Hertz Lab

• Noam Shental, Shlomia Levy, Vered Wuvshet, Shosh Skorniakov, Bar Shalem, Aner Ottolenghi, Yariv Greenshpan, Rachel Steinberg, Avishay Edri, Roni Gillis, Michal Goldhirsh, Khen Moscovici, Sinai Sachren, Lilach M. Friedman, Lior Nesher, Yonat Shemer-Avni, Angel Porgador and Tomer Hertz. Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Science Advances  21 Aug 2020: eabc5961. DOI: 10.1126/sciadv.abc5961

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• Maria Littmann, Katharina Selig, Liel Cohen-Lavi, Yotam Frank, Peter Hönigschmid, Evans Kataka, Anja Mösch, Kun Qian, Avihai Ron, Sebastian Schmid, Adam Sorbie, Liran Szlak, Ayana Dagan-Wiener, Nir Ben-Tal, Masha Y. Niv, Daniel Razansky, Björn W. Schuller, Donna Ankerst, Tomer Hertz & Burkhard Rost. Validity of machine learning in biology and medicine increased through collaborations across fields of expertise. Nature Machine Intelligence. 2020 Jan. doi:10.1038/s42256-019-0139-8

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• Liel Cohen†, Andrew Fiore-Gartland†, Adrienne G. Randolph, Angela Panoskaltsis-Mortari, Sook-San Wong, Jacqui Ralston, Timothy Wood, Ruth Seeds, Q. Sue Huang, Richard J. Webby, Paul G. Thomas and Tomer Hertz. A Modular Cytokine Analysis Method Reveals Novel Associations With Clinical Phenotypes and Identifies Sets of Co-signaling Cytokines Across Influenza Natural Infection Cohorts and Healthy Controls. Front Immunol. 2019 Jun 18;10:1338. doi: 10.3389/fimmu.2019.01338. PubMed PMID: 31275311; PubMed Central PMCID: PMC6594355.

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• Andrew Fiore-Gartland, Angela Panoskaltsis-Mortari, Anna A. Agan, Anushay J. Mistry, Paul G. Thomas, Michael A. Matthay, PALISI PICFlu Investigators, Tomer Hertz,† and Adrienne G. Randolph†. Cytokine Profiles of Severe Influenza Virus-Related Complications in Children. Front Immunol. 2017; 8: 1423. Published online 2017 Nov 6. doi:  10.3389/fimmu.2017.01423

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• Pradyot Dash, Andrew J. Fiore-Gartland, Tomer Hertz, George C. Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E. Bridie Clemens, Thi H. O. Nguyen, Katherine Kedzierska, Nicole L. La Gruta, Philip Bradley and Paul G. Thomas. Quantifiable predictive features define epitope- specific T cell receptor repertoires. Nature. 2017 Jul 6;547(7661):89-93. doi: 10.1038/nature22383. Epub 2017 Jun 21. PMID:28636592.

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• Tomer Hertz†, P. Robert Beatty†, Zachary MacMillen, Sarah S. Killingbeck, Chunling Wang, and Eva Harris. Antibody Epitopes Identified in Critical Regions of Dengue Virus Nonstructural 1 Protein in Mouse Vaccination and Natural Human Infections. Journal of Immunology 2017; 198:4025-4035; Pre-published online 5 April 2017; [† equally contributing authors]

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• Tomer Hertz†, Murray G. Logan†, Morganne Rolland, Craig A. Magaret, Cecilia Rademeyer, Andrew Fiore-Gartland, Paul T. Edlefsen, Allan DeCamp, Hasan Ahmed, Nobu Ngandu, Breandon B. Larsen, Nicole Frahm, J Marais, R Thebus, Daniel Geraghty, John Hural, Larry Corey, James Kublin, Glenda Gray, M. Julie McElrath, James I. Mullins, Peter B. Gilbert, and Carolyn Williamson.  A Study of Vaccine-induced Immune Pressure on Breakthrough Infections in the Phambili Phase 2b HIV-1 Vaccine Efficacy Trial. Accepted to Vaccine, July 2016.  

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• Erik Karlsson, Tomer Hertz, Cydney Johnson, Andrew Mehle, Florian Krammer, and Stacey Schultz-Cherry. Obesity outweighs protection conferred by adjuvanted influenza vaccination. mBio. 2016 Aug 2;7(4). pii: e01144-16. doi: 10.1128/mBio.01144-16. 

