BibTeX records: Sheida Nabavi

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@article{DBLP:journals/tcbb/HamzeheiBRTON25,
  author       = {Sahand Hamzehei and
                  Jun Bai and
                  Gianna Raimondi and
                  Rebecca Tripp and
                  Linnaea Ostroff and
                  Sheida Nabavi},
  title        = {Advanced Feature Extraction and Outlier Detection for 3D Biological/Biomedical
                  Image Registration},
  journal      = {{IEEE} Trans. Comput. Biol. Bioinform.},
  volume       = {22},
  number       = {4},
  pages        = {1335--1346},
  year         = {2025},
  url          = {https://doi.org/10.1109/tcbbio.2024.3517596},
  doi          = {10.1109/TCBBIO.2024.3517596},
  timestamp    = {Tue, 03 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/tcbb/HamzeheiBRTON25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/JenyHKBRYN25,
  author       = {Afsana Ahsan Jeny and
                  Sahand Hamzehei and
                  Mostafa Karami and
                  Stephen Andrew Baker and
                  Tucker Van Rathe and
                  Clifford Yang and
                  Sheida Nabavi},
  editor       = {Xinghua Mindy Shi and
                  Xiaoning Qian and
                  Minghan Chen and
                  Jacob M. Luber and
                  Gail L. Rosen and
                  Yunan Luo},
  title        = {Longitudinal Tumor Generation in Mammograms via Dual Encoder {GAN}
                  and Learnable Blending},
  booktitle    = {Proceedings of the 16th {ACM} International Conference on Bioinformatics,
                  Computational Biology, and Health Informatics, {BCB} 2025, Element
                  Philadelphia Downtown, Philadelphia, PA, USA, October 12-15, 2025},
  pages        = {21:1--21:10},
  publisher    = {{ACM}},
  year         = {2025},
  url          = {https://doi.org/10.1145/3765612.3767232},
  doi          = {10.1145/3765612.3767232},
  timestamp    = {Wed, 25 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/JenyHKBRYN25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/isbi/Martinez-Martinez25,
  author       = {Josu{\'{e}} Mart{\'{\i}}nez{-}Mart{\'{\i}}nez and
                  Olivia Brown and
                  Jun Bai and
                  Sheida Nabavi},
  title        = {Robust Training of Deep Learning Models for Mammogram Classification},
  booktitle    = {22nd {IEEE} International Symposium on Biomedical Imaging, {ISBI}
                  2025, Houston, TX, USA, April 14-17, 2025},
  pages        = {1--4},
  publisher    = {{IEEE}},
  year         = {2025},
  url          = {https://doi.org/10.1109/ISBI60581.2025.10980787},
  doi          = {10.1109/ISBI60581.2025.10980787},
  timestamp    = {Sat, 15 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/isbi/Martinez-Martinez25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/miccai/KaramiHARON25,
  author       = {Mostafa Karami and
                  Sahand Hamzehei and
                  David Arce and
                  Gianna Raimondi and
                  Linnaea Ostroff and
                  Sheida Nabavi},
  editor       = {James C. Gee and
                  Daniel C. Alexander and
                  Jaesung Hong and
                  Juan Eugenio Iglesias and
                  Carole H. Sudre and
                  Archana Venkataraman and
                  Polina Golland and
                  Jong Hyo Kim and
                  Jinah Park},
  title        = {Bayesian Transformers and Higher-Order Graph Matching for Cell Tracking
                  in Serial Tissue Sections},
  booktitle    = {Medical Image Computing and Computer Assisted Intervention - {MICCAI}
                  2025 - 28th International Conference, Daejeon, South Korea, September
                  23-27, 2025, Proceedings, Part {XII}},
  series       = {Lecture Notes in Computer Science},
  volume       = {15971},
  pages        = {87--97},
  publisher    = {Springer},
  year         = {2025},
  url          = {https://doi.org/10.1007/978-3-032-05162-2\_9},
  doi          = {10.1007/978-3-032-05162-2\_9},
  timestamp    = {Mon, 06 Oct 2025 08:05:55 +0200},
  biburl       = {https://dblp.org/rec/conf/miccai/KaramiHARON25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/miccai/JunayedVWNN25,
  author       = {Masum Shah Junayed and
                  John Derek Van Vessem and
                  Qian Wan and
                  Gahie Nam and
                  Sheida Nabavi},
  editor       = {James C. Gee and
                  Daniel C. Alexander and
                  Jaesung Hong and
                  Juan Eugenio Iglesias and
                  Carole H. Sudre and
                  Archana Venkataraman and
                  Polina Golland and
                  Jong Hyo Kim and
                  Jinah Park},
  title        = {Graph Laplacian Transformer with Progressive Sampling for Prostate
                  Cancer Grading},
  booktitle    = {Medical Image Computing and Computer Assisted Intervention - {MICCAI}
                  2025 - 28th International Conference, Daejeon, South Korea, September
                  23-27, 2025, Proceedings, Part {XII}},
  series       = {Lecture Notes in Computer Science},
  volume       = {15971},
  pages        = {362--372},
  publisher    = {Springer},
  year         = {2025},
  url          = {https://doi.org/10.1007/978-3-032-05162-2\_35},
  doi          = {10.1007/978-3-032-05162-2\_35},
  timestamp    = {Tue, 14 Oct 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/miccai/JunayedVWNN25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2506-17133,
  author       = {Josu{\'{e}} Mart{\'{\i}}nez{-}Mart{\'{\i}}nez and
                  Olivia Brown and
                  Mostafa Karami and
                  Sheida Nabavi},
  title        = {Robust Training with Data Augmentation for Medical Imaging Classification},
  journal      = {CoRR},
  volume       = {abs/2506.17133},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2506.17133},
