Publications

2022

  1. Deep learning-enabled assessment of cardiac allograft rejection from endomyocardial biopsies
    Jana Lipkova, Tiffany Y Chen, Ming Y Lu, Richard J Chen, Maha Shady, Mane Williams, Jingwen Wang, Zahra Noor, Richard N Mitchell, Mehmet Turan, and others
    Nature medicine
    [ bibtex | software | demo | html | abstract ]
  2. Modelling glioma progression, mass effect and intracranial pressure in patient anatomy
    Jana Lipková, Bjoern Menze, Benedikt Wiestler, Petros Koumoutsakos, and John S Lowengrub
    Journal of the Royal Society Interface
    [ bibtex | software | html | abstract ]
  3. Federated learning for computational pathology on gigapixel whole slide images
    Ming Y Lu, Richard J Chen, Dehan Kong, Jana Lipkova, Rajendra Singh, Drew FK Williamson, Tiffany Y Chen, and Faisal Mahmood
    Medical image analysis
    [ bibtex | software | html | arXiv | abstract ]

2021

  1. AI-based pathology predicts origins for cancers of unknown primary
    Ming Y Lu, Tiffany Y Chen, Drew FK Williamson, Melissa Zhao, Maha Shady, Jana Lipkova, and Faisal Mahmood
    Nature
    [ bibtex | software | demo | html | abstract ]
  2. Algorithm fairness in ai for medicine and healthcare
    Richard J Chen, Tiffany Y Chen, Jana Lipkova, Judy J Wang, Drew FK Williamson, Ming Y Lu, Sharifa Sahai, and Faisal Mahmood
    arXiv preprint arXiv:2110.00603
    [ bibtex | html | abstract ]
  3. Pan-cancer integrative histology-genomic analysis via interpretable multimodal deep learning
    Richard J Chen, Ming Y Lu, Drew FK Williamson, Tiffany Y Chen, Jana Lipkova, Muhammad Shaban, Maha Shady, Mane Williams, Bumjin Joo, Zahra Noor, and others
    arXiv preprint arXiv:2108.02278
    [ bibtex | software | demo | html | abstract ]

2020

  1. CXCR4-targeted PET imaging of central nervous system B-cell lymphoma
    Peter Herhaus, Jana Lipkova, Felicitas Lammer, Igor Yakushev, Tibor Vag, Julia Slotta-Huspenina, Stefan Habringer, Constantin Lapa, Tobias Pukrop, Dirk Hellwig, and others
    Journal of Nuclear Medicine
    [ bibtex | html | abstract ]
  2. Predicting glioblastoma recurrence from preoperative MR scans using fractional-anisotropy maps with free-water suppression
    Marie-Christin Metz, Miguel Molina-Romero, Jana Lipkova, Jens Gempt, Friederike Liesche-Starnecker, Paul Eichinger, Lioba Grundl, Bjoern Menze, Stephanie E Combs, Claus Zimmer, and others
    Cancers
    [ bibtex | html | abstract ]
  3. BraTS Toolkit: translating BraTS brain tumor segmentation algorithms into clinical and scientific practice
    Florian Kofler, Christoph Berger, Diana Waldmannstetter, Jana Lipkova, Ivan Ezhov, Giles Tetteh, Jan Kirschke, Claus Zimmer, Benedikt Wiestler, and Bjoern H Menze
    Frontiers in neuroscience
    [ bibtex | html | abstract ]
  4. Red-GAN: Attacking class imbalance via conditioned generation. Yet another medical imaging perspective.
    Ahmad B Qasim, Ivan Ezhov, Suprosanna Shit, Oliver Schoppe, Johannes C Paetzold, Anjany Sekuboyina, Florian Kofler, Jana Lipkova, Hongwei Li, and Bjoern Menze
    Medical Imaging with Deep Learning
    [ bibtex | software | html | abstract ]

2019

  1. Personalized radiotherapy design for glioblastoma: Integrating mathematical tumor models, multimodal scans, and bayesian inference
    Jana Lipková, Panagiotis Angelikopoulos, Stephen Wu, Esther Alberts, Benedikt Wiestler, Christian Diehl, Christine Preibisch, Thomas Pyka, Stephanie E Combs, Panagiotis Hadjidoukas, and others
    IEEE transactions on medical imaging
    [ bibtex | software | html | abstract ]
  2. Neural parameters estimation for brain tumor growth modeling
    Ivan Ezhov, Jana Lipkova, Suprosanna Shit, Florian Kofler, Nore Collomb, Benjamin Lemasson, Emmanuel Barbier, and Bjoern Menze
    International Conference on Medical Image Computing and Computer-Assisted Intervention
    [ bibtex | html | arXiv | abstract ]
  3. The liver tumor segmentation benchmark (lits)
    Patrick Bilic, Patrick Ferdinand Christ, Eugene Vorontsov, Grzegorz Chlebus, Hao Chen, Qi Dou, Chi-Wing Fu, Xiao Han, Pheng-Ann Heng, Jürgen Hesser, and others
    arXiv preprint arXiv:1901.04056
    [ bibtex | html | abstract ]

2018

  1. Identifying the best machine learning algorithms for brain tumor segmentation
    Spyridon Bakas, Mauricio Reyes, András Jakab, Stefan Bauer, Markus Rempfler, Alessandro Crimi, RT Shinohara, Christoph Berger, SM Ha, Martin Rozycki, and others
    Progression Assessment, and Overall Survival Prediction in the BRATS Challenge
    [ bibtex | html | abstract ]
  2. S-Leaping: An Adaptive, Accelerated Stochastic Simulation Algorithm, Bridging \backslashtau-Leaping and R-Leaping
    Jana Lipkova, Georgios Arampatzis, Philippe Chatelain, Bjoern Menze, and Petros Koumoutsakos
    Bulletin of Mathematical Biology
    [ bibtex | software | html | arXiv | abstract ]
  3. Automated whole-body bone lesion detection for multiple myeloma on 68Ga-pentixafor PET/CT imaging using deep learning methods
    Lina Xu, Giles Tetteh, Jana Lipkova, Yu Zhao, Hongwei Li, Patrick Christ, Marie Piraud, Andreas Buck, Kuangyu Shi, and Bjoern H Menze
    Contrast media & molecular imaging
    [ bibtex | html | abstract ]

2017

  1. Automatic liver and tumor segmentation of CT and MRI volumes using cascaded fully convolutional neural networks
    Patrick Ferdinand Christ, Florian Ettlinger, Felix Grün, Mohamed Ezzeldin A Elshaera, Jana Lipkova, Sebastian Schlecht, Freba Ahmaddy, Sunil Tatavarty, Marc Bickel, Patrick Bilic, and others
    arXiv preprint arXiv:1702.05970
    [ bibtex | html | abstract ]
  2. Automated unsupervised segmentation of liver lesions in ct scans via cahn-hilliard phase separation
    Jana Lipková, Markus Rempfler, Patrick Christ, John Lowengrub, and Bjoern H Menze
    arXiv preprint arXiv:1704.02348
    [ bibtex | html | abstract ]

2011

  1. Analysis of Brownian dynamics simulations of reversible bimolecular reactions
    Jana Lipková, Konstantinos C Zygalakis, S Jonathan Chapman, and Radek Erban
    SIAM Journal on Applied Mathematics
    [ bibtex | html | arXiv | abstract ]