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2020 – today
- 2025
[j30]Burcu Bakir-Gungor, Mustafa Temiz
, Beyza Canakcimaksutoglu, Malik Yousef:
Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach. Comput. Biol. Medicine 187: 109813 (2025)- [j29]Cihan Kuzudisli, Burcu Bakir-Gungor, Bahjat Qaqish, Malik Yousef:
RCE-IFE: recursive cluster elimination with intra-cluster feature elimination. PeerJ Comput. Sci. 11: e2528 (2025) - [c25]Maham Khokhar, Burcu Bakir-Gungor, Malik Yousef:
Enhancing the Efficiency of the Grouping-Scoring-Modeling Framework with Statistical Pre-Scoring Component for Transcriptomic Data Analysis. BIOSTEC (1) 2025: 479-488 - [c24]Nur Sebnem Ersoz, Burcu Bakir-Gungor, Malik Yousef:
Identifying Inflammatory Bowel Disease-Associated Gene Ontology Groups Using Biological Knowledge-Based Machine Learning. BIOSTEC (1) 2025: 586-593 - [c23]Emma Qumsiyeh, Burcu Bakir-Gungor, Malik Yousef:
PathDisGene: Discovering Informative Gene Groups for Disease Diagnosis Using Pathway-Disease Associations and a Grouping, Scoring, Modeling-Based Machine Learning Approach. BIOSTEC (1) 2025: 676-683 - [e3]Jungsil Kim, Raquel C. Conceição, Malik Yousef, Arnav Bhavsar, Sylvia Pelayo, Ana Fred, Hugo Gamboa:
Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2025 - Volume 1, Porto, Portugal, February 20-22, 2025. SCITEPRESS 2025, ISBN 978-989-758-731-3 [contents] - [e2]Jungsil Kim, Raquel C. Conceição, Malik Yousef, Arnav Bhavsar, Sylvia Pelayo, Ana Fred, Hugo Gamboa:
Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2025 - Volume 2: HEALTHINF, Porto, Portugal, February 20-22, 2025. SCITEPRESS 2025, ISBN 978-989-758-731-3 [contents] - 2024
- [j28]Burcu Bakir-Gungor, Mustafa Temiz, Yasin Inal, Emre Cicekyurt, Malik Yousef:
CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques. Comput. Biol. Medicine 182: 109098 (2024) - [j27]Ümmü Gülsüm Söylemez, Malik Yousef, Zülal Kesmen, Burcu Bakir-Gungor:
Novel Antimicrobial Peptide Design Using Motif Match Score Representation. IEEE ACM Trans. Comput. Biol. Bioinform. 21(6): 1656-1666 (2024) - [c22]Emma Qumsiyeh, Miar Yousef, Malik Yousef:
ReScore Disease Groups Based on Multiple Machine Learnings Utilizing the Grouping-Scoring-Modeling Approach. BIOSTEC (1) 2024: 446-453 - [c21]Daniel Voskergian, Burcu Bakir-Gungor, Malik Yousef:
SEMANT - Feature Group Selection Utilizing FastText-Based Semantic Word Grouping, Scoring, and Modeling Approach for Text Classification. DEXA (2) 2024: 69-75 - [c20]Daniel Voskergian, Burcu Bakir-Gungor, Malik Yousef:
TextNetTopics-SFTS-SBTS: TextNetTopics Scoring Approaches Based Sequential Forward and Backward. IWBBIO (2) 2024: 343-355 - [c19]Nur Sebnem Ersoz, Cihan Kuzudisli, Malik Yousef, Burcu Bakir-Gungor:
Metagenomic Data Analysis with Machine Learning to Discover Colorectal Cancer-Associated Enzymes. SIU 2024: 1-4 - [c18]Emma Qumsiyeh, Burcu Bakir-Gungor, Malik Yousef:
Classification of Breast Cancer Molecular Subtypes with Grouping-Scoring-Modeling Approach that Incorporates Disease-Disease Association Information. SIU 2024: 1-4 - [c17]Mustafa Temiz, Cihan Kuzudisli, Malik Yousef, Burcu Bakir-Gungor:
Prediction of Type 2 Diabetes using Metagenomic Data and Identification of Taxonomic Biomarkers. SIU 2024: 1-4 - [e1]Maria Pedro Guarino, Kazuhiro Hotta, Malik Yousef, Hui Liu, Giovanni Saggio, Ana Fred, Hugo Gamboa:
Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2024, Volume 1, Rome, Italy, February 21-23, 2024. SCITEPRESS 2024, ISBN 978-989-758-688-0 [contents] - 2023
- [j26]Malik Yousef, Fatma Ozdemir, Amhar Jaber, Jens Allmer, Burcu Bakir-Gungor:
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. BMC Bioinform. 24(1): 60 (2023) - [c16]Emma Qumsiyeh, Malik Yousef, Zaidoun Salah, Rashid Jayousi:
Detecting Semantic Similarity of Diseases based Machine Learning. BIBM 2023: 3118-3124 - [c15]Miray Unlu Yazici, Malik Yousef, J. S. Marron, Burcu Bakir-Gungor:
miRcorrNetPro: Unraveling Algorithmic Insights through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis. BIBM 2023: 3234-3240 - [c14]Ümmü Gülsüm Söylemez, Malik Yousef, Burcu Bakir-Gungor:
Prediction of Antimicrobial Peptides Using Deep Neural Networks. BIOINFORMATICS 2023: 188-194 - [c13]Emma Qumsiyeh, Miray Unlu Yazici, Malik Yousef:
GediNETPro: Discovering Patterns of Disease Groups. BIOINFORMATICS 2023: 195-203 - 2021
- [j25]Malik Yousef, Jens Allmer:
Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features. Algorithms 14(5): 132 (2021) - [j24]Loai AbedAllah, Murad Badarna, Waleed Khalifa, Malik Yousef:
MultiKOC: Multi-One-Class Classifier Based K-Means Clustering. Algorithms 14(5): 134 (2021) - [j23]Rohit Satyam, Malik Yousef, Sahar Qazi, Adil Manzoor Bhat, Khalid Raza:
COVIDium: a COVID-19 resource compendium. Database J. Biol. Databases Curation 2021 (2021) - [j22]Malik Yousef, Abhishek Kumar, Burcu Bakir-Gungor:
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data. Entropy 23(1): 2 (2021) - [j21]Malik Yousef, Louise C. Showe, Izhar Ben Shlomo:
Clinical presentation of COVID-19 - a model derived by a machine learning algorithm. J. Integr. Bioinform. 18(1): 3-8 (2021) - [j20]Anusha Uttarilli, Sridhar Amalakanti, Phaneeswara-Rao Kommoju, Srihari Sharma, Pankaj Goyal, Gowrang Kasaba Manjunath, Vineet Upadhayay, Alisha Parveen, Ravi Tandon, Kumar Suranjit Prasad, Tikam Chand Dakal, Izhar Ben Shlomo, Malik Yousef, Muniasamy Neerathilingam, Abhishek Kumar:
Super-rapid race for saving lives by developing COVID-19 vaccines. J. Integr. Bioinform. 18(1): 27-43 (2021) - [j19]Malik Yousef, Ege Ülgen, Osman Ugur Sezerman:
CogNet: classification of gene expression data based on ranked active-subnetwork-oriented KEGG pathway enrichment analysis. PeerJ Comput. Sci. 7: e336 (2021) - [c12]Malik Yousef, Ahmet Sayici, Burcu Bakir-Gungor:
Integrating Gene Ontology Based Grouping and Ranking into the Machine Learning Algorithm for Gene Expression Data Analysis. DEXA Workshops 2021: 205-214 - [c11]Malik Yousef, Amhar Jabeer, Burcu Bakir-Gungor:
SVM-RCE-R-OPT: Optimization of Scoring Function for SVM-RCE-R. DEXA Workshops 2021: 215-224 - [i2]Malik Yousef, Jamal Al Qundus, Silvio Peikert, Adrian Paschke:
TopicsRanksDC: Distance-based Topic Ranking applied on Two-Class Data. CoRR abs/2105.07826 (2021) - 2020
- [j18]Loai AbedAllah, Malik Yousef:
GrpClassifierEC: a novel classification approach based on the ensemble clustering space. Algorithms Mol. Biol. 15(1): 3 (2020) - [j17]Jamal Al Qundus, Adrian Paschke, Shivam Gupta, Ahmad M. Alzouby, Malik Yousef:
Exploring the impact of short-text complexity and structure on its quality in social media. J. Enterp. Inf. Manag. 33(6): 1443-1466 (2020) - [c10]Luise Odenthal, Jens Allmer, Malik Yousef:
A Machine Learning-based Approach for the Categorization of MicroRNAs to Their Species of Origin. BIOINFORMATICS 2020: 150-157 - [c9]Malik Yousef, Jamal Al Qundus, Silvio Peikert, Adrian Paschke:
TopicsRanksDC: Distance-Based Topic Ranking Applied on Two-Class Data. DEXA Workshops 2020: 11-21 - [i1]Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Gokhan Goy, Rehman Qureshi, Louise C. Showe:
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME. F1000Research 9: 1255 (2020)
2010 – 2019
- 2019
- [j16]Malik Yousef, Loai AbdAllah, Jens Allmer:
maTE: discovering expressed interactions between microRNAs and their targets. Bioinform. 35(20): 4020-4028 (2019) - [c8]Malik Yousef, Walid Khaleifa, Tugba Onal Suzek:
In Silico Validation of ncRNA-ncRNA Interaction Sites with ncRNAs Represented by k-mers Features. BIOINFORMATICS 2019: 168-173 - [c7]Malik Yousef, Jens Allmer:
Classification of Pre-cursor microRNAs from Different Species Using a New Set of Features. DEXA Workshops 2019: 15-20 - [c6]Loai AbedAllah, Murad Badarna, Waleed Khalifa, Malik Yousef:
K - Means Based One-Class SVM Classifier. DEXA Workshops 2019: 45-53 - 2018
- [c5]Malik Yousef, Dalit Levy, Jens Allmer:
Species Categorization via MicroRNAs - Based on 3'UTR Target Sites using Sequence Features. BIOINFORMATICS 2018: 112-118 - [c4]Loai AbedAllah, Malik Yousef:
Ensemble Clustering Based Dimensional Reduction. DEXA Workshops 2018: 115-125 - 2017
- [j15]Malik Yousef, Waleed Khalifa, Ilhan Erkin Acar, Jens Allmer:
MicroRNA categorization using sequence motifs and k-mers. BMC Bioinform. 18(1): 170:1-170:9 (2017) - [j14]Dawit Nigatu, Patrick Sobetzko, Malik Yousef, Werner Henkel:
Sequence-based information-theoretic features for gene essentiality prediction. BMC Bioinform. 18(1): 473 (2017) - [j13]Malik Yousef, Dawit Nigatu, Dalit Levy, Jens Allmer, Werner Henkel:
Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers. EURASIP J. Adv. Signal Process. 2017: 70 (2017) - [c3]Malik Yousef, Waleed Khalifa, Ilhan Erkin Acar, Jens Allmer:
Distinguishing between MicroRNA Targets from Diverse Species using Sequence Motifs and K-mers. BIOINFORMATICS 2017: 133-139 - 2016
- [j12]Malik Yousef, Muserref Duygu Saçar, Waleed Khalifa, Jens Allmer:
Feature Selection Has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants. Adv. Bioinformatics 2016: 5670851:1-5670851:6 (2016) - [j11]Jens Allmer, Malik Yousef:
Editorial: Computational miRNomics. J. Integr. Bioinform. 13(5) (2016) - [j10]Malik Yousef, Waleed Khalifa, Loai AbdAllah:
Ensemble Clustering Classification compete SVM and One-Class classifiers applied on plant microRNAs Data. J. Integr. Bioinform. 13(5) (2016) - [c2]Malik Yousef, Jens Allmer, Waleed Khalifa:
Feature Selection for MicroRNA Target Prediction - Comparison of One-Class Feature Selection Methodologies. BIOINFORMATICS 2016: 216-225
2000 – 2009
- 2009
- [j9]Malik Yousef, Mohamed Ketany, Larry M. Manevitz, Louise C. Showe, Michael K. Showe:
Classification and biomarker identification using gene network modules and support vector machines. BMC Bioinform. 10: 337 (2009) - 2008
- [j8]Malik Yousef, Segun Jung, Louise C. Showe, Michael K. Showe:
Learning from positive examples when the negative class is undetermined- microRNA gene identification. Algorithms Mol. Biol. 3 (2008) - 2007
- [j7]Jiajing Wang, Huai Li, Yitan Zhu, Malik Yousef, Michael Nebozhyn, Michael M. Showe, Louise C. Showe, Jianhua Xuan, Robert Clarke, Yue Joseph Wang:
VISDA: an open-source caBIGTM analytical tool for data clustering and beyond. Bioinform. 23(15): 2024-2027 (2007) - [j6]Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe, Michael K. Showe:
Naïve Bayes for microRNA target predictions - machine learning for microRNA targets. Bioinform. 23(22): 2987-2992 (2007) - [j5]Malik Yousef, Segun Jung, Louise C. Showe, Michael K. Showe:
Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data. BMC Bioinform. 8 (2007) - [j4]Larry M. Manevitz, Malik Yousef:
One-class document classification via Neural Networks. Neurocomputing 70(7-9): 1466-1481 (2007) - 2006
- [j3]Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, Michael K. Showe:
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier. Bioinform. 22(11): 1325-1334 (2006) - 2004
- [j2]Larry M. Manevitz, Malik Yousef:
A web navigation system based on a neural network user-model trained with only positive web documents. Web Intell. Agent Syst. 2(2): 137-144 (2004) - 2001
- [j1]Larry M. Manevitz, Malik Yousef:
One-Class SVMs for Document Classification. J. Mach. Learn. Res. 2: 139-154 (2001) - 2000
- [c1]Larry M. Manevitz, Malik Yousef:
Document classification on neural networks using only positive examples. SIGIR 2000: 304-306
Coauthor Index
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