  doi          = {10.48550/ARXIV.2506.17133},
  eprinttype    = {arXiv},
  eprint       = {2506.17133},
  timestamp    = {Mon, 14 Jul 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2506-17133.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2512-10808,
  author       = {Masum Shah Junayed and
                  John Derek Van Vessem and
                  Qian Wan and
                  Gahie Nam and
                  Sheida Nabavi},
  title        = {Graph Laplacian Transformer with Progressive Sampling for Prostate
                  Cancer Grading},
  journal      = {CoRR},
  volume       = {abs/2512.10808},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2512.10808},
  doi          = {10.48550/ARXIV.2512.10808},
  eprinttype    = {arXiv},
  eprint       = {2512.10808},
  timestamp    = {Fri, 23 Jan 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2512-10808.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/WeinerLN24,
  author       = {Samson Weiner and
                  Bingjun Li and
                  Sheida Nabavi},
  title        = {Improved allele-specific single-cell copy number estimation in low-coverage
                  DNA-sequencing},
  journal      = {Bioinform.},
  volume       = {40},
  number       = {8},
  year         = {2024},
  url          = {https://doi.org/10.1093/bioinformatics/btae506},
  doi          = {10.1093/BIOINFORMATICS/BTAE506},
  timestamp    = {Tue, 28 Oct 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/WeinerLN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/LiN24,
  author       = {Bingjun Li and
                  Sheida Nabavi},
  title        = {A multimodal graph neural network framework for cancer molecular subtype
                  classification},
  journal      = {{BMC} Bioinform.},
  volume       = {25},
  number       = {1},
  pages        = {27},
  year         = {2024},
  url          = {https://doi.org/10.1186/s12859-023-05622-4},
  doi          = {10.1186/S12859-023-05622-4},
  timestamp    = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/LiN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bspc/BehzadiMWBBTYNN24,
  author       = {Mohammad Mahdi Behzadi and
                  Mohammad Madani and
                  Hanzhang Wang and
                  Jun Bai and
                  Ankit Bhardwaj and
                  Anna Tarakanova and
                  Harold Yamase and
                  Ga Hie Nam and
                  Sheida Nabavi},
  title        = {Weakly-supervised deep learning model for prostate cancer diagnosis
                  and Gleason grading of histopathology images},
  journal      = {Biomed. Signal Process. Control.},
  volume       = {95},
  pages        = {106351},
  year         = {2024},
  url          = {https://doi.org/10.1016/j.bspc.2024.106351},
  doi          = {10.1016/J.BSPC.2024.106351},
  timestamp    = {Thu, 04 Jul 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bspc/BehzadiMWBBTYNN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/cmig/BaiJAYN24,
  author       = {Jun Bai and
                  Annie Jin and
                  Madison Adams and
                  Clifford Yang and
                  Sheida Nabavi},
  title        = {Unsupervised feature correlation model to predict breast abnormal
                  variation maps in longitudinal mammograms},
  journal      = {Comput. Medical Imaging Graph.},
  volume       = {113},
  pages        = {102341},
  year         = {2024},
  url          = {https://doi.org/10.1016/j.compmedimag.2024.102341},
  doi          = {10.1016/J.COMPMEDIMAG.2024.102341},
  timestamp    = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/cmig/BaiJAYN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/KaramiLWHN24,
  author       = {Mostafa Karami and
                  Bingjun Li and
                  Samson Weiner and
                  Sahand Hamzehei and
                  Sheida Nabavi},
  title        = {{DCCNV:} Enhanced {CNV} Detection in Single-Cell Sequencing Using
                  Diffusion Process and Contrastive Learning},
  booktitle    = {Proceedings of the 15th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2024, Shenzhen,
                  China, November 22-25, 2024},
  pages        = {48:1--48:6},
  publisher    = {{ACM}},
  year         = {2024},
  url          = {https://doi.org/10.1145/3698587.3701395},
  doi          = {10.1145/3698587.3701395},
  timestamp    = {Sun, 22 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/KaramiLWHN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/HamzeheiRKON24,
  author       = {Sahand Hamzehei and
                  Gianna Raimondi and
                  Mostafa Karami and
                  Linnaea Ostroff and
                  Sheida Nabavi},
  title        = {{CAPTURE:} {A} Clustered Adaptive Patchwork Technique for Unified
                  Registration Enhancement in Biological Imaging},
  booktitle    = {Proceedings of the 15th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2024, Shenzhen,
                  China, November 22-25, 2024},
  pages        = {62:1--62:6},
  publisher    = {{ACM}},
  year         = {2024},
  url          = {https://doi.org/10.1145/3698587.3701369},
  doi          = {10.1145/3698587.3701369},
  timestamp    = {Sun, 22 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/HamzeheiRKON24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/HamzeheiJJYN24,
  author       = {Sahand Hamzehei and
                  Afsana Ahsan Jeny and
                  Annie Jin and
                  Clifford Yang and
                  Sheida Nabavi},
  editor       = {Mario Cannataro and
                  Huiru Jane Zheng and
                  Lin Gao and
                  Jianlin Cheng and
                  Jo{\~{a}}o Lu{\'{\i}}s de Miranda and
                  Ester Zumpano and
                  Xiaohua Hu and
                  Young{-}Rae Cho and
                  Taesung Park},
  title        = {Benchmarking Distance Functions in Siamese Networks for Current and
                  Prior Mammogram Image Analysis},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2024, Lisbon, Portugal, December 3-6, 2024},
  pages        = {1996--2003},
  publisher    = {{IEEE}},
  year         = {2024},
  url          = {https://doi.org/10.1109/BIBM62325.2024.10822291},
  doi          = {10.1109/BIBM62325.2024.10822291},
  timestamp    = {Mon, 03 Feb 2025 17:16:55 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/HamzeheiJJYN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/JunayedN24,
  author       = {Masum Shah Junayed and
                  Sheida Nabavi},
  editor       = {Mario Cannataro and
                  Huiru Jane Zheng and
                  Lin Gao and
                  Jianlin Cheng and
                  Jo{\~{a}}o Lu{\'{\i}}s de Miranda and
                  Ester Zumpano and
                  Xiaohua Hu and
                  Young{-}Rae Cho and
                  Taesung Park},
  title        = {A Scaled Mask Attention-based Hybrid model for Survival Prediction},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2024, Lisbon, Portugal, December 3-6, 2024},
  pages        = {2100--2107},
  publisher    = {{IEEE}},
  year         = {2024},
  url          = {https://doi.org/10.1109/BIBM62325.2024.10822154},
  doi          = {10.1109/BIBM62325.2024.10822154},
  timestamp    = {Mon, 03 Feb 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/JunayedN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/LiKJN24,
  author       = {Bingjun Li and
                  Mostafa Karami and
                  Masum Shah Junayed and
                  Sheida Nabavi},
  editor       = {Mario Cannataro and
                  Huiru Jane Zheng and
                  Lin Gao and
                  Jianlin Cheng and
                  Jo{\~{a}}o Lu{\'{\i}}s de Miranda and
                  Ester Zumpano and
                  Xiaohua Hu and
                  Young{-}Rae Cho and
                  Taesung Park},
  title        = {Multi-modal Spatial Clustering for Spatial Transcriptomics Utilizing
                  High-resolution Histology Images},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2024, Lisbon, Portugal, December 3-6, 2024},
  pages        = {3469--3474},
  publisher    = {{IEEE}},
  year         = {2024},
  url          = {https://doi.org/10.1109/BIBM62325.2024.10822051},
  doi          = {10.1109/BIBM62325.2024.10822051},
  timestamp    = {Mon, 03 Feb 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/LiKJN24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/JunayedJNM24,
  author       = {Masum Shah Junayed and
                  Afsana Ahsan Jeny and
                  Sheida Nabavi and
                  Ion Mandoiu},
  editor       = {Mario Cannataro and
                  Huiru Jane Zheng and
                  Lin Gao and
                  Jianlin Cheng and
                  Jo{\~{a}}o Lu{\'{\i}}s de Miranda and
                  Ester Zumpano and
                  Xiaohua Hu and
                  Young{-}Rae Cho and
                  Taesung Park},
  title        = {A Fused Transformer-based Model for Gene Expression Prediction using
                  Histopathology Images},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2024, Lisbon, Portugal, December 3-6, 2024},
  pages        = {4942--4949},
  publisher    = {{IEEE}},
  year         = {2024},
  url          = {https://doi.org/10.1109/BIBM62325.2024.10821923},
  doi          = {10.1109/BIBM62325.2024.10821923},
  timestamp    = {Tue, 04 Feb 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/JunayedJNM24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2411-02534,
  author       = {Bingjun Li and
                  Mostafa Karami and
                  Masum Shah Junayed and
                  Sheida Nabavi},
  title        = {Multi-modal Spatial Clustering for Spatial Transcriptomics Utilizing
                  High-resolution Histology Images},
  journal      = {CoRR},
  volume       = {abs/2411.02534},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2411.02534},
  doi          = {10.48550/ARXIV.2411.02534},
  eprinttype    = {arXiv},
  eprint       = {2411.02534},
  timestamp    = {Wed, 01 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2411-02534.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/HamzeheiBRTON23,
  author       = {Sahand Hamzehei and
                  Jun Bai and
                  Gianna Raimondi and
                  Rebecca Tripp and
                  Linnaea Ostroff and
                  Sheida Nabavi},
  editor       = {May D. Wang and
                  Byung{-}Jun Yoon},
  title        = {3D Biological/Biomedical Image Registration with enhanced Feature
                  Extraction and Outlier Detection},
  booktitle    = {Proceedings of the 14th {ACM} International Conference on Bioinformatics,
                  Computational Biology, and Health Informatics, {BCB} 2023, Houston,
                  TX, USA, September 3-6, 2023},
  pages        = {1:1--1:10},
  publisher    = {{ACM}},
  year         = {2023},
  url          = {https://doi.org/10.1145/3584371.3612965},
  doi          = {10.1145/3584371.3612965},
  timestamp    = {Fri, 27 Oct 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bcb/HamzeheiBRTON23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/LiN23,
  author       = {Bingjun Li and
                  Sheida Nabavi},
  editor       = {May D. Wang and
                  Byung{-}Jun Yoon},
  title        = {Contrastive Learning in Single-cell Multiomics Clustering},
  booktitle    = {Proceedings of the 14th {ACM} International Conference on Bioinformatics,
                  Computational Biology, and Health Informatics, {BCB} 2023, Houston,
                  TX, USA, September 3-6, 2023},
  pages        = {65:1},
  publisher    = {{ACM}},
  year         = {2023},
  url          = {https://doi.org/10.1145/3584371.3613010},
  doi          = {10.1145/3584371.3613010},
  timestamp    = {Fri, 27 Oct 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bcb/LiN23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/LiN23a,
  author       = {Bingjun Li and
                  Sheida Nabavi},
  editor       = {Xingpeng Jiang and
                  Haiying Wang and
                  Reda Alhajj and
                  Xiaohua Hu and
                  Felix Engel and
                  Mufti Mahmud and
                  Nadia Pisanti and
                  Xuefeng Cui and
                  Hong Song},
  title        = {scGEMOC, {A} Graph Embedded Contrastive Learning Single-cell Multiomics
                  Clustering Model},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2023, Istanbul, Turkiye, December 5-8, 2023},
  pages        = {2075--2080},
  publisher    = {{IEEE}},
  year         = {2023},
  url          = {https://doi.org/10.1109/BIBM58861.2023.10385267},
  doi          = {10.1109/BIBM58861.2023.10385267},
  timestamp    = {Thu, 14 Mar 2024 16:59:09 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/LiN23a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/ieeecai/MartinezMartinezN23,
  author       = {Josu{\'{e}} Mart{\'{\i}}nez{-}Mart{\'{\i}}nez and
                  Sheida Nabavi},
  title        = {Addressing Vulnerability in Medical Deep Learning through Robust Training},
  booktitle    = {{IEEE} Conference on Artificial Intelligence, {CAI} 2023, Santa Clara,
                  CA, USA, June 5-6, 2023},
  pages        = {341--342},
  publisher    = {{IEEE}},
  year         = {2023},
  url          = {https://doi.org/10.1109/CAI54212.2023.00150},
  doi          = {10.1109/CAI54212.2023.00150},
  timestamp    = {Tue, 14 Oct 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/ieeecai/MartinezMartinezN23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/isqed/AgrignanZBINXD23,
  author       = {Ya{-}sine Agrignan and
                  Shanglin Zhou and
                  Jun Bai and
                  Sahidul Islam and
                  Sheida Nabavi and
                  Mimi Xie and
                  Caiwen Ding},
  title        = {A Deep Learning Approach for Ventricular Arrhythmias Classification
                  using Microcontroller},
  booktitle    = {24th International Symposium on Quality Electronic Design, {ISQED}
                  2023, San Francisco, CA, USA, April 5-7, 2023},
  pages        = {1--5},
  publisher    = {{IEEE}},
  year         = {2023},
  url          = {https://doi.org/10.1109/ISQED57927.2023.10129313},
  doi          = {10.1109/ISQED57927.2023.10129313},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/isqed/AgrignanZBINXD23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/mlmi-ws/JunayedN23,
  author       = {Masum Shah Junayed and
                  Sheida Nabavi},
  editor       = {Xiaohuan Cao and
                  Xuanang Xu and
                  Islem Rekik and
                  Zhiming Cui and
                  Xi Ouyang},
  title        = {A Scaled Denoising Attention-Based Transformer for Breast Cancer Detection
                  and Classification},
  booktitle    = {Machine Learning in Medical Imaging - 14th International Workshop,
                  {MLMI} 2023, Held in Conjunction with {MICCAI} 2023, Vancouver, BC,
                  Canada, October 8, 2023, Proceedings, Part {II}},
  series       = {Lecture Notes in Computer Science},
  volume       = {14349},
  pages        = {346--356},
  publisher    = {Springer},
  year         = {2023},
  url          = {https://doi.org/10.1007/978-3-031-45676-3\_35},
  doi          = {10.1007/978-3-031-45676-3\_35},
  timestamp    = {Thu, 15 Jan 2026 20:22:57 +0100},
  biburl       = {https://dblp.org/rec/conf/mlmi-ws/JunayedN23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2302-12838,
  author       = {Bingjun Li and
                  Sheida Nabavi},
  title        = {A Multimodal Graph Neural Network Framework for Cancer Molecular Subtype
                  Classification},
  journal      = {CoRR},
  volume       = {abs/2302.12838},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2302.12838},
  doi          = {10.48550/ARXIV.2302.12838},
  eprinttype    = {arXiv},
  eprint       = {2302.12838},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2302-12838.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2312-16772,
  author       = {Jun Bai and
                  Annie Jin and
                  Madison Adams and
                  Clifford Yang and
                  Sheida Nabavi},
  title        = {Unsupversied feature correlation model to predict breast abnormal
                  variation maps in longitudinal mammograms},
  journal      = {CoRR},
  volume       = {abs/2312.16772},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2312.16772},
  doi          = {10.48550/ARXIV.2312.16772},
  eprinttype    = {arXiv},
  eprint       = {2312.16772},
  timestamp    = {Wed, 10 Jan 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2312-16772.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/BaiJJWYN22,
  author       = {Jun Bai and
                  Annie Jin and
                  Andre Jin and
                  Tianyu Wang and
                  Clifford Yang and
                  Sheida Nabavi},
  title        = {Applying graph convolution neural network in digital breast tomosynthesis
                  for cancer classification},
  booktitle    = {{BCB} '22: 13th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, Northbrook, Illinois,
                  USA, August 7 - 10, 2022},
  pages        = {37:1--37:10},
  publisher    = {{ACM}},
  year         = {2022},
  url          = {https://doi.org/10.1145/3535508.3545549},
  doi          = {10.1145/3535508.3545549},
  timestamp    = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/BaiJJWYN22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/BaiLN22,
  author       = {Jun Bai and
                  Bingjun Li and
                  Sheida Nabavi},
  title        = {Semi-supervised classification of disease prognosis using {CR} images
                  with clinical data structured graph},
