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Publications

May 2023.PNG

US National Institutes of Health Prioritization of SARS-CoV-2 Variants

  Emerging Infectious Diseases ,May 2023

Sam Turner, Arghavan Alisoltani, Debbie Bratt, Liel Cohen-Lavi, Bethany L. Dearlove, Christian Drosten, Will M. Fischer, Ron A.M. Fouchier, Ana Silvia Gonzalez-Reiche, Lukasz Jaroszewski, Zain Khalil, Eric LeGresley, Marc Johnson, Terry C. Jones, Barbara Mühlemann, David O’Connor, Mayya Sedova, Maulik Shukla, James Theiler, Zachary S. Wallace, Hyejin Yoon, Yun Zhang, Harm van Bakel, Marciela M. Degrace, Elodie Ghedin, Adam Godzik, Tomer Hertz, Bette Korber, Jacob Lemieux, Anna M. Niewiadomska, Diane J. Post, Morgane Rolland, Richard Scheuermann, and Derek J. Smith.

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FLU-LISA: High throughput antibody profiling using antigen microarrays

Immunology & Cell Biology  25 December 2022

Shlomia Levy, Marwa Abd Alhadi, Asaf Azulay, Amit Kahana, Nir Bujanover, Roi Gazit, Maureen A McGargill, Lilach M Friedman, Tomer Hertz

Febuary 2022.PNG

Brain-immune axis regulation is responsive to cognitive behavioral therapy and mindfulness intervention: Observations from a randomized controlled trial in patients with Crohn's disease

 Brain, Behavior, & Immunity - Health February 2022

Anna Nemirovsky , Karny Ilan , Livnat Lerner , Liel Cohen-Lavi , Doron Schwartz , Ganit Goren , Ruslan Sergienko , Dan Greenberg, Vered Slonim,Nevo , Orly Sarid , Michael Friger 

, Shirley Regev , Shmuel Odes , Tomer Hertz , Alon Monsonego , on behalf of the Israeli IBD Research Nucleus (IIRN).

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 Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers

Science Advances  21 Aug 2020

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

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Validity of machine learning in biology and medicine increased through collaborations across fields of expertise

Nature Machine Intelligence. 2020 Jan.

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.

fimmu-10-01338-g001.jpeg

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

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.

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Cytokine Profiles of Severe Influenza Virus-Related Complications in Children.

Front Immunol. 2017 November 06

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.

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Quantifiable predictive features define epitope- specific T cell receptor repertoires

Nature. 2017 Jul 06

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.

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Antibody Epitopes Identified in Critical Regions of Dengue Virus Nonstructural 1 Protein in Mouse Vaccination and Natural Human Infections.

Journal of Immunology 2017 May 15

Tomer Hertz, P. Robert Beatty, Zachary MacMillen, Sarah S. Killingbeck, Chunling Wang, and Eva Harris.

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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.  

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.

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Obesity outweighs protection conferred by adjuvanted influenza vaccination.

mBio. 2016 Aug 2

Erik Karlsson, Tomer Hertz, Cydney Johnson, Andrew Mehle, Florian Krammer, and Stacey Schultz-Cherry.

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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

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.

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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.

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.

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Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus.

Scientific Reports 5,  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.

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Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.

PLoS Comp. Biol, 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.

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Analysis of HLA A*02 Association with Vaccine Efficacy in the RV144 HIV-1 Vaccine Trial.

Journal of Virology, 2014.

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*

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Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load.

American Journal of Respiratory and Critical Care Medicine, 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. 

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The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection with influenza virus.

Nat. Immunology, 2013.

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.

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HLA Targeting Efficiency Correlates with Human T-Cell Response Magnitude and with Mortality from Influenza A Infection,

PNAS editorial feature, Quanta Magazine, 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.

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HIV-1 Vaccine Induced T-cell Reponses Cluster in Epitope Hotspots that Differ From Those Induced in Natural Infection with HIV-1,

PLoS Pathogens, 2013. 

Tomer Hertz*, Hasan Ahmed, Dave Friedrich, Helen Horton, Nicole Frahm, Julie McElrath, Larry Corey and Peter Gilbert.

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 Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design

PLoS ONE, 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.

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Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2,

Nature, 2012.

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

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 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, 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.

