {209},
pages = {6--18},
publisher = {{PMLR}},
year = {2023},
url = {https://proceedings.mlr.press/v209/ali23a.html},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/chil/AliBCPCKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccci/AhmedSAAPK23,
author = {Mansoor Ahmed and
Usama Sardar and
Sarwan Ali and
Shafiq Alam and
Murray Patterson and
Imdadullah Khan},
editor = {Ngoc Thanh Nguyen and
J{\'{a}}nos Botzheim and
L{\'{a}}szl{\'{o}} Guly{\'{a}}s and
Manuel N{\'{u}}{\~{n}}ez and
Jan Treur and
Gottfried Vossen and
Adrianna Kozierkiewicz},
title = {Robust Brain Age Estimation via Regression Models and MRI-Derived
Features},
booktitle = {Advances in Computational Collective Intelligence - 15th International
Conference, {ICCCI} 2023, Budapest, Hungary, September 27-29, 2023,
Proceedings},
series = {Communications in Computer and Information Science},
volume = {1864},
pages = {661--674},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-41774-0\_52},
doi = {10.1007/978-3-031-41774-0\_52},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccci/AhmedSAAPK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/AliCP23,
author = {Sarwan Ali and
Prakash Chourasia and
Murray Patterson},
editor = {Krystal Maughan and
Rosanne Liu and
Thomas F. Burns},
title = {When Biology has Chemistry: Solubility And Drug Subcategory Prediction
using {SMILES} Strings},
booktitle = {The First Tiny Papers Track at {ICLR} 2023, Tiny Papers @ {ICLR} 2023,
Kigali, Rwanda, May 5, 2023},
publisher = {OpenReview.net},
year = {2023},
url = {https://openreview.net/forum?id=28si4RXwDt1},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iclr/AliCP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iconip/TayebiACMP23,
author = {Zahra Tayebi and
Sarwan Ali and
Prakash Chourasia and
Taslim Murad and
Murray Patterson},
editor = {Biao Luo and
Long Cheng and
Zheng{-}Guang Wu and
Hongyi Li and
Chaojie Li},
title = {T Cell Receptor Protein Sequences and Sparse Coding: {A} Novel Approach
to Cancer Classification},
booktitle = {Neural Information Processing - 30th International Conference, {ICONIP}
2023, Changsha, China, November 20-23, 2023, Proceedings, Part {X}},
series = {Communications in Computer and Information Science},
volume = {1964},
pages = {215--227},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-8141-0\_17},
doi = {10.1007/978-981-99-8141-0\_17},
timestamp = {Mon, 27 Nov 2023 17:35:45 +0100},
biburl = {https://dblp.org/rec/conf/iconip/TayebiACMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/AliMP23,
author = {Sarwan Ali and
Taslim Murad and
Murray Patterson},
title = {PCD2Vec: {A} Poisson Correction Distance Based Approach for Viral
Host Classification},
booktitle = {International Joint Conference on Neural Networks, {IJCNN} 2023, Gold
Coast, Australia, June 18-23, 2023},
pages = {1--8},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/IJCNN54540.2023.10191311},
doi = {10.1109/IJCNN54540.2023.10191311},
timestamp = {Wed, 09 Aug 2023 16:25:09 +0200},
biburl = {https://dblp.org/rec/conf/ijcnn/AliMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/ChourasiaTAP23,
author = {Prakash Chourasia and
Zahra Tayebi and
Sarwan Ali and
Murray Patterson},
title = {Empowering Pandemic Response with Federated Learning for Protein Sequence
Data Analysis},
booktitle = {International Joint Conference on Neural Networks, {IJCNN} 2023, Gold
Coast, Australia, June 18-23, 2023},
pages = {1--8},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/IJCNN54540.2023.10191721},
doi = {10.1109/IJCNN54540.2023.10191721},
timestamp = {Wed, 09 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ijcnn/ChourasiaTAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/inns-dlia/MuradAP23,
author = {Taslim Murad and
Sarwan Ali and
Murray Patterson},
editor = {Chrisina Jayne and
Danilo P. Mandic and
Richard J. Duro},
title = {A New Direction in Membranolytic Anticancer Peptides classification:
Combining Spaced k-mers with Chaos Game Representation},
booktitle = {International Neural Network Society Workshop on Deep Learning Innovations
and Applications, {INNS} DLIA@IJCNN 2023, Gold Coast, Australia, 23
June 2023},
series = {Procedia Computer Science},
volume = {222},
pages = {666--675},
publisher = {Elsevier},
year = {2023},
url = {https://doi.org/10.1016/j.procs.2023.08.204},
doi = {10.1016/J.PROCS.2023.08.204},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/inns-dlia/MuradAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AliCP23,
author = {Sarwan Ali and
Pin{-}Yu Chen and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Unveiling the Robustness of Machine Learning Models in Classifying
{COVID-19} Spike Sequences},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {1--15},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_1},
doi = {10.1007/978-981-99-7074-2\_1},
timestamp = {Tue, 10 Oct 2023 15:52:57 +0200},
biburl = {https://dblp.org/rec/conf/isbra/AliCP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AliSKP23,
author = {Sarwan Ali and
Usama Sardar and
Imdadullah Khan and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Efficient Sequence Embedding for SARS-CoV-2 Variants Classification},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {16--30},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_2},
doi = {10.1007/978-981-99-7074-2\_2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/isbra/AliSKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/SardarAASBKP23,
author = {Usama Sardar and
Sarwan Ali and
Muhammad Sohaib Ayub and
Muhammad Shoaib and
Khurram Bashir and
Imdadullah Khan and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Sequence-Based Nanobody-Antigen Binding Prediction},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {227--240},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_18},
doi = {10.1007/978-981-99-7074-2\_18},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/SardarAASBKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AliCP23a,
author = {Sarwan Ali and
Prakash Chourasia and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {PDB2Vec: Using 3D Structural Information for Improved Protein Analysis},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {376--386},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_29},
doi = {10.1007/978-981-99-7074-2\_29},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/AliCP23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AliMCP23,
author = {Sarwan Ali and
Haris Mansoor and
Prakash Chourasia and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {387--397},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_30},
doi = {10.1007/978-981-99-7074-2\_30},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/AliMCP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/ChourasiaMAP23,
author = {Prakash Chourasia and
Taslim Murad and
Sarwan Ali and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Enhancing t-SNE Performance for Biological Sequencing Data Through
Kernel Selection},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {442--452},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_35},
doi = {10.1007/978-981-99-7074-2\_35},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/ChourasiaMAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/TayebiJZP23,
author = {Zahra Tayebi and
Akshay Juyal and
Alexander Zelikovsky and
Murray Patterson},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Simulating Tumor Evolution from scDNA-Seq as an Accumulation of both
SNVs and CNAs},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {530--540},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_43},
doi = {10.1007/978-981-99-7074-2\_43},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/TayebiJZP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdh/AliCP23,
author = {Sarwan Ali and
Prakash Chourasia and
Murray Patterson},
editor = {Zina M. Ibrahim and
Honghan Wu and
Nirmalie Wiratunga},
title = {Anderson Acceleration for Bioinformatics-Based Machine Learning},
booktitle = {Proceedings of the 6th International Workshop on Knowledge Discovery
from Healthcare Data co-located with 32nd International Joint Conference
on Artificial Intelligence {(IJCAI} 2023), Macao, China, August 20,
2023},
series = {{CEUR} Workshop Proceedings},
volume = {3479},
publisher = {CEUR-WS.org},
year = {2023},
url = {https://ceur-ws.org/Vol-3479/paper4.pdf},
timestamp = {Wed, 13 Sep 2023 16:08:43 +0200},
biburl = {https://dblp.org/rec/conf/kdh/AliCP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pakdd/AliSPK23,
author = {Sarwan Ali and
Usama Sardar and
Murray Patterson and
Imdadullah Khan},
editor = {Hisashi Kashima and
Tsuyoshi Id{\'{e}} and
Wen{-}Chih Peng},
title = {BioSequence2Vec: Efficient Embedding Generation for Biological Sequences},
booktitle = {Advances in Knowledge Discovery and Data Mining - 27th Pacific-Asia
Conference on Knowledge Discovery and Data Mining, {PAKDD} 2023, Osaka,
Japan, May 25-28, 2023, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {13936},
pages = {173--185},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-33377-4\_14},
doi = {10.1007/978-3-031-33377-4\_14},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pakdd/AliSPK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/isbra/2023,
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2},
doi = {10.1007/978-981-99-7074-2},
isbn = {978-981-99-7073-5},
timestamp = {Tue, 10 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/2023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-00347,
author = {Sarwan Ali and
Prakash Chourasia and
Murray Patterson},
title = {Anderson Acceleration For Bioinformatics-Based Machine Learning},
journal = {CoRR},
volume = {abs/2302.00347},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.00347},
doi = {10.48550/ARXIV.2302.00347},
eprinttype = {arXiv},
eprint = {2302.00347},
timestamp = {Thu, 09 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-00347.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-08688,
author = {Prakash Chourasia and
Taslim Murad and
Zahra Tayebi and
Sarwan Ali and
Imdadullah Khan and
Murray Patterson},
title = {Efficient Classification of SARS-CoV-2 Spike Sequences Using Federated
Learning},
journal = {CoRR},
volume = {abs/2302.08688},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.08688},
doi = {10.48550/ARXIV.2302.08688},
eprinttype = {arXiv},
eprint = {2302.08688},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-08688.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2303-02421,
author = {Taslim Murad and
Sarwan Ali and
Murray Patterson},
title = {Exploring The Potential Of GANs In Biological Sequence Analysis},
journal = {CoRR},
volume = {abs/2303.02421},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2303.02421},
doi = {10.48550/ARXIV.2303.02421},
eprinttype = {arXiv},
eprint = {2303.02421},
timestamp = {Tue, 14 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2303-02421.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-00291,
author = {Sarwan Ali and
Usama Sardar and
Murray Patterson and
Imdadullah Khan},
title = {BioSequence2Vec: Efficient Embedding Generation For Biological Sequences},
journal = {CoRR},
volume = {abs/2304.00291},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.00291},
doi = {10.48550/ARXIV.2304.00291},
eprinttype = {arXiv},
eprint = {2304.00291},
timestamp = {Mon, 17 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-00291.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-02891,
author = {Sarwan Ali and
Prakash Chourasia and
Zahra Tayebi and
Babatunde Bello and
Murray Patterson},
title = {ViralVectors: Compact and Scalable Alignment-free Virome Feature Generation},
journal = {CoRR},
volume = {abs/2304.02891},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.02891},
doi = {10.48550/ARXIV.2304.02891},
eprinttype = {arXiv},
eprint = {2304.02891},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-02891.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-06731,
author = {Sarwan Ali and
Taslim Murad and
Murray Patterson},
title = {PCD2Vec: {A} Poisson Correction Distance-Based Approach for Viral
Host Classification},
journal = {CoRR},
volume = {abs/2304.06731},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.06731},
doi = {10.48550/ARXIV.2304.06731},
eprinttype = {arXiv},
eprint = {2304.06731},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-06731.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-12328,
author = {Sarwan Ali and
Babatunde Bello and
Prakash Chourasia and
Ria Thazhe Punathil and
Pin{-}Yu Chen and
Imdadullah Khan and
Murray Patterson},
title = {Virus2Vec: Viral Sequence Classification Using Machine Learning},
journal = {CoRR},
volume = {abs/2304.12328},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.12328},
doi = {10.48550/ARXIV.2304.12328},
eprinttype = {arXiv},
eprint = {2304.12328},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-12328.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-13145,
author = {Zahra Tayebi and
Sarwan Ali and
Prakash Chourasia and
Taslim Murad and
Murray Patterson},
title = {T Cell Receptor Protein Sequences and Sparse Coding: {A} Novel Approach
to Cancer Classification},
journal = {CoRR},
volume = {abs/2304.13145},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.13145},
doi = {10.48550/ARXIV.2304.13145},
eprinttype = {arXiv},
eprint = {2304.13145},
timestamp = {Wed, 03 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-13145.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-05514,
author = {Mansoor Ahmed and
Usama Sardar and
Sarwan Ali and
Shafiq Alam and
Murray Patterson and
Imdadullah Khan},
title = {Robust Brain Age Estimation via Regression Models and MRI-derived
Features},
journal = {CoRR},
volume = {abs/2306.05514},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.05514},
doi = {10.48550/ARXIV.2306.05514},
eprinttype = {arXiv},
eprint = {2306.05514},
timestamp = {Wed, 14 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-05514.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2308-01920,
author = {Usama Sardar and
Sarwan Ali and
Muhammad Sohaib Ayub and
Muhammad Shoaib and
Khurram Bashir and
Imdadullah Khan and
Murray Patterson},
title = {Sequence-Based Nanobody-Antigen Binding Prediction},
journal = {CoRR},
volume = {abs/2308.01920},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2308.01920},
doi = {10.48550/ARXIV.2308.01920},
eprinttype = {arXiv},
eprint = {2308.01920},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2308-01920.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KhandaiNSBBP22,
author = {Kaustubh Khandai and
Cristian Navarro{-}Martinez and
Brendan Smith and
Rebecca Buonopane and
S. Ashley Byun and
Murray Patterson},
title = {Determining Significant Correlation Between Pairs of Extant Characters
in a Small Parsimony Framework},
journal = {J. Comput. Biol.},
volume = {29},
number = {10},
pages = {1132--1154},
year = {2022},
url = {https://doi.org/10.1089/cmb.2022.0141},
doi = {10.1089/CMB.2022.0141},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KhandaiNSBBP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mbec/AliZP22,
author = {Sarwan Ali and
Yijing Zhou and
Murray Patterson},
title = {Efficient analysis of {COVID-19} clinical data using machine learning
models},
journal = {Medical Biol. Eng. Comput.},
volume = {60},
number = {7},
pages = {1881--1896},
year = {2022},
url = {https://doi.org/10.1007/s11517-022-02570-8},
doi = {10.1007/S11517-022-02570-8},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mbec/AliZP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acml/MuradCAP22,
author = {Taslim Murad and
Prakash Chourasia and
Sarwan Ali and
Murray Patterson},
editor = {Vineeth N. Balasubramanian and
Ivor W. Tsang},
title = {Hashing2Vec: Fast Embedding Generation for SARS-CoV-2 Spike Sequence
Classification},
booktitle = {Asian Conference on Machine Learning, {ACML} 2022, 12-14 December
2022, Hyderabad, India},
series = {Proceedings of Machine Learning Research},
volume = {189},
pages = {754--769},
publisher = {{PMLR}},
year = {2022},
url = {https://proceedings.mlr.press/v189/taslim23a.html},
timestamp = {Tue, 07 May 2024 20:11:56 +0200},
biburl = {https://dblp.org/rec/conf/acml/MuradCAP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bigdataconf/ChourasiaAP22,
author = {Prakash Chourasia and
Sarwan Ali and
Murray Patterson},
editor = {Shusaku Tsumoto and
Yukio Ohsawa and
Lei Chen and
Dirk Van den Poel and
Xiaohua Hu and
Yoichi Motomura and
Takuya Takagi and
Lingfei Wu and
Ying Xie and
Akihiro Abe and
Vijay Raghavan},
title = {Informative Initialization and Kernel Selection Improves t-SNE for
Biological Sequences},
booktitle = {{IEEE} International Conference on Big Data, Big Data 2022, Osaka,
Japan, December 17-20, 2022},
pages = {101--106},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/BigData55660.2022.10020217},
doi = {10.1109/BIGDATA55660.2022.10020217},
timestamp = {Tue, 11 Jun 2024 10:44:02 +0200},
biburl = {https://dblp.org/rec/conf/bigdataconf/ChourasiaAP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bigdataservice/AliMCP22,
author = {Sarwan Ali and
Taslim Murad and
Prakash Chourasia and
Murray Patterson},
title = {Spike2Signal: Classifying Coronavirus Spike Sequences with Deep Learning},
booktitle = {Eighth {IEEE} International Conference on Big Data Computing Service
and Applications, BigDataService 2022, Newark, CA, USA, August 15-18,
2022},
pages = {81--88},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/BigDataService55688.2022.00020},
doi = {10.1109/BIGDATASERVICE55688.2022.00020},
timestamp = {Thu, 06 Oct 2022 22:35:08 +0200},
biburl = {https://dblp.org/rec/conf/bigdataservice/AliMCP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iconip/AliMP22,
author = {Sarwan Ali and
Taslim Murad and
Murray Patterson},
editor = {Mohammad Tanveer and
Sonali Agarwal and
Seiichi Ozawa and
Asif Ekbal and
Adam Jatowt},
title = {PSSM2Vec: {A} Compact Alignment-Free Embedding Approach for Coronavirus
Spike Sequence Classification},
booktitle = {Neural Information Processing - 29th International Conference, {ICONIP}
2022, Virtual Event, November 22-26, 2022, Proceedings, Part {VII}},
series = {Communications in Computer and Information Science},
volume = {1794},
pages = {420--432},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-981-99-1648-1\_35},
doi = {10.1007/978-981-99-1648-1\_35},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iconip/AliMP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/iccabs/2021,
editor = {Mukul S. Bansal and
Ion I. Mandoiu and
Marmar Moussa and
Murray Patterson and
Sanguthevar Rajasekaran and
Pavel Skums and
Alexander Zelikovsky},
title = {Computational Advances in Bio and Medical Sciences: 11th International
Conference, {ICCABS} 2021, Virtual Event, December 16-18, 2021, Revised
Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {13254},
publisher = {Springer International Publishing},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-17531-2},
doi = {10.1007/978-3-031-17531-2},
isbn = {978-3-031-17530-5},
timestamp = {Thu, 04 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/2021.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2201-02273,
author = {Sarwan Ali and
Babatunde Bello and
Prakash Chourasia and
Ria Thazhe Punathil and
Yijing Zhou and
Murray Patterson},
title = {PWM2Vec: An Efficient Embedding Approach for Viral Host Specification
from Coronavirus Spike Sequences},
journal = {CoRR},
volume = {abs/2201.02273},
year = {2022},
url = {https://arxiv.org/abs/2201.02273},
eprinttype = {arXiv},
eprint = {2201.02273},
timestamp = {Mon, 10 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2201-02273.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2207-08898,
author = {Sarwan Ali and
Bikram Sahoo and
Alexander Zelikovskiy and
Pin{-}Yu Chen and
Murray Patterson},
title = {Benchmarking Machine Learning Robustness in Covid-19 Genome Sequence
Classification},
journal = {CoRR},
volume = {abs/2207.08898},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2207.08898},
doi = {10.48550/ARXIV.2207.08898},
eprinttype = {arXiv},
eprint = {2207.08898},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2207-08898.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2209-04952,
author = {Sarwan Ali and
Bikram Sahoo and
Muhammad Asad Khan and
Alexander Zelikovsky and
Imdadullah Khan and
Murray Patterson},
title = {Efficient Approximate Kernel Based Spike Sequence Classification},
journal = {CoRR},
volume = {abs/2209.04952},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2209.04952},
doi = {10.48550/ARXIV.2209.04952},
eprinttype = {arXiv},
eprint = {2209.04952},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2209-04952.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2211-08267,
author = {Prakash Chourasia and
Sarwan Ali and
Simone Ciccolella and
Gianluca Della Vedova and
Murray Patterson},
title = {Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads
Data},
journal = {CoRR},
volume = {abs/2211.08267},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2211.08267},
doi = {10.48550/ARXIV.2211.08267},
eprinttype = {arXiv},
eprint = {2211.08267},
timestamp = {Thu, 24 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2211-08267.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2211-09263,
author = {Prakash Chourasia and
Sarwan Ali and
Murray Patterson},
title = {Informative Initialization and Kernel Selection Improves t-SNE for
Biological Sequences},
journal = {CoRR},
volume = {abs/2211.09263},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2211.09263},
doi = {10.48550/ARXIV.2211.09263},
eprinttype = {arXiv},
eprint = {2211.09263},
timestamp = {Wed, 23 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2211-09263.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/TayebiAP21,
author = {Zahra Tayebi and
Sarwan Ali and
Murray Patterson},
title = {Robust Representation and Efficient Feature Selection Allows for Effective
Clustering of SARS-CoV-2 Variants},
journal = {Algorithms},
volume = {14},
number = {12},
pages = {348},
year = {2021},
url = {https://doi.org/10.3390/a14120348},
doi = {10.3390/A14120348},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithms/TayebiAP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CiccolellaRGPSB21,
author = {Simone Ciccolella and
Camir Ricketts and
Mauricio Soto Gomez and
Murray Patterson and
Dana Silverbush and
Paola Bonizzoni and
Iman Hajirasouliha and
Gianluca Della Vedova},
title = {Inferring cancer progression from Single-Cell Sequencing while allowing
mutation losses},
journal = {Bioinform.},
volume = {37},
number = {3},
pages = {326--333},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa722},
doi = {10.1093/BIOINFORMATICS/BTAA722},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CiccolellaRGPSB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MelnykMKSHSZP21,
author = {Andrew Melnyk and
Fatemeh Mohebbi and
Sergey Knyazev and
Bikram Sahoo and
Roya Hosseini and
Pavel Skums and
Alex Zelikovsky and
Murray Patterson},
title = {From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2
Via Clustering},
journal = {J. Comput. Biol.},
volume = {28},
number = {11},
pages = {1113--1129},
year = {2021},
url = {https://doi.org/10.1089/cmb.2021.0302},
doi = {10.1089/CMB.2021.0302},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/MelnykMKSHSZP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AliCLVP21,
author = {Sarwan Ali and
Simone Ciccolella and
Lorenzo Lucarella and
Gianluca Della Vedova and
Murray Patterson},
title = {Simpler and Faster Development of Tumor Phylogeny Pipelines},
journal = {J. Comput. Biol.},
volume = {28},
number = {11},
pages = {1142--1155},
year = {2021},
url = {https://doi.org/10.1089/cmb.2021.0271},
doi = {10.1089/CMB.2021.0271},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/AliCLVP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/titb/CiccolellaPBV21,
author = {Simone Ciccolella and
Murray Patterson and
Paola Bonizzoni and
Gianluca Della Vedova},
title = {Effective Clustering for Single Cell Sequencing Cancer Data},
journal = {{IEEE} J. Biomed. Health Informatics},
volume = {25},
number = {11},
pages = {4068--4078},
year = {2021},
url = {https://doi.org/10.1109/JBHI.2021.3081380},
doi = {10.1109/JBHI.2021.3081380},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/titb/CiccolellaPBV21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bigdataconf/AliP21,
author = {Sarwan Ali and
Murray Patterson},
editor = {Yixin Chen and
Heiko Ludwig and
Yicheng Tu and
Usama M. Fayyad and
Xingquan Zhu and
Xiaohua Hu and
Suren Byna and
Xiong Liu and
Jianping Zhang and
Shirui Pan and
Vagelis Papalexakis and
Jianwu Wang and
Alfredo Cuzzocrea and
Carlos Ordonez},
title = {Spike2Vec: An Efficient and Scalable Embedding Approach for {COVID-19}
Spike Sequences},
booktitle = {2021 {IEEE} International Conference on Big Data (Big Data), Orlando,
FL, USA, December 15-18, 2021},
pages = {1533--1540},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/BigData52589.2021.9671848},
doi = {10.1109/BIGDATA52589.2021.9671848},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bigdataconf/AliP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/ChourasiaACVP21,
author = {Prakash Chourasia and
Sarwan Ali and
Simone Ciccolella and
Gianluca Della Vedova and
Murray Patterson},
editor = {Mukul S. Bansal and
Ion I. Mandoiu and
Marmar Moussa and
Murray Patterson and
Sanguthevar Rajasekaran and
Pavel Skums and
Alexander Zelikovsky},
title = {Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing
Reads Data},
booktitle = {Computational Advances in Bio and Medical Sciences: 11th International
Conference, {ICCABS} 2021, Virtual Event, December 16-18, 2021, Revised
Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {13254},
pages = {133--148},
publisher = {Springer International Publishing},
year = {2021},
url = {https://doi.org/10.1007/978-3-031-17531-2\_11},
doi = {10.1007/978-3-031-17531-2\_11},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/ChourasiaACVP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AliSUZPK21,
author = {Sarwan Ali and
Bikram Sahoo and
Naimat Ullah and
Alexander Zelikovskiy and
Murray Patterson and
Imdadullah Khan},
editor = {Yanjie Wei and
Min Li and
Pavel Skums and
Zhipeng Cai},
title = {A k-mer Based Approach for SARS-CoV-2 Variant Identification},
booktitle = {Bioinformatics Research and Applications - 17th International Symposium,
{ISBRA} 2021, Shenzhen, China, November 26-28, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13064},
pages = {153--164},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-91415-8\_14},
doi = {10.1007/978-3-030-91415-8\_14},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/AliSUZPK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/SmithNBBP21,
author = {Brendan Smith and
Cristian Navarro{-}Martinez and
Rebecca Buonopane and
S. Ashley Byun and
Murray Patterson},
editor = {Yanjie Wei and
Min Li and
Pavel Skums and
Zhipeng Cai},
title = {Correlated Evolution in the Small Parsimony Framework},
booktitle = {Bioinformatics Research and Applications - 17th International Symposium,
{ISBRA} 2021, Shenzhen, China, November 26-28, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13064},
pages = {608--619},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-91415-8\_51},
doi = {10.1007/978-3-030-91415-8\_51},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/isbra/SmithNBBP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2108-03465,
author = {Sarwan Ali and
Bikram Sahoo and
Naimat Ullah and
Alexander Zelikovskiy and
Murray Patterson and
Imdadullah Khan},
title = {A k-mer Based Approach for SARS-CoV-2 Variant Identification},
journal = {CoRR},
volume = {abs/2108.03465},
year = {2021},
url = {https://arxiv.org/abs/2108.03465},
eprinttype = {arXiv},
eprint = {2108.03465},
timestamp = {Wed, 11 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2108-03465.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2108-08143,
author = {Sarwan Ali and
Tamkanat E. Ali and
Muhammad Asad Khan and
Imdadullah Khan and
Murray Patterson},
title = {Effective and scalable clustering of SARS-CoV-2 sequences},
journal = {CoRR},
volume = {abs/2108.08143},
year = {2021},
url = {https://arxiv.org/abs/2108.08143},
eprinttype = {arXiv},
eprint = {2108.08143},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2108-08143.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2109-05019,
author = {Sarwan Ali and
Murray Patterson},
title = {Spike2Vec: An Efficient and Scalable Embedding Approach for {COVID-19}
Spike Sequences},
journal = {CoRR},
volume = {abs/2109.05019},
year = {2021},
url = {https://arxiv.org/abs/2109.05019},
eprinttype = {arXiv},
eprint = {2109.05019},
timestamp = {Wed, 22 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2109-05019.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-00809,
author = {Sarwan Ali and
Babatunde Bello and
Murray Patterson},
title = {Classifying {COVID-19} Spike Sequences from Geographic Location Using
Deep Learning},
journal = {CoRR},
volume = {abs/2110.00809},
year = {2021},
url = {https://arxiv.org/abs/2110.00809},
eprinttype = {arXiv},
eprint = {2110.00809},
timestamp = {Fri, 08 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-00809.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-09606,
author = {Sarwan Ali and
Yijing Zhou and
Murray Patterson},
title = {Efficient Analysis of {COVID-19} Clinical Data using Machine Learning
Models},
journal = {CoRR},
volume = {abs/2110.09606},
year = {2021},
url = {https://arxiv.org/abs/2110.09606},
eprinttype = {arXiv},
eprint = {2110.09606},
timestamp = {Mon, 25 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-09606.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-09622,
author = {Zahra Tayebi and
Sarwan Ali and
Murray Patterson},
title = {Robust Representation and Efficient Feature Selection Allows for Effective
Clustering of SARS-CoV-2 Variants},
journal = {CoRR},
volume = {abs/2110.09622},
year = {2021},
url = {https://arxiv.org/abs/2110.09622},
eprinttype = {arXiv},
eprint = {2110.09622},