  booktitle    = {{BCB} '22: 13th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, Northbrook, Illinois,
                  USA, August 7 - 10, 2022},
  pages        = {44:1--44:9},
  publisher    = {{ACM}},
  year         = {2022},
  url          = {https://doi.org/10.1145/3535508.3545548},
  doi          = {10.1145/3535508.3545548},
  timestamp    = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/BaiLN22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2212-12844,
  author       = {Mohammad Mahdi Behzadi and
                  Mohammad Madani and
                  Hanzhang Wang and
                  Jun Bai and
                  Ankit Bhardwaj and
                  Anna Tarakanova and
                  Harold Yamase and
                  Ga Hie Nam and
                  Sheida Nabavi},
  title        = {Weakly-Supervised Deep Learning Model for Prostate Cancer Diagnosis
                  and Gleason Grading of Histopathology Images},
  journal      = {CoRR},
  volume       = {abs/2212.12844},
  year         = {2022},
  url          = {https://doi.org/10.48550/arXiv.2212.12844},
  doi          = {10.48550/ARXIV.2212.12844},
  eprinttype    = {arXiv},
  eprint       = {2212.12844},
  timestamp    = {Mon, 02 Jan 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2212-12844.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/WangBN21,
  author       = {Tianyu Wang and
                  Jun Bai and
                  Sheida Nabavi},
  title        = {Single-cell classification using graph convolutional networks},
  journal      = {{BMC} Bioinform.},
  volume       = {22},
  number       = {1},
  pages        = {364},
  year         = {2021},
  url          = {https://doi.org/10.1186/s12859-021-04278-2},
  doi          = {10.1186/S12859-021-04278-2},
  timestamp    = {Tue, 16 Aug 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/WangBN21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/mia/BaiPWYN21,
  author       = {Jun Bai and
                  Russell Posner and
                  Tianyu Wang and
                  Clifford Yang and
                  Sheida Nabavi},
  title        = {Applying deep learning in digital breast tomosynthesis for automatic
                  breast cancer detection: {A} review},
  journal      = {Medical Image Anal.},
  volume       = {71},
  pages        = {102049},
  year         = {2021},
  url          = {https://doi.org/10.1016/j.media.2021.102049},
  doi          = {10.1016/J.MEDIA.2021.102049},
  timestamp    = {Sun, 16 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/mia/BaiPWYN21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/ZareSN21,
  author       = {Fatima Zare and
                  Jacob Stark and
                  Sheida Nabavi},
  editor       = {Hongmei Jiang and
                  Xiuzhen Huang and
                  Jiajie Zhang},
  title        = {Copy number variation detection using single cell sequencing data},
  booktitle    = {{BCB} '21: 12th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, Gainesville, Florida,
                  USA, August 1-4, 2021},
  pages        = {26:1--26:6},
  publisher    = {{ACM}},
  year         = {2021},
  url          = {https://doi.org/10.1145/3459930.3469556},
  doi          = {10.1145/3459930.3469556},
  timestamp    = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/ZareSN21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/LiWN21,
  author       = {Bingjun Li and
                  Tianyu Wang and
                  Sheida Nabavi},
  editor       = {Hongmei Jiang and
                  Xiuzhen Huang and
                  Jiajie Zhang},
  title        = {Cancer molecular subtype classification by graph convolutional networks
                  on multi-omics data},
  booktitle    = {{BCB} '21: 12th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, Gainesville, Florida,
                  USA, August 1-4, 2021},
  pages        = {50:1--50:9},
  publisher    = {{ACM}},
  year         = {2021},
  url          = {https://doi.org/10.1145/3459930.3469542},
  doi          = {10.1145/3459930.3469542},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bcb/LiWN21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/WangLN21,
  author       = {Tianyu Wang and
                  Bingjun Li and
                  Sheida Nabavi},
  editor       = {Yufei Huang and
                  Lukasz A. Kurgan and
                  Feng Luo and
                  Xiaohua Hu and
                  Yidong Chen and
                  Edward R. Dougherty and
                  Andrzej Kloczkowski and
                  Yaohang Li},
  title        = {Single-cell {RNA} sequencing data clustering using graph convolutional
                  networks},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2021, Houston, TX, USA, December 9-12, 2021},
  pages        = {2163--2170},
  publisher    = {{IEEE}},
  year         = {2021},
  url          = {https://doi.org/10.1109/BIBM52615.2021.9669529},
  doi          = {10.1109/BIBM52615.2021.9669529},
  timestamp    = {Tue, 20 Aug 2024 07:54:45 +0200},
  biburl       = {https://dblp.org/rec/conf/bibm/WangLN21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/AbdelhafizBAYN20,
  author       = {Dina Abdelhafiz and
                  Jinbo Bi and
                  Reda Ammar and
                  Clifford Yang and
                  Sheida Nabavi},
  title        = {Convolutional neural network for automated mass segmentation in mammography},
  journal      = {{BMC} Bioinform.},
  volume       = {21-S},
  number       = {1},
  pages        = {192},
  year         = {2020},
  url          = {https://doi.org/10.1186/s12859-020-3521-y},
  doi          = {10.1186/S12859-020-3521-Y},
  timestamp    = {Tue, 29 Dec 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/AbdelhafizBAYN20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/tcbb/ZareANN20,
  author       = {Fatima Zare and
                  Sardar Ansari and
                  Kayvan Najarian and
                  Sheida Nabavi},
  title        = {Preprocessing Sequence Coverage Data for More Precise Detection of
                  Copy Number Variations},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {17},
  number       = {3},
  pages        = {868--876},
  year         = {2020},
  url          = {https://doi.org/10.1109/TCBB.2018.2869738},
  doi          = {10.1109/TCBB.2018.2869738},
  timestamp    = {Mon, 03 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/ZareANN20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/ZareNWCN20,
  author       = {Fatima Zare and
                  Javad Noorbakhsh and
                  Tianyu Wang and
                  Jeffrey H. Chuang and
                  Sheida Nabavi},
  title        = {Integrative Deep Learning for PanCancer Molecular Subtype Classification
                  Using Histopathological Images and RNAseq Data},
  booktitle    = {{BCB} '20: 11th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, Virtual Event, USA,
                  September 21-24, 2020},
  pages        = {8:1--8:8},
  publisher    = {{ACM}},
  year         = {2020},
  url          = {https://doi.org/10.1145/3388440.3412414},
  doi          = {10.1145/3388440.3412414},
  timestamp    = {Fri, 13 Nov 2020 11:27:35 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/ZareNWCN20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/WangLNN19,
  author       = {Tianyu Wang and
                  Boyang Li and
                  Craig E. Nelson and
                  Sheida Nabavi},
  title        = {Comparative analysis of differential gene expression analysis tools
                  for single-cell {RNA} sequencing data},
  journal      = {{BMC} Bioinform.},
  volume       = {20},
  number       = {1},
  pages        = {40:1--40:16},
  year         = {2019},
  url          = {https://doi.org/10.1186/s12859-019-2599-6},
  doi          = {10.1186/S12859-019-2599-6},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/WangLNN19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/AbdelhafizYAN19,
  author       = {Dina Abdelhafiz and
                  Clifford Yang and
                  Reda Ammar and
                  Sheida Nabavi},
  title        = {Deep convolutional neural networks for mammography: advances, challenges
                  and applications},
  journal      = {{BMC} Bioinform.},
  volume       = {20-S},
  number       = {11},
  pages        = {281:1--281:20},
  year         = {2019},
  url          = {https://doi.org/10.1186/s12859-019-2823-4},
  doi          = {10.1186/S12859-019-2823-4},
  timestamp    = {Tue, 29 Dec 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/AbdelhafizYAN19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/ZareN19,
  author       = {Fatima Zare and
                  Sheida Nabavi},
  editor       = {Xinghua Mindy Shi and
                  Michael Buck and
                  Jian Ma and
                  Pierangelo Veltri},
  title        = {Copy Number Variation Detection Using Total Variation},
  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        = {423--428},
  publisher    = {{ACM}},
  year         = {2019},
  url          = {https://doi.org/10.1145/3307339.3342181},
  doi          = {10.1145/3307339.3342181},
  timestamp    = {Thu, 13 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bcb/ZareN19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/AbdelhafizNAYB19,
  author       = {Dina Abdelhafiz and
                  Sheida Nabavi and
                  Reda Ammar and
                  Clifford Yang and
                  Jinbo Bi},
  editor       = {Xinghua Mindy Shi and
                  Michael Buck and
                  Jian Ma and
                  Pierangelo Veltri},
  title        = {Residual Deep Learning System for Mass Segmentation and Classification
                  in Mammography},
  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        = {475--484},
  publisher    = {{ACM}},
  year         = {2019},
  url          = {https://doi.org/10.1145/3307339.3342157},
  doi          = {10.1145/3307339.3342157},
  timestamp    = {Sun, 19 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/AbdelhafizNAYB19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/WangN19,
  author       = {Tianyu Wang and
                  Sheida Nabavi},
  editor       = {Illhoi Yoo and
                  Jinbo Bi and
                  Xiaohua Hu},
  title        = {Single-cell RNAseq Imputation Based on Matrix Completion with Side
                  Information},
  booktitle    = {2019 {IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2019, San Diego, CA, USA, November 18-21, 2019},
  pages        = {2763--2770},
  publisher    = {{IEEE}},
  year         = {2019},
  url          = {https://doi.org/10.1109/BIBM47256.2019.8983268},
  doi          = {10.1109/BIBM47256.2019.8983268},
  timestamp    = {Fri, 09 Apr 2021 17:11:15 +0200},
  biburl       = {https://dblp.org/rec/conf/bibm/WangN19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/ZareHN18,
  author       = {Fatima Zare and
                  Abdelrahman Hosny and
                  Sheida Nabavi},
  title        = {Noise cancellation using total variation for copy number variation
                  detection},
  journal      = {{BMC} Bioinform.},
  volume       = {19-S},
  number       = {11},
  pages        = {361:1--361:12},
  year         = {2018},
  url          = {https://doi.org/10.1186/s12859-018-2332-x},
  doi          = {10.1186/S12859-018-2332-X},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/ZareHN18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/WangN18,
  author       = {Tianyu Wang and
                  Sheida Nabavi},
  editor       = {Amarda Shehu and
                  Cathy H. Wu and
                  Christina Boucher and
                  Jing Li and
                  Hongfang Liu and
                  Mihai Pop},
  title        = {Single-cell Clustering Based on Word Embedding and Nonparametric Methods},
  booktitle    = {Proceedings of the 2018 {ACM} International Conference on Bioinformatics,