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• Andrew Fiore-Gartland, Bryce A. Manso, Dave P. Friedrich DP, Erin E. Gabriel, Greg Finak, Zoe Moodie, Tomer Hertz, Steve C. De Rosa, Nicole Frahm, Peter B. Gilbert, M. Juliana McElrath. Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials. PLoS One. 2016 Feb 10;11(2):e0147812. doi: 10.1371/journal.pone.0147812.

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• Stephen R. Walsh, Zoe Moodie, Andrew J. Fiore-Gartland, Cecilia Morgan, Marissa B. Wilck, Scott M. Hammer, Susan P. Buchbinder, Spyros A. Kalams, Paul A. Goepfert, Mark J. Mulligan, Michael C. Keefer, Lindsey R.Baden, Edith M. Swann, Shannon Grant, Hasan Ahmed, Fusheng L, Tomer Hertz, Steven G. Self, David Friedrich, Nicole Frahm, Hua-Xin Liao,David C.Montefiori, Georgia D. Tomaras, M. Juliana McElrath, John Hural, Barney S. Graham, Xia Jin, the HVTN 083 Study Group, and the NIAID HIV Vaccine Trials Network. Vaccination with heterologous HIV envelope sequences and heterologous adenovirus vectors increases T cell responses to conserved regions (HVTN 083). Journal of Infectious Diseases. October 2015.

 

• Sun-Woo Yoon, Noam Chen, Mariette F. Ducatez, Ryan McBride, Subrata Barman, Thomas P. Fabrizi, Robert G. Webster, Turkan Haliloglu, James C. Paulson, Charles J. Russell, Tomer Hertz, Nir Ben-Tal,  Richard J. Webby. Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus. Scientific Reports 5, Article number: 12828. doi:10.1038/srep12828l, 2015.

 

• Paul T. Edlefsen*, Morgane Rolland*, Tomer Hertz*, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, RV144 Sequencing Team, MiguelA. Arroyo, Robert J. O’Connell, Sorachai Nitayaphan, Punnee Pitisuttithum,Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin S. Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson L. Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert. Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. PLoS Comp. Biol, 11(2): e1003973. doi:10.1371/jour- nal.pcbi.1003973, 2015. 

   

• Andrew J. Gartland , Sue Li , John McNevin, Georgia D. Tomaras, Raphael Gottardo, Holly Janes, Youyi Fong, Darril D. Morris , Dan E. Geraghty, Gustavo H. Kijak, Paul T. Edlefsen, Nicole Frahm, Branden B. Larsen, Sodsai Tovanabutra, Eric Sanders-Buell, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Jodie P. Goodridge, Lennie Chen, Philip Konopa, S. Nariya, Jill N. Stoddard, Kim Wong, Hong Zhao ,Wenjie Deng, Brandon S. Maust, Meera Bose, Shana Howell, Adam Bates, Michelle Lazzaro, Annemarie O’Sullivan, Esther Lei, Andrea Bradfield, Grace Ibitamuno, Vatcharain Assawadarachai, Robert J. O’Connell , Mark S. deSouza, Sorchai Nitayaphan, Supachai Rerks-Ngarm, Merlin L. Robb, John Sidney, Alessandro Sette, Suzan Zolla-Pazner, David Montefiori, M. Juliana McElrath, Jim I. Mullins, Jerome H. Kim, Peter B. Gilbert and Tomer Hertz*. Analysis of HLA A*02 Association with Vaccine Efficacy in the RV144 HIV-1 Vaccine Trial. Journal of Virology, 88(15), 2014.

 

• Christine M. Oshansky, Sook-San Wong, Andrew J. Gartland, Trushar Jeevan, David Wang, Philippa L. Roddam, Miguela A. Caniza, Tomer Hertz, John P. DeVincenzo, Richard J. Webby and Paul G. Thomas. Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load. American Journal of Respiratory and Critical Care Medicine, 189(4):449-62., 2014 .  

 

• Rachael Keating, Tomer Hertz, Marie Wehenkel, Tarsha L. Harris, Benjamin A. Edwards, Jennifer L. McClaren, Scott A. Brown, Sherri Surman, Zachary S. Wilson, Philip Bradley, Julia Hurwitz, Hongbo Chi, Peter C. Doherty, Paul G. Thomas and Maureen A. McGargill. The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection with influenza virus. Nat. Immunology,  14(12):1266-76., 2013.