timestamp = {Mon, 25 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-09622.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CiccolellaGPVHB20,
author = {Simone Ciccolella and
Mauricio Soto Gomez and
Murray D. Patterson and
Gianluca Della Vedova and
Iman Hajirasouliha and
Paola Bonizzoni},
title = {gpps: an ILP-based approach for inferring cancer progression with
mutation losses from single cell data},
journal = {{BMC} Bioinform.},
volume = {21-S},
number = {1},
pages = {413},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03736-7},
doi = {10.1186/S12859-020-03736-7},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CiccolellaGPVHB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/MelnykMKSHSZP20,
author = {Andrew Melnyk and
Fatemeh Mohebbi and
Sergey Knyazev and
Bikram Sahoo and
Roya Hosseini and
Pavel Skums and
Alex Zelikovsky and
Murray Patterson},
editor = {Sumit Kumar Jha and
Ion I. Mandoiu and
Sanguthevar Rajasekaran and
Pavel Skums and
Alex Zelikovsky},
title = {Clustering Based Identification of SARS-CoV-2 Subtypes},
booktitle = {Computational Advances in Bio and Medical Sciences - 10th International
Conference, {ICCABS} 2020, Virtual Event, December 10-12, 2020, Revised
Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {12686},
pages = {127--141},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-79290-9\_11},
doi = {10.1007/978-3-030-79290-9\_11},
timestamp = {Thu, 29 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccabs/MelnykMKSHSZP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/quanbio/RizziBPPPVB19,
author = {Raffaella Rizzi and
Stefano Beretta and
Murray Patterson and
Yuri Pirola and
Marco Previtali and
Gianluca Della Vedova and
Paola Bonizzoni},
title = {Overlap graphs and de Bruijn graphs: data structures for de novo genome
assembly in the big data era},
journal = {Quant. Biol.},
volume = {7},
number = {4},
pages = {278--292},
year = {2019},
url = {https://doi.org/10.1007/s40484-019-0181-x},
doi = {10.1007/S40484-019-0181-X},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/quanbio/RizziBPPPVB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/CiccolellaPBV19,
author = {Simone Ciccolella and
Murray D. Patterson and
Paola Bonizzoni and
Gianluca Della Vedova},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Effective Clustering for Single Cell Sequencing Cancer Data},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {437--446},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3342149},
doi = {10.1145/3307339.3342149},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/CiccolellaPBV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/0001BVP19,
author = {Giulia Bernardini and
Paola Bonizzoni and
Gianluca Della Vedova and
Murray Patterson},
editor = {Nadia Pisanti and
Solon P. Pissis},
title = {A Rearrangement Distance for Fully-Labelled Trees},
booktitle = {30th Annual Symposium on Combinatorial Pattern Matching, {CPM} 2019,
June 18-20, 2019, Pisa, Italy},
series = {LIPIcs},
volume = {128},
pages = {28:1--28:15},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.CPM.2019.28},
doi = {10.4230/LIPICS.CPM.2019.28},
timestamp = {Wed, 21 Aug 2024 22:46:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/0001BVP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1904-01321,
author = {Giulia Bernardini and
Paola Bonizzoni and
Gianluca Della Vedova and
Murray Patterson},
title = {A rearrangement distance for fully-labelled trees},
journal = {CoRR},
volume = {abs/1904.01321},
year = {2019},
url = {http://arxiv.org/abs/1904.01321},
eprinttype = {arXiv},
eprint = {1904.01321},
timestamp = {Thu, 02 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1904-01321.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BerettaPZVB18,
author = {Stefano Beretta and
Murray Patterson and
Simone Zaccaria and
Gianluca Della Vedova and
Paola Bonizzoni},
title = {HapCHAT: adaptive haplotype assembly for efficiently leveraging high
coverage in long reads},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {252:1--252:19},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2253-8},
doi = {10.1186/S12859-018-2253-8},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BerettaPZVB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/CiccolellaGPVHB18,
author = {Simone Ciccolella and
Mauricio Soto Gomez and
Murray Patterson and
Gianluca Della Vedova and
Iman Hajirasouliha and
Paola Bonizzoni},
title = {gpps: an ILP-based approach for inferring cancer progression with
mutation losses from single cell data},
booktitle = {8th {IEEE} International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2018, Las Vegas, NV, USA, October 18-20,
2018},
pages = {1},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.org/10.1109/ICCABS.2018.8542058},
doi = {10.1109/ICCABS.2018.8542058},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/CiccolellaGPVHB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cie/VedovaPRS17,
author = {Gianluca Della Vedova and
Murray Patterson and
Raffaella Rizzi and
Mauricio Soto Gomez},
editor = {Jarkko Kari and
Florin Manea and
Ion Petre},
title = {Character-Based Phylogeny Construction and Its Application to Tumor
Evolution},
booktitle = {Unveiling Dynamics and Complexity - 13th Conference on Computability
in Europe, CiE 2017, Turku, Finland, June 12-16, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10307},
pages = {3--13},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-58741-7\_1},
doi = {10.1007/978-3-319-58741-7\_1},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cie/VedovaPRS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BraccialiAPMPMT16,
author = {Andrea Bracciali and
Marco Aldinucci and
Murray Patterson and
Tobias Marschall and
Nadia Pisanti and
Ivan Merelli and
Massimo Torquati},
title = {{PWHATSHAP:} efficient haplotyping for future generation sequencing},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-11}},
pages = {342},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1170-y},
