High-Resolution Modeling of Energy-Services Supply Systems Using deeco: Overview and Application to Policy Development. - Thomas Bruckner; Robbie Morrison; Chris Handley; Murray Patterson (Ann. Oper. Res., 2003)

Grounding for Model Expansion in k-Guarded Formulas with Inductive Definitions. - Murray Patterson; Yongmei Liu 001; Eugenia Ternovska; Arvind Gupta (IJCAI, 2007)

On the Generalised Character Compatibility Problem for Non-branching Character Trees. - Ján Manuch; Murray Patterson; Arvind Gupta (COCOON, 2009)

Hardness Results for the Gapped Consecutive-Ones Property - Cédric Chauve; Ján Manuch; Murray Patterson (CoRR, 2009)

On the Gapped Consecutive-Ones Property. - Cédric Chauve; Ján Manuch; Murray Patterson (Electron. Notes Discret. Math., 2009)

Complexity of Finding Non-Planar Rectilinear Drawings of Graphs. - Ján Manuch; Murray Patterson; Sheung-Hung Poon; Chris Thachuk (GD, 2010)

Tractability Results for the Consecutive-Ones Property with Multiplicity. - Cédric Chauve; Ján Manuch; Murray Patterson; Roland Wittler (CPM, 2011)

Towards a Characterisation of the Generalised Cladistic Character Compatibility Problem for Non-branching Character Trees. - Ján Manuch; Murray Patterson; Arvind Gupta (ISBRA, 2011)

The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree. - Ján Manuch; Murray Patterson (J. Comput. Biol., 2011)

Consistency of Sequence-Based Gene Clusters. - Roland Wittler; Ján Manuch; Murray Patterson; Jens Stoye (J. Comput. Biol., 2011)

Linearization of ancestral multichromosomal genomes. - Ján Manuch; Murray Patterson; Roland Wittler; Cédric Chauve; Eric Tannier (BMC Bioinform., 2012)

Hardness results on the gapped consecutive-ones property problem. - Ján Manuch; Murray Patterson; Cédric Chauve (Discret. Appl. Math., 2012)

Hypergraph Covering Problems Motivated by Genome Assembly Questions. - Cédric Chauve; Murray Patterson; Ashok Rajaraman (IWOCA, 2013)

Mapping proteins in the presence of paralogs using units of coevolution. - Mohammed El-Kebir; Tobias Marschall; Inken Wohlers; Murray Patterson; Jaap Heringa; Alexander Schönhuth; Gunnar W. Klau (BMC Bioinform., 2013)

Lateral gene transfer, rearrangement, reconciliation. - Murray Patterson; Gergely J. Szöllosi; Vincent Daubin; Eric Tannier (BMC Bioinform., 2013)

High-Performance Haplotype Assembly. - Marco Aldinucci; Andrea Bracciali; Tobias Marschall; Murray Patterson; Nadia Pisanti; Massimo Torquati (CIBB, 2014)

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. - Murray Patterson; Tobias Marschall; Nadia Pisanti; Leo van Iersel; Leen Stougie; Gunnar W. Klau; Alexander Schönhuth (RECOMB, 2014)

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. - Murray Patterson; Tobias Marschall; Nadia Pisanti; Leo van Iersel; Leen Stougie; Gunnar W. Klau; Alexander Schönhuth (J. Comput. Biol., 2015)

PWHATSHAP: efficient haplotyping for future generation sequencing. - Andrea Bracciali; Marco Aldinucci; Murray Patterson; Tobias Marschall; Nadia Pisanti; Ivan Merelli; Massimo Torquati (BMC Bioinform., 2016)

Character-Based Phylogeny Construction and Its Application to Tumor Evolution. - Gianluca Della Vedova; Murray Patterson; Raffaella Rizzi; Mauricio Soto Gomez (CiE, 2017)

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. - Stefano Beretta 001; Murray Patterson; Simone Zaccaria; Gianluca Della Vedova; Paola Bonizzoni (BMC Bioinform., 2018)

A Rearrangement Distance for Fully-Labelled Trees. - Giulia Bernardini 001; Paola Bonizzoni; Gianluca Della Vedova; Murray Patterson (CPM, 2019)

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. - Raffaella Rizzi; Stefano Beretta 001; Murray Patterson; Yuri Pirola; Marco Previtali; Gianluca Della Vedova; Paola Bonizzoni (Quant. Biol., 2019)

Clustering Based Identification of SARS-CoV-2 Subtypes. - Andrew Melnyk; Fatemeh Mohebbi; Sergey Knyazev; Bikram Sahoo; Roya Hosseini; Pavel Skums; Alex Zelikovsky; Murray Patterson (ICCABS, 2020)

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. - Simone Ciccolella; Mauricio Soto Gomez; Murray D. Patterson; Gianluca Della Vedova; Iman Hajirasouliha; Paola Bonizzoni (BMC Bioinform., 2020)

Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences. - Sarwan Ali; Murray Patterson (IEEE BigData, 2021)

Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data. - Prakash Chourasia; Sarwan Ali; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 2021)

A k-mer Based Approach for SARS-CoV-2 Variant Identification. - Sarwan Ali; Bikram Sahoo; Naimat Ullah; Alexander Zelikovskiy; Murray Patterson; Imdadullah Khan (ISBRA, 2021)

Correlated Evolution in the Small Parsimony Framework. - Brendan Smith; Cristian Navarro-Martinez; Rebecca Buonopane; S. Ashley Byun; Murray Patterson (ISBRA, 2021)

Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants. - Zahra Tayebi; Sarwan Ali; Murray Patterson (Algorithms, 2021)

Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. - Simone Ciccolella; Camir Ricketts; Mauricio Soto Gomez; Murray Patterson; Dana Silverbush; Paola Bonizzoni; Iman Hajirasouliha; Gianluca Della Vedova (Bioinform., 2021)

Effective and scalable clustering of SARS-CoV-2 sequences. - Sarwan Ali; Tamkanat E. Ali; Muhammad Asad Khan; Imdadullah Khan; Murray Patterson (CoRR, 2021)

Classifying COVID-19 Spike Sequences from Geographic Location Using Deep Learning. - Sarwan Ali; Babatunde Bello; Murray Patterson (CoRR, 2021)

Simpler and Faster Development of Tumor Phylogeny Pipelines. - Sarwan Ali; Simone Ciccolella; Lorenzo Lucarella; Gianluca Della Vedova; Murray Patterson (J. Comput. Biol., 2021)

From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. - Andrew Melnyk; Fatemeh Mohebbi; Sergey Knyazev; Bikram Sahoo; Roya Hosseini; Pavel Skums; Alex Zelikovsky; Murray Patterson (J. Comput. Biol., 2021)

Effective Clustering for Single Cell Sequencing Cancer Data. - Simone Ciccolella; Murray Patterson; Paola Bonizzoni; Gianluca Della Vedova (IEEE J. Biomed. Health Informatics, 2021)

Hashing2Vec: Fast Embedding Generation for SARS-CoV-2 Spike Sequence Classification. - Taslim Murad; Prakash Chourasia; Sarwan Ali; Murray Patterson (ACML, 2022)

Informative Initialization and Kernel Selection Improves t-SNE for Biological Sequences. - Prakash Chourasia; Sarwan Ali; Murray Patterson (IEEE Big Data, 2022)

Spike2Signal: Classifying Coronavirus Spike Sequences with Deep Learning. - Sarwan Ali; Taslim Murad; Prakash Chourasia; Murray Patterson (BigDataService, 2022)

PSSM2Vec: A Compact Alignment-Free Embedding Approach for Coronavirus Spike Sequence Classification. - Sarwan Ali; Taslim Murad; Murray Patterson (ICONIP (7), 2022)

PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences. - Sarwan Ali; Babatunde Bello; Prakash Chourasia; Ria Thazhe Punathil; Yijing Zhou; Murray Patterson (CoRR, 2022)

Benchmarking Machine Learning Robustness in Covid-19 Genome Sequence Classification. - Sarwan Ali; Bikram Sahoo; Alexander Zelikovskiy; Pin-Yu Chen; Murray Patterson (CoRR, 2022)

Determining Significant Correlation Between Pairs of Extant Characters in a Small Parsimony Framework. - Kaustubh Khandai; Cristian Navarro-Martinez; Brendan Smith; Rebecca Buonopane; S. Ashley Byun; Murray Patterson (J. Comput. Biol., 2022)

Efficient analysis of COVID-19 clinical data using machine learning models. - Sarwan Ali; Yijing Zhou; Murray Patterson (Medical Biol. Eng. Comput., 2022)

Circular Arc Length-Based Kernel Matrix For Protein Sequence Classification. - Taslim Murad; Sarwan Ali; Prakash Chourasia; Haris Mansoor; Murray Patterson (IEEE Big Data, 2023)

Counterfactually Guided Policy Transfer in Clinical Settings. - Sarwan Ali; Babatunde Bello; Prakash Chourasia; Ria Thazhe Punathil; Pin-Yu Chen; Imdadullah Khan; Murray Patterson (CHIL, 2023)

Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines. - Akshay Juyal; Zahra Tayebi; Alexander Zelikovsky; Mauricio Soto Gomez; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 2023)

Robust Brain Age Estimation via Regression Models and MRI-Derived Features. - Mansoor Ahmed; Usama Sardar; Sarwan Ali; Shafiq Alam; Murray Patterson; Imdad Ullah Khan (ICCCI (CCIS Volume), 2023)

When Biology has Chemistry: Solubility And Drug Subcategory Prediction using SMILES Strings. - Sarwan Ali; Prakash Chourasia; Murray Patterson (Tiny Papers @ ICLR, 2023)

T Cell Receptor Protein Sequences and Sparse Coding: A Novel Approach to Cancer Classification. - Zahra Tayebi; Sarwan Ali; Prakash Chourasia; Taslim Murad; Murray Patterson (ICONIP (10), 2023)

PCD2Vec: A Poisson Correction Distance Based Approach for Viral Host Classification. - Sarwan Ali; Taslim Murad; Murray Patterson (IJCNN, 2023)

Empowering Pandemic Response with Federated Learning for Protein Sequence Data Analysis. - Prakash Chourasia; Zahra Tayebi; Sarwan Ali; Murray Patterson (IJCNN, 2023)

A New Direction in Membranolytic Anticancer Peptides classification: Combining Spaced k-mers with Chaos Game Representation. - Taslim Murad; Sarwan Ali; Murray Patterson (INNS DLIA@IJCNN, 2023)

Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences. - Sarwan Ali; Pin-Yu Chen; Murray Patterson (ISBRA, 2023)

PDB2Vec: Using 3D Structural Information for Improved Protein Analysis. - Sarwan Ali; Prakash Chourasia; Murray Patterson (ISBRA, 2023)

Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification. - Sarwan Ali; Haris Mansoor; Prakash Chourasia; Murray Patterson (ISBRA, 2023)

Efficient Sequence Embedding for SARS-CoV-2 Variants Classification. - Sarwan Ali; Usama Sardar; Imdad Ullah Khan; Murray Patterson (ISBRA, 2023)

Enhancing t-SNE Performance for Biological Sequencing Data Through Kernel Selection. - Prakash Chourasia; Taslim Murad; Sarwan Ali; Murray Patterson (ISBRA, 2023)

Sequence-Based Nanobody-Antigen Binding Prediction. - Usama Sardar; Sarwan Ali; Muhammad Sohaib Ayub; Muhammad Shoaib; Khurram Bashir; Imdad Ullah Khan; Murray Patterson (ISBRA, 2023)

Simulating Tumor Evolution from scDNA-Seq as an Accumulation of both SNVs and CNAs. - Zahra Tayebi; Akshay Juyal; Alexander Zelikovsky; Murray Patterson (ISBRA, 2023)

Anderson Acceleration for Bioinformatics-Based Machine Learning. - Sarwan Ali; Prakash Chourasia; Murray Patterson (KDH@IJCAI, 2023)

BioSequence2Vec: Efficient Embedding Generation for Biological Sequences. - Sarwan Ali; Usama Sardar; Murray Patterson; Imdad Ullah Khan (PAKDD (2), 2023)

Efficient Classification of SARS-CoV-2 Spike Sequences Using Federated Learning. - Prakash Chourasia; Taslim Murad; Zahra Tayebi; Sarwan Ali; Imdad Ullah Khan; Murray Patterson (CoRR, 2023)

Exploring The Potential Of GANs In Biological Sequence Analysis. - Taslim Murad; Sarwan Ali; Murray Patterson (CoRR, 2023)

Virus2Vec: Viral Sequence Classification Using Machine Learning. - Sarwan Ali; Babatunde Bello; Prakash Chourasia; Ria Thazhe Punathil; Pin-Yu Chen; Imdad Ullah Khan; Murray Patterson (CoRR, 2023)

Efficient Approximate Kernel Based Spike Sequence Classification. - Sarwan Ali; Bikram Sahoo; Muhammad Asad Khan; Alexander Zelikovsky; Imdad Ullah Khan; Murray Patterson (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location. - Sarwan Ali; Babatunde Bello; Zahra Tayebi; Murray Patterson (J. Comput. Biol., 2023)

Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). - Mukul S. Bansal; Ion I. Mandoiu; Marmar Moussa; Murray Patterson; Sanguthevar Rajasekaran; Pavel Skums; Alexander Zelikovsky (J. Comput. Biol., 2023)

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. - Prakash Chourasia; Sarwan Ali; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (J. Comput. Biol., 2023)

ViralVectors: compact and scalable alignment-free virome feature generation. - Sarwan Ali; Prakash Chourasia; Zahra Tayebi; Babatunde Bello; Murray Patterson (Medical Biol. Eng. Comput., 2023)

Spike2CGR: an efficient method for spike sequence classification using chaos game representation. - Taslim Murad; Sarwan Ali; Imdadullah Khan; Murray Patterson (Mach. Learn., 2023)

An Interactive Lambda Calculus Interpreter and Visualization Tool. - Bhashithe Abeysinghe; Murray Patterson; Rajshekhar Sunderraman (COMPUTE, 2024)

Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach. - Sarwan Ali; Haris Mansoor; Prakash Chourasia; Yasir Ali; Murray Patterson (ISBRA (1), 2024)

MIK: Modified Isolation Kernel for Biological Sequence Visualization, Classification, and Clustering. - Sarwan Ali; Prakash Chourasia; Haris Mansoor; Bipin Koirala; Murray Patterson (ML4H@NeurIPS, 2024)

A Universal Non-parametric Approach for Improved Molecular Sequence Analysis. - Sarwan Ali; Tamkanat E. Ali; Prakash Chourasia; Murray Patterson (PKDD (4), 2024)

Weighted Chaos Game Representation for Molecular Sequence Classification. - Taslim Murad; Sarwan Ali; Murray Patterson (PKDD (4), 2024)

Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting. - Sarwan Ali; Prakash Chourasia; Murray Patterson (CoRR, 2024)

Nearest Neighbor CCP-Based Molecular Sequence Analysis. - Sarwan Ali; Prakash Chourasia; Bipin Koirala; Murray Patterson (CoRR, 2024)

DANCE: Deep Learning-Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images. - Taslim Murad; Prakash Chourasia; Sarwan Ali; Murray Patterson (CoRR, 2024)

Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks. - Sarwan Ali; Taslim Murad; Prakash Chourasia; Haris Mansoor; Imdad Ullah Khan; Pin-Yu Chen; Murray Patterson (CoRR, 2024)

EPIC: Enhancing Privacy through Iterative Collaboration. - Prakash Chourasia; Heramb Lonkar; Sarwan Ali; Murray Patterson (CoRR, 2024)

DWFL: Enhancing Federated Learning through Dynamic Weighted Averaging. - Prakash Chourasia; Tamkanat E. Ali; Sarwan Ali; Murray Patterson (CoRR, 2024)

An alignment problem. - Emma Louise McDaniel; Armin R. Mikler; Chetan Tiwari; Murray Patterson (CoRR, 2024)

Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm. - Sarwan Ali; Haris Mansoor; Prakash Chourasia; Imdad Ullah Khan; Murray Patterson (CoRR, 2024)

Converting Time Series Data to Numeric Representations Using Alphabetic Mapping and k-mer strategy. - Sarwan Ali; Tamkanat E. Ali; Imdad Ullah Khan; Murray Patterson (CoRR, 2024)

Molecular sequence classification using efficient kernel based embedding. - Sarwan Ali; Tamkanat E. Ali; Taslim Murad; Haris Mansoor; Murray Patterson (Inf. Sci., 2024)

Special Issue, Part I 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023). - Murray Patterson (J. Comput. Biol., 2024)

Elliptic geometry-based kernel matrix for improved biological sequence classification. - Sarwan Ali; Madiha Shabbir; Haris Mansoor; Prakash Chourasia; Murray Patterson (Knowl. Based Syst., 2024)

TCellR2Vec: efficient feature selection for TCR sequences for cancer classification. - Zahra Tayebi; Sarwan Ali; Murray Patterson (PeerJ Comput. Sci., 2024)

PseAAC2Vec protein encoding for TCR protein sequence classification. - Zahra Tayebi; Sarwan Ali; Taslim Murad; Imdadullah Khan; Murray Patterson (Comput. Biol. Medicine, 2024)

From PDB files to protein features: a comparative analysis of PDB bind and STCRDAB datasets. - Sarwan Ali; Prakash Chourasia; Murray Patterson (Medical Biol. Eng. Comput., 2024)

Hilbert Curve Based Molecular Sequence Analysis. - Sarwan Ali; Tamkanat E. Ali; Imdad Ullah Khan; Murray Patterson (PAKDD (2), 2025)

Hist2Vec: A histogram and kernel-based embedding method for molecular sequence analysis. - Sarwan Ali; Tamkanat E. Ali; Haris Mansoor; Prakash Chourasia; Murray Patterson (Expert Syst. Appl., 2025)

Special Section: 12th International Computational Advances in Bio and Medical Sciences (ICCABS 2023). - Mukul S. Bansal; Wei Chen; Yury Khudyakov; Ion I. Mandoiu; Marmar Moussa; Murray Patterson; Sanguthevar Rajasekaran; Pavel Skums; Sharma V. Thankachan; Alex Zelikovsky (J. Comput. Biol., 2025)

Special Issue, Part 2 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023). - Murray Patterson (J. Comput. Biol., 2025)

Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences. - Taslim Murad; Prakash Chourasia; Sarwan Ali; Imdad Ullah Khan; Murray Patterson (CoRR, 2025)

Sequence Analysis Using the Bezier Curve. - Taslim Murad; Sarwan Ali; Murray Patterson (CoRR, 2025)

Hash-binding: DNA-protein binding prediction using hashing-based embedding. - Sarwan Ali; Tamkanat E. Ali; Murray Patterson (Neural Comput. Appl., 2025)