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Constrained evolution drives limited influenza diversity

BMC Biology, 2012.

Paul Thomas and Tomer Hertz

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Machine learning competition in immunology -- Prediction of HLA class I binding peptides.

Journal of immunological methods, 2011.

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.

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Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population.

PNAS U S A. 2011

Daphna Meroz, Sun-Woo Yoon, Marriette F. Ducatez, Thomas P. Fazrizio, Rihard J Webby, Tomer Hertz* and Nir Ben-Tal.

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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, 2011.

Tomer Hertz , David Nolan, Ian James, Mina John, Silvana Gaudieri, Elizabeth Phillips, Jim C Huang, Gonzalo Riadi, Simon Mallal and Nebojsa Jojic.

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Category Learning from Equivalence Constraints.

Cognitive Processing, 2009.

Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall.

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Portably solving file races with hardness amplification.

ACM Transactions on Storage (TOS), 2008.

Dan Tsafrir, Tomer Hertz, Dilma Da Silva and David Wagner.

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Comparison Processes in Category Learning: From Theory to Behavior.

Brain Research, 2008.

Ruby Hammer, Aharon Bar-Hillel, Tomer Hertz, Daphna Weinshall and Shaul Hochstein.

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Population Sequencing Using Short Reads: HIV as a Case Study.

Pacific Symposium on Biocomputing (PSB), 2008. 

Vladimir Jojic, Tomer Hertz and Nebojsa Jojic.

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Portably Solving File TOCTTOU Races with Hardness Amplification.

6th USENIX Conference on File and Storage Technologies, 2008.

Dan Tsafrir, Tomer Hertz, David Wagner and Dilma Da Silva.

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Classification with Positive and Negative Equivalence onstraints: Theory, Computation and Human Experiments,

BVAI, 2007.

Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall.

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Identifying HLA Supertypes by Learning Distance Functions.

European Conference on Computational Biology (ECCB), 2006.

Tomer Hertz and Chen Yanover. 

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 Learning a kernel function for classification with small training samples.

International Conference on Machine Learning (ICML), 2006.

Tomer Hertz, Aharon Bar Hillel and Daphna Weinshall.

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Analyzing Auditory Neurons by Learning Distance Functions.

Advances in Neural Information Processing Systems (NIPS), 2005.

Inna Weiner, Tomer Hertz, Israel Nelken and Daphna Weinshall. 

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Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions.

The Ninth Annual Conference on Research in Computational Biology (RECOMB), 2005.

Chen Yanover and Tomer Hertz.

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Object Class Recognition by Boosting a Part-Based Model.

Conf. on Computer Vision and Pattern Recognition (CVPR), 2005.

Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.

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Learning a Mahalanobis Metric from Equivalence Constraints. 

Journal of Machine Learning Research, 2005.

Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall.

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Efficient learning of relational object class models.

International Conference on Computer Vision (ICCV), 2005.

Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.

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Category Learning from Equivalence Constraints.

XXVII Anuual Meeting of the Cognitive Science Society, Stresa Italy, 2005.

Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall.

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Boosting Margin Based Distance Functions for Clustering.

International Conference on Machine Learning (ICML), 2004.

Tomer Hertz, Aharon Bar-Hillel and Daphna Weinshall.

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Learning Distance Functions for Image Retrieval,

,Conf. on Computer Vision and Pattern Recognition (CVPR), 2004.

Tomer Hertz, Aharon Bar-Hillel and Daphna Weinshall.

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Pairwise clustering and graphical models. 

Advances in Neural Information Processing Systems (NIPS), 2004.

Noam Shental, Assaf Zomet, Tomer Hertz and Yair Weiss.

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Computing Gaussian mixture models with EM using equivalence constraints.

Advances in Neural Information Processing Systems (NIPS), 2004.

Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.

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Enhancing image and video retrieval: learning via equivalence constraints.

Conf. on Computer Vision and Pattern Recognition (CVPR), 2003.

Tomer Hertz, Noam Shental, Aharon Bar-Hillel and Daphna Weinshall.

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Learning distance functions using equivalence relations.

International Conference on Machine Learning (ICML), 2003.

Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall.

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Learning and inferring image segmentations using the GBP Typical Cut. 

International Conference on Computer Vision (ICCV), 2003.