doi = {10.1186/S12859-016-1170-Y},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BraccialiAPMPMT16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/PattersonMPISKS15,
author = {Murray Patterson and
Tobias Marschall and
Nadia Pisanti and
Leo van Iersel and
Leen Stougie and
Gunnar W. Klau and
Alexander Sch{\"{o}}nhuth},
title = {WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing
Reads},
journal = {J. Comput. Biol.},
volume = {22},
number = {6},
pages = {498--509},
year = {2015},
url = {https://doi.org/10.1089/cmb.2014.0157},
doi = {10.1089/CMB.2014.0157},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/PattersonMPISKS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/AldinucciBMPPT14,
author = {Marco Aldinucci and
Andrea Bracciali and
Tobias Marschall and
Murray Patterson and
Nadia Pisanti and
Massimo Torquati},
editor = {Clelia Di Serio and
Pietro Li{\`{o}} and
Alessandro Nonis and
Roberto Tagliaferri},
title = {High-Performance Haplotype Assembly},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics
- 11th International Meeting, {CIBB} 2014, Cambridge, UK, June 26-28,
2014, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {8623},
pages = {245--258},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-24462-4\_21},
doi = {10.1007/978-3-319-24462-4\_21},
timestamp = {Wed, 25 Sep 2019 18:13:08 +0200},
biburl = {https://dblp.org/rec/conf/cibb/AldinucciBMPPT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PattersonMPISKS14,
author = {Murray Patterson and
Tobias Marschall and
Nadia Pisanti and
Leo van Iersel and
Leen Stougie and
Gunnar W. Klau and
Alexander Sch{\"{o}}nhuth},
editor = {Roded Sharan},
title = {WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads},
booktitle = {Research in Computational Molecular Biology - 18th Annual International
Conference, {RECOMB} 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8394},
pages = {237--249},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-05269-4\_19},
doi = {10.1007/978-3-319-05269-4\_19},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PattersonMPISKS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/El-KebirMWPHSK13,
author = {Mohammed El{-}Kebir and
Tobias Marschall and
Inken Wohlers and
Murray Patterson and
Jaap Heringa and
Alexander Sch{\"{o}}nhuth and
Gunnar W. Klau},
title = {Mapping proteins in the presence of paralogs using units of coevolution},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-15}},
pages = {S18},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S15-S18},
doi = {10.1186/1471-2105-14-S15-S18},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/El-KebirMWPHSK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PattersonSDT13,
author = {Murray Patterson and
Gergely J. Sz{\"{o}}llosi and
Vincent Daubin and
Eric Tannier},
title = {Lateral gene transfer, rearrangement, reconciliation},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-15}},
pages = {S4},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S15-S4},
doi = {10.1186/1471-2105-14-S15-S4},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PattersonSDT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/ChauvePR13,
author = {C{\'{e}}dric Chauve and
Murray Patterson and
Ashok Rajaraman},
editor = {Thierry Lecroq and
Laurent Mouchard},
title = {Hypergraph Covering Problems Motivated by Genome Assembly Questions},
booktitle = {Combinatorial Algorithms - 24th International Workshop, {IWOCA} 2013,
Rouen, France, July 10-12, 2013, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {8288},
pages = {428--432},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-45278-9\_37},
doi = {10.1007/978-3-642-45278-9\_37},
timestamp = {Wed, 25 Sep 2019 18:08:04 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/ChauvePR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/colognetwente/ManuchPWCT13,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Roland Wittler and
C{\'{e}}dric Chauve and
Eric Tannier},
editor = {Kamiel Cornelissen and
Ruben Hoeksma and
Johann L. Hurink and
Bodo Manthey},
title = {Linearization of ancestral multichromosomal genomes},
booktitle = {12th Cologne-Twente Workshop on Graphs and Combinatorial Optimization,
Enschede, Netherlands, May 21-23, 2013},
series = {{CTIT} Workshop Proceedings},
volume = {{WP} 13-01},
pages = {169--173},
year = {2013},
timestamp = {Mon, 06 Apr 2020 17:04:26 +0200},
biburl = {https://dblp.org/rec/conf/colognetwente/ManuchPWCT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauvePR13,
author = {C{\'{e}}dric Chauve and
Murray Patterson and
Ashok Rajaraman},
title = {Hypergraph covering problems motivated by genome assembly questions},
journal = {CoRR},
volume = {abs/1306.4353},
year = {2013},
url = {http://arxiv.org/abs/1306.4353},
eprinttype = {arXiv},
eprint = {1306.4353},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ChauvePR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ManuchPWCT12,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Roland Wittler and
C{\'{e}}dric Chauve and
Eric Tannier},
title = {Linearization of ancestral multichromosomal genomes},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-19}},
pages = {S11},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S19-S11},
doi = {10.1186/1471-2105-13-S19-S11},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ManuchPWCT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/ManuchPC12,
author = {J{\'{a}}n Manuch and
Murray Patterson and
C{\'{e}}dric Chauve},
title = {Hardness results on the gapped consecutive-ones property problem},
journal = {Discret. Appl. Math.},
volume = {160},
number = {18},
pages = {2760--2768},
year = {2012},
url = {https://doi.org/10.1016/j.dam.2012.03.019},
doi = {10.1016/J.DAM.2012.03.019},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/ManuchPC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/WittlerMPS11,
author = {Roland Wittler and
J{\'{a}}n Manuch and
Murray Patterson and
Jens Stoye},
title = {Consistency of Sequence-Based Gene Clusters},
journal = {J. Comput. Biol.},
volume = {18},
number = {9},
pages = {1023--1039},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0083},
doi = {10.1089/CMB.2011.0083},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/WittlerMPS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ManuchP11,
author = {J{\'{a}}n Manuch and
Murray Patterson},
title = {The Complexity of the Gapped Consecutive-Ones Property Problem for
Matrices of Bounded Maximum Degree},
journal = {J. Comput. Biol.},
volume = {18},
number = {9},
pages = {1243--1253},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0128},
doi = {10.1089/CMB.2011.0128},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ManuchP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/ChauveMPW11,
author = {C{\'{e}}dric Chauve and
J{\'{a}}n Manuch and
Murray Patterson and
Roland Wittler},
editor = {Raffaele Giancarlo and
Giovanni Manzini},
title = {Tractability Results for the Consecutive-Ones Property with Multiplicity},
booktitle = {Combinatorial Pattern Matching - 22nd Annual Symposium, {CPM} 2011,
Palermo, Italy, June 27-29, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6661},
pages = {90--103},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21458-5\_10},
doi = {10.1007/978-3-642-21458-5\_10},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/ChauveMPW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/ManuchPG11,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Arvind Gupta},
editor = {Jianer Chen and
Jianxin Wang and
Alexander Zelikovsky},
title = {Towards a Characterisation of the Generalised Cladistic Character
Compatibility Problem for Non-branching Character Trees},
booktitle = {Bioinformatics Research and Applications - 7th International Symposium,
{ISBRA} 2011, Changsha, China, May 27-29, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6674},
pages = {440--451},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21260-4\_41},
doi = {10.1007/978-3-642-21260-4\_41},
timestamp = {Fri, 21 Aug 2020 17:12:20 +0200},
biburl = {https://dblp.org/rec/conf/isbra/ManuchPG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gd/ManuchPPT10,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Sheung{-}Hung Poon and
Chris Thachuk},
editor = {Ulrik Brandes and
Sabine Cornelsen},
title = {Complexity of Finding Non-Planar Rectilinear Drawings of Graphs},
booktitle = {Graph Drawing - 18th International Symposium, {GD} 2010, Konstanz,
Germany, September 21-24, 2010. Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {6502},
pages = {305--316},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-18469-7\_28},
doi = {10.1007/978-3-642-18469-7\_28},
timestamp = {Sun, 13 Nov 2022 09:57:29 +0100},
biburl = {https://dblp.org/rec/conf/gd/ManuchPPT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ManuchP10,
author = {J{\'{a}}n Manuch and
Murray Patterson},
editor = {Eric Tannier},
title = {The Complexity of the Gapped Consecutive-Ones Property Problem for
Matrices of Bounded Maximum Degree},
booktitle = {Comparative Genomics - International Workshop, {RECOMB-CG} 2010, Ottawa,
Canada, October 9-11, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6398},
pages = {278--289},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-16181-0\_23},
doi = {10.1007/978-3-642-16181-0\_23},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ManuchP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/endm/ChauveMP09,
author = {C{\'{e}}dric Chauve and
J{\'{a}}n Manuch and
Murray Patterson},
title = {On the Gapped Consecutive-Ones Property},
journal = {Electron. Notes Discret. Math.},
volume = {34},
pages = {121--125},
year = {2009},
url = {https://doi.org/10.1016/j.endm.2009.07.020},
doi = {10.1016/J.ENDM.2009.07.020},
timestamp = {Thu, 20 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/endm/ChauveMP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/ManuchPG09,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Arvind Gupta},
editor = {Hung Q. Ngo},
title = {On the Generalised Character Compatibility Problem for Non-branching
Character Trees},
booktitle = {Computing and Combinatorics, 15th Annual International Conference,
{COCOON} 2009, Niagara Falls, NY, USA, July 13-15, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5609},
pages = {268--276},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02882-3\_27},
doi = {10.1007/978-3-642-02882-3\_27},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/ManuchPG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0912-0309,
author = {C{\'{e}}dric Chauve and
J{\'{a}}n Manuch and
Murray Patterson},
title = {Hardness Results for the Gapped Consecutive-Ones Property},
journal = {CoRR},
volume = {abs/0912.0309},
year = {2009},
url = {http://arxiv.org/abs/0912.0309},
eprinttype = {arXiv},
eprint = {0912.0309},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0912-0309.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcai/PattersonLTG07,
author = {Murray Patterson and
Yongmei Liu and
Eugenia Ternovska and
Arvind Gupta},
editor = {Manuela M. Veloso},
title = {Grounding for Model Expansion in k-Guarded Formulas with Inductive
Definitions},
booktitle = {{IJCAI} 2007, Proceedings of the 20th International Joint Conference
on Artificial Intelligence, Hyderabad, India, January 6-12, 2007},
pages = {161--166},
year = {2007},
url = {http://ijcai.org/Proceedings/07/Papers/024.pdf},
timestamp = {Tue, 20 Aug 2019 16:17:11 +0200},
biburl = {https://dblp.org/rec/conf/ijcai/PattersonLTG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/anor/BrucknerMHP03,
author = {Thomas Bruckner and
Robbie Morrison and
Chris Handley and
Murray Patterson},
title = {High-Resolution Modeling of Energy-Services Supply Systems Using \emph{deeco}:
Overview and Application to Policy Development},
journal = {Ann. Oper. Res.},
volume = {121},
number = {1-4},
pages = {151--180},
year = {2003},
url = {https://doi.org/10.1023/A:1023359303704},
doi = {10.1023/A:1023359303704},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/anor/BrucknerMHP03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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