 

• Tomer Hertz*, Christine Oshansky-Weilnau, Philippa L. Roddam, John P. DeVincenzo, Miguela A. Caniza, Nebojsa Jojic, Simon Mallal, Elizabeth Phillips, Ian James, Paul Thomas, Betz Halloran and Larry Corey. HLA Targeting Efficiency Correlates with Human T-Cell Response Magnitude and with Mortality from Influenza A Infection, PNAS,13;110(33):13492-7, 2013.  PNAS editorial feature, Quanta Magazine.

 

• Tomer Hertz*, Hasan Ahmed, Dave Friedrich, Helen Horton, Nicole Frahm, Julie McElrath, Larry Corey and Peter Gilbert. HIV-1 Vaccine Induced T-cell Reponses Cluster in Epitope Hotspots that Differ From Those Induced in Natural Infection with HIV-1, PLoS Pathogens, 9, e1003404, 2013. 

 

• Pratima Kunwar, Natalie Hawkins, Warren L. Dinges, Yi Liu, Erin E. Gabriel, David A. Swan, Claire E. Stevens, Janine Maenza, Ann C. Collier, James I. Mullins, Tomer Hertz, Xuesong Yu and Helen Horton. Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design, PLoS ONE, 8, e64405, 2013.

 

• Morgane Rolland, Paul T Edlefsen, Brendan B Larsen, Sodsai Tovanabutra, Eric Sanders-Buell, Tomer Hertz, Allan C DeCamp, Chris Carrico, Sergey Menis, Craig A Magaret, Hasan Ahmed, Michal Juraska, Lennie Chen, Philip Konopa, Snehal Nariya, Julia N Stoddard, Kim Wong, Hong Zhao, Wenjie Deng, Brandon S Maust, Meera Bose, Shana Howell, Adam Bates, Michelle Lazzaro, Annemarie O'Sullivan, Esther Lei, Andrea Bradfield, Grace Ibitamuno, Vatcharain Assawadarachai, Robert J O'Connell, Mark S deSouza, Sorachai Nitayaphan, Supachai Rerks-Ngarm, Merlin L Robb, Jason S McLellan, Ivelin Georgiev, Peter D Kwong, Jonathan M Carlson, Nelson L Michael, William R Schief, Peter B Gilbert, James I Mullins and Jerome H Kim. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2, Nature, 490, 417--420, 2012.

 

• Holly Janes, Nicole Frahm, Allan DeCamp, Morgane Rolland, Erin Gabriel, Julian Wolfson, Tomer Hertz, Esper Kallas, Paul Goepfert, David P. Friedrich, Lawrence Corey, James I. Mullins, M. Juliana McElrath and Peter Gilbert. MRKAd5 HIV-1 Gag/Pol/Nef Vaccine-Induced T-Cell Responses Inadequately Predict Distance of Breakthrough HIV-1 Sequences to the Vaccine or Viral Load, PLoS ONE, 7, e43396, 2012.

 

• Paul Thomas and Tomer Hertz. Constrained evolution drives limited influenza diversity, BMC Biology, 10, 43, 2012.

 

• Guang Lan Zhang, Hifzur Rahman Ansari, Phil Bradley, Gavin C Cawley, Tomer Hertz, Xihao Hu, Nebojsa Jojic, Yohan Kim, Oliver Kohlbacher, Ole Lund, Claus Lundegaard, Craig A Magaret, Morten Nielsen, Harris Papadopoulos, G P S Raghava, Vider-Shalit Tal, Li C Xue, Chen Yanover, Shanfeng Zhu, Michael T Rock, James E Crowe Jr., Christos Panayiotou, Marios M Polycarpou, Wlodzisaw Duch and Vladimir Brusic. Machine learning competition in immunology -- Prediction of HLA class I binding peptides, Journal of immunological methods, 374, 1--4, 2011.

 

• Daphna Meroz, Sun-Woo Yoon, Marriette F. Ducatez, Thomas P. Fazrizio, Rihard J Webby, Tomer Hertz* and Nir Ben-Tal. Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population. PNAS U S A. 2011;108(33):13522-7. PMCid: 3158228. PMCid: 3158228.  PNAS editorial feature, Jerusalem Post article, Supp. material.

 

• Tomer Hertz , David Nolan, Ian James, Mina John, Silvana Gaudieri, Elizabeth Phillips, Jim C Huang, Gonzalo Riadi, Simon Mallal and Nebojsa Jojic. Mapping the landscape of host-pathogen co-evolution: HLA class I binding and its relationship with evolutionary conservation in human and viral proteins. J. Virol,85(3):1310-21, 2011. PMCid: 3020499. Featured in MSR's 20th anniversary research connections

 

• Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall. Category Learning from Equivalence Constraints. Cognitive Processing, 10, 211-232, 2009.

 

• Dan Tsafrir, Tomer Hertz, Dilma Da Silva and David Wagner. Portably solving file races with hardness amplification. ACM Transactions on Storage (TOS), 4, 2008.

 

• Ruby Hammer, Aharon Bar-Hillel, Tomer Hertz, Daphna Weinshall and Shaul Hochstein. Comparison Processes in Category Learning: From Theory to Behavior. Brain Research, 2008.

 

• Vladimir Jojic, Tomer Hertz and Nebojsa Jojic. Population Sequencing Using Short Reads: HIV as a Case Study. Pacific Symposium on Biocomputing (PSB), 2008.

 

• Dan Tsafrir, Tomer Hertz, David Wagner and Dilma Da Silva. Portably Solving File TOCTTOU Races with Hardness Amplification. 6th USENIX Conference on File and Storage Technologies, 2008.

 

• Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall. Classification with Positive and Negative Equivalence onstraints: Theory, Computation and Human Experiments, BVAI, 264-276, 2007.

 

• Tomer Hertz and Chen Yanover. Identifying HLA Supertypes by Learning Distance Functions. European Conference on Computational Biology (ECCB), 2006.

 

• Tomer Hertz, Aharon Bar Hillel and Daphna Weinshall. Learning a kernel function for classification with small training samples. International Conference on Machine Learning (ICML), 2006.

 

• Tomer Hertz and Chen Yanover. PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions. BMC Bioinformatics, 7(Suppl 1):S3, 2006.

 

• Inna Weiner, Tomer Hertz, Israel Nelken and Daphna Weinshall. Analyzing Auditory Neurons by Learning Distance Functions. Advances in Neural Information Processing Systems (NIPS), 2005.

 

• Chen Yanover and Tomer Hertz. Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions. The Ninth Annual Conference on Research in Computational Biology (RECOMB), 2005.

 

• Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall. Object Class Recognition by Boosting a Part-Based Model. Conf. on Computer Vision and Pattern Recognition (CVPR), 2005.

 

• Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall. Learning a Mahalanobis Metric from Equivalence Constraints. Journal of Machine Learning Research, 6, 937--965, 2005.

 

• Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall. Efficient learning of relational object class models. International Conference on Computer Vision (ICCV), 2005.

 

• Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall. Category Learning from Equivalence Constraints. XXVII Anuual Meeting of the Cognitive Science Society, Stresa Italy, 2005.

 

• Tomer Hertz, Aharon Bar-Hillel and Daphna Weinshall. Boosting Margin Based Distance Functions for Clustering. International Conference on Machine Learning (ICML), 2004.

 

• Tomer Hertz, Aharon Bar-Hillel and Daphna Weinshall. Learning Distance Functions for Image Retrieval,Conf. on Computer Vision and Pattern Recognition (CVPR), 2004.

 

• Noam Shental, Assaf Zomet, Tomer Hertz and Yair Weiss. Pairwise clustering and graphical models. Advances in Neural Information Processing Systems (NIPS), 185--192, 2004.

 

• Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall. Computing Gaussian mixture models with EM using equivalence constraints. Advances in Neural Information Processing Systems (NIPS), 465--472, 2004.

 

• Tomer Hertz, Noam Shental, Aharon Bar-Hillel and Daphna Weinshall. Enhancing image and video retrieval: learning via equivalence constraints. Conf. on Computer Vision and Pattern Recognition (CVPR), 668--674, 2003.

 

• Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall. Learning distance functions using equivalence relations. International Conference on Machine Learning (ICML), 11--18, 2003.

 

• Noam Shental, Aassaf Zomet, Tomer Hertz and Yair Weiss. Learning and inferring image segmentations using the GBP Typical Cut. International Conference on Computer Vision (ICCV), 1243--1250, 2003.

 

• Noam Shental, Tomer Hertz, Daphna Weinshall and Misha Pavel. Adjustment learning and relevant component analysis. European Conf. on Computer Vision (ECCV), 2002.