                  Computational Biology, and Health Informatics, {BCB} 2018, Washington,
                  DC, USA, August 29 - September 01, 2018},
  pages        = {130--138},
  publisher    = {{ACM}},
  year         = {2018},
  url          = {https://doi.org/10.1145/3233547.3233590},
  doi          = {10.1145/3233547.3233590},
  timestamp    = {Mon, 10 Jun 2024 20:41:10 +0200},
  biburl       = {https://dblp.org/rec/conf/bcb/WangN18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/TursynbekGNZ18,
  author       = {Nurislam Tursynbek and
                  Ghazal Ghahramany and
                  Sheida Nabavi and
                  Amin Zollanvari},
  editor       = {Huiru Jane Zheng and
                  Zoraida Callejas and
                  David Griol and
                  Haiying Wang and
                  Xiaohua Hu and
                  Harald H. H. W. Schmidt and
                  Jan Baumbach and
                  Julie Dickerson and
                  Le Zhang},
  title        = {Predictive Meta-analysis of Multiple Microarray Datasets: An Application
                  to Classification of Malignant Gliomas},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2018, Madrid, Spain, December 3-6, 2018},
  pages        = {2423--2428},
  publisher    = {{IEEE} Computer Society},
  year         = {2018},
  url          = {https://doi.ieeecomputersociety.org/10.1109/BIBM.2018.8621503},
  doi          = {10.1109/BIBM.2018.8621503},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/TursynbekGNZ18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/ZareANN18,
  author       = {Fatima Zare and
                  Sardar Ansari and
                  Kayvan Najarian and
                  Sheida Nabavi},
  editor       = {Huiru Jane Zheng and
                  Zoraida Callejas and
                  David Griol and
                  Haiying Wang and
                  Xiaohua Hu and
                  Harald H. H. W. Schmidt and
                  Jan Baumbach and
                  Julie Dickerson and
                  Le Zhang},
  title        = {Copy number variation detection using partial alignment information},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2018, Madrid, Spain, December 3-6, 2018},
  pages        = {2435--2441},
  publisher    = {{IEEE} Computer Society},
  year         = {2018},
  url          = {https://doi.ieeecomputersociety.org/10.1109/BIBM.2018.8621529},
  doi          = {10.1109/BIBM.2018.8621529},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/ZareANN18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/iccabs/AbdelhafizNAYB18,
  author       = {Dina Abdelhafiz and
                  Sheida Nabavi and
                  Reda Ammar and
                  Clifford Yang and
                  Jinbo Bi},
  title        = {Convolutional Neural Network for Automated Mass Segmentation in Mammography},
  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.2018.8542071},
  doi          = {10.1109/ICCABS.2018.8542071},
  timestamp    = {Thu, 23 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/iccabs/AbdelhafizNAYB18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/ZareDMHN17,
  author       = {Fatima Zare and
                  Michelle Dow and
                  Nicholas Monteleone and
                  Abdelrahman Hosny and
                  Sheida Nabavi},
  title        = {An evaluation of copy number variation detection tools for cancer
                  using whole exome sequencing data},
  journal      = {{BMC} Bioinform.},
  volume       = {18},
  number       = {1},
  pages        = {286:1--286:13},
  year         = {2017},
  url          = {https://doi.org/10.1186/s12859-017-1705-x},
  doi          = {10.1186/S12859-017-1705-X},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/ZareDMHN17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/HosnyZN17,
  author       = {Abdelrahman Hosny and
                  Fatima Zare and
                  Sheida Nabavi},
  editor       = {Nurit Haspel and
                  Lenore J. Cowen and
                  Amarda Shehu and
                  Tamer Kahveci and
                  Giuseppe Pozzi},
  title        = {Varsimlab: {A} Docker-based Pipeline to Automatically Synthesize Short
                  Reads with Genomic Aberrations},
  booktitle    = {Proceedings of the 8th {ACM} International Conference on Bioinformatics,
                  Computational Biology, and Health Informatics, {BCB} 2017, Boston,
                  MA, USA, August 20-23, 2017},
  pages        = {581},
  publisher    = {{ACM}},
  year         = {2017},
  url          = {https://doi.org/10.1145/3107411.3108188},
  doi          = {10.1145/3107411.3108188},
  timestamp    = {Tue, 06 Nov 2018 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/HosnyZN17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bcb/ZareANN17,
  author       = {Fatima Zare and
                  Sardar Ansari and
                  Kayvan Najarian and
                  Sheida Nabavi},
  editor       = {Nurit Haspel and
                  Lenore J. Cowen and
                  Amarda Shehu and
                  Tamer Kahveci and
                  Giuseppe Pozzi},
  title        = {Bias and Noise Cancellation for Robust Copy Number Variation Detection},
  booktitle    = {Proceedings of the 8th {ACM} International Conference on Bioinformatics,
                  Computational Biology, and Health Informatics, {BCB} 2017, Boston,
                  MA, USA, August 20-23, 2017},
  pages        = {591},
  publisher    = {{ACM}},
  year         = {2017},
  url          = {https://doi.org/10.1145/3107411.3108199},
  doi          = {10.1145/3107411.3108199},
  timestamp    = {Tue, 06 Nov 2018 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/ZareANN17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/WangN17,
  author       = {Tianyu Wang and
                  Sheida Nabavi},
  editor       = {Xiaohua Hu and
                  Chi{-}Ren Shyu and
                  Yana Bromberg and
                  Jean Gao and
                  Yang Gong and
                  Dmitry Korkin and
                  Illhoi Yoo and
                  Huiru Jane Zheng},
  title        = {Differential gene expression analysis in single-cell {RNA} sequencing
                  data},
  booktitle    = {2017 {IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2017, Kansas City, MO, USA, November 13-16, 2017},
  pages        = {202--207},
  publisher    = {{IEEE} Computer Society},
  year         = {2017},
  url          = {https://doi.org/10.1109/BIBM.2017.8217650},
  doi          = {10.1109/BIBM.2017.8217650},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/WangN17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/bibm/ZareANN17,
  author       = {Fatima Zare and
                  Sardar Ansari and
                  Kayvan Najarian and
                  Sheida Nabavi},
  editor       = {Xiaohua Hu and
                  Chi{-}Ren Shyu and
                  Yana Bromberg and
                  Jean Gao and
                  Yang Gong and
                  Dmitry Korkin and
                  Illhoi Yoo and
                  Huiru Jane Zheng},
  title        = {Noise cancellation for robust copy number variation detection using
                  next generation sequencing data},
  booktitle    = {2017 {IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2017, Kansas City, MO, USA, November 13-16, 2017},
  pages        = {230--236},
  publisher    = {{IEEE} Computer Society},
  year         = {2017},
  url          = {https://doi.org/10.1109/BIBM.2017.8217654},
  doi          = {10.1109/BIBM.2017.8217654},
  timestamp    = {Fri, 24 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bibm/ZareANN17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/iccabs/AbdelhafizNAY17,
  author       = {Dina Abdelhafiz and
                  Sheida Nabavi and
                  Reda Ammar and
                  Clifford Yang},
  title        = {Survey on deep convolutional neural networks in mammography},
  booktitle    = {7th {IEEE} International Conference on Computational Advances in Bio
                  and Medical Sciences, {ICCABS} 2017, Orlando, FL, USA, October 19-21,
                  2017},
  pages        = {1},
  publisher    = {{IEEE} Computer Society},
  year         = {2017},
  url          = {https://doi.org/10.1109/ICCABS.2017.8114310},
  doi          = {10.1109/ICCABS.2017.8114310},
  timestamp    = {Wed, 16 Oct 2019 14:14:55 +0200},
  biburl       = {https://dblp.org/rec/conf/iccabs/AbdelhafizNAY17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/NabaviSMMB16,
  author       = {Sheida Nabavi and
                  Daniel Schmolze and
                  Mayinuer Maitituoheti and
                  Sadhika Malladi and
                  Andrew H. Beck},
  title        = {EMDomics: a robust and powerful method for the identification of genes
                  differentially expressed between heterogeneous classes},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {4},
  pages        = {533--541},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btv634},
  doi          = {10.1093/BIOINFORMATICS/BTV634},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/NabaviSMMB16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/globalsip/NabaviB15,
  author       = {Sheida Nabavi and
                  Andrew H. Beck},
  title        = {Earth mover's distance for differential analysis of heterogeneous
                  genomics data},
  booktitle    = {2015 {IEEE} Global Conference on Signal and Information Processing,
                  GlobalSIP 2015, Orlando, FL, USA, December 14-16, 2015},
  pages        = {963--966},
  publisher    = {{IEEE}},
  year         = {2015},
  url          = {https://doi.org/10.1109/GlobalSIP.2015.7418340},
  doi          = {10.1109/GLOBALSIP.2015.7418340},
  timestamp    = {Wed, 16 Oct 2019 14:14:51 +0200},
  biburl       = {https://dblp.org/rec/conf/globalsip/NabaviB15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jsac/NabaviJK10,
  author       = {Sheida Nabavi and
                  Seungjune Jeon and
                  B. V. K. Vijaya Kumar},
  title        = {An Analytical Approach for Performance Evaluation of Bit-Patterned
                  Media Channels},
  journal      = {{IEEE} J. Sel. Areas Commun.},
  volume       = {28},
  number       = {2},
  pages        = {135--142},
  year         = {2010},
  url          = {https://doi.org/10.1109/JSAC.2010.100202},
  doi          = {10.1109/JSAC.2010.100202},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jsac/NabaviJK10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/icc/NabaviKB08,
  author       = {Sheida Nabavi and
                  B. V. K. Vijaya Kumar and
                  James A. Bain},
  title        = {Mitigating the Effects of Track Mis-Registration in Bit-Patterned
                  Media},
  booktitle    = {Proceedings of {IEEE} International Conference on Communications,
                  {ICC} 2008, Beijing, China, 19-23 May 2008},
  pages        = {2061--2065},
  publisher    = {{IEEE}},
  year         = {2008},
  url          = {https://doi.org/10.1109/ICC.2008.395},
  doi          = {10.1109/ICC.2008.395},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icc/NabaviKB08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/icc/NabaviK07,
  author       = {Sheida Nabavi and
                  B. V. K. Vijaya Kumar},
  title        = {Two-Dimensional Generalized Partial Response Equalizer for Bit-Patterned
                  Media},
  booktitle    = {Proceedings of {IEEE} International Conference on Communications,
                  {ICC} 2007, Glasgow, Scotland, UK, 24-28 June 2007},
  pages        = {6249--6254},
  publisher    = {{IEEE}},
  year         = {2007},
  url          = {https://doi.org/10.1109/ICC.2007.1035},
  doi          = {10.1109/ICC.2007.1035},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icc/NabaviK07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

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