Noam Shental, Aassaf Zomet, Tomer Hertz and Yair Weiss.

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Adjustment learning and relevant component analysis. 

European Conf. on Computer Vision (ECCV), 2002.

Noam Shental, Tomer Hertz, Daphna Weinshall and Misha Pavel.

Publications

May 2023.PNG

US National Institutes of Health Prioritization of SARS-CoV-2 Variants

  Emerging Infectious Diseases ,May 2023

Sam Turner, Arghavan Alisoltani, Debbie Bratt, Liel Cohen-Lavi, Bethany L. Dearlove, Christian Drosten, Will M. Fischer, Ron A.M. Fouchier, Ana Silvia Gonzalez-Reiche, Lukasz Jaroszewski, Zain Khalil, Eric LeGresley, Marc Johnson, Terry C. Jones, Barbara Mühlemann, David O’Connor, Mayya Sedova, Maulik Shukla, James Theiler, Zachary S. Wallace, Hyejin Yoon, Yun Zhang, Harm van Bakel, Marciela M. Degrace, Elodie Ghedin, Adam Godzik, Tomer Hertz, Bette Korber, Jacob Lemieux, Anna M. Niewiadomska, Diane J. Post, Morgane Rolland, Richard Scheuermann, and Derek J. Smith.

Screen Shot 2023-01-16 at 20.53.37.png

FLU-LISA: High throughput antibody profiling using antigen microarrays

Immunology & Cell Biology  25 December 2022

Shlomia Levy, Marwa Abd Alhadi, Asaf Azulay, Amit Kahana, Nir Bujanover, Roi Gazit, Maureen A McGargill, Lilach M Friedman, Tomer Hertz

Febuary 2022.PNG

Brain-immune axis regulation is responsive to cognitive behavioral therapy and mindfulness intervention: Observations from a randomized controlled trial in patients with Crohn's disease

 Brain, Behavior, & Immunity - Health February 2022

Anna Nemirovsky , Karny Ilan , Livnat Lerner , Liel Cohen-Lavi , Doron Schwartz , Ganit Goren , Ruslan Sergienko , Dan Greenberg, Vered Slonim,Nevo , Orly Sarid , Michael Friger 

, Shirley Regev , Shmuel Odes , Tomer Hertz , Alon Monsonego , on behalf of the Israeli IBD Research Nucleus (IIRN).

pub.jpg

 Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers

Science Advances  21 Aug 2020

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

42256_2019_139_Fig1_HTML.png

Validity of machine learning in biology and medicine increased through collaborations across fields of expertise

Nature Machine Intelligence. 2020 Jan.

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.

fimmu-10-01338-g001.jpeg

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

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.

fimmu-08-01423-g002.jpeg

Cytokine Profiles of Severe Influenza Virus-Related Complications in Children.

Front Immunol. 2017 November 06

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.

41586_2017_Article_BFnature22383_Fig1_HTML.jpeg

Quantifiable predictive features define epitope- specific T cell receptor repertoires

Nature. 2017 Jul 06

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.

m_ji_1700029_f2.jpeg

Antibody Epitopes Identified in Critical Regions of Dengue Virus Nonstructural 1 Protein in Mouse Vaccination and Natural Human Infections.

Journal of Immunology 2017 May 15

Tomer Hertz, P. Robert Beatty, Zachary MacMillen, Sarah S. Killingbeck, Chunling Wang, and Eva Harris.

Screen Shot 2023-01-31 at 20.31.03.png

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.  

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.

mbo0041629290001.jpeg

Obesity outweighs protection conferred by adjuvanted influenza vaccination.

mBio. 2016 Aug 2

Erik Karlsson, Tomer Hertz, Cydney Johnson, Andrew Mehle, Florian Krammer, and Stacey Schultz-Cherry.

pone.0147812.g004.png

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

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.

Screen Shot 2023-01-31 at 20.37.05.png

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.

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.

Screen Shot 2023-01-31 at 20.39.15.png

Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus.

Scientific Reports 5,  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.

pcbi.1003973.g003.png

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.

PLoS Comp. Biol, 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.

Screen Shot 2023-01-31 at 20.44.19.png

Analysis of HLA A*02 Association with Vaccine Efficacy in the RV144 HIV-1 Vaccine Trial.

Journal of Virology, 2014.

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*

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Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load.

American Journal of Respiratory and Critical Care Medicine, 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. 

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The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection with influenza virus.

Nat. Immunology, 2013.

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.

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HLA Targeting Efficiency Correlates with Human T-Cell Response Magnitude and with Mortality from Influenza A Infection,

PNAS editorial feature, Quanta Magazine, 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.

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HIV-1 Vaccine Induced T-cell Reponses Cluster in Epitope Hotspots that Differ From Those Induced in Natural Infection with HIV-1,

PLoS Pathogens, 2013. 

Tomer Hertz*, Hasan Ahmed, Dave Friedrich, Helen Horton, Nicole Frahm, Julie McElrath, Larry Corey and Peter Gilbert.

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 Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design

PLoS ONE, 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.

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Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2,

Nature, 2012.

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

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 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, 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.

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Constrained evolution drives limited influenza diversity

BMC Biology, 2012.

Paul Thomas and Tomer Hertz

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Machine learning competition in immunology -- Prediction of HLA class I binding peptides.

Journal of immunological methods, 2011.

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.

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Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population.

PNAS U S A. 2011

Daphna Meroz, Sun-Woo Yoon, Marriette F. Ducatez, Thomas P. Fazrizio, Rihard J Webby, Tomer Hertz* and Nir Ben-Tal.

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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, 2011.

Tomer Hertz , David Nolan, Ian James, Mina John, Silvana Gaudieri, Elizabeth Phillips, Jim C Huang, Gonzalo Riadi, Simon Mallal and Nebojsa Jojic.

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Category Learning from Equivalence Constraints.

Cognitive Processing, 2009.

Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall.

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Portably solving file races with hardness amplification.

ACM Transactions on Storage (TOS), 2008.

Dan Tsafrir, Tomer Hertz, Dilma Da Silva and David Wagner.

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Comparison Processes in Category Learning: From Theory to Behavior.

Brain Research, 2008.

Ruby Hammer, Aharon Bar-Hillel, Tomer Hertz, Daphna Weinshall and Shaul Hochstein.

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Population Sequencing Using Short Reads: HIV as a Case Study.

Pacific Symposium on Biocomputing (PSB), 2008. 

Vladimir Jojic, Tomer Hertz and Nebojsa Jojic.

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Portably Solving File TOCTTOU Races with Hardness Amplification.

6th USENIX Conference on File and Storage Technologies, 2008.

Dan Tsafrir, Tomer Hertz, David Wagner and Dilma Da Silva.

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Classification with Positive and Negative Equivalence onstraints: Theory, Computation and Human Experiments,

BVAI, 2007.

Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall.

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Identifying HLA Supertypes by Learning Distance Functions.

European Conference on Computational Biology (ECCB), 2006.

Tomer Hertz and Chen Yanover. 

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 Learning a kernel function for classification with small training samples.

International Conference on Machine Learning (ICML), 2006.

Tomer Hertz, Aharon Bar Hillel and Daphna Weinshall.

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Analyzing Auditory Neurons by Learning Distance Functions.

Advances in Neural Information Processing Systems (NIPS), 2005.

Inna Weiner, Tomer Hertz, Israel Nelken and Daphna Weinshall. 

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Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions.

The Ninth Annual Conference on Research in Computational Biology (RECOMB), 2005.

Chen Yanover and Tomer Hertz.

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Object Class Recognition by Boosting a Part-Based Model.

Conf. on Computer Vision and Pattern Recognition (CVPR), 2005.

Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.

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Learning a Mahalanobis Metric from Equivalence Constraints. 

Journal of Machine Learning Research, 2005.

Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall.

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Efficient learning of relational object class models.

International Conference on Computer Vision (ICCV), 2005.

Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.

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Category Learning from Equivalence Constraints.

XXVII Anuual Meeting of the Cognitive Science Society, Stresa Italy, 2005.

Rubi Hammer, Tomer Hertz, Shaul Hochstein and Daphna Weinshall.

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Boosting Margin Based Distance Functions for Clustering.

International Conference on Machine Learning (ICML), 2004.

Tomer Hertz, Aharon Bar-Hillel and Daphna Weinshall.

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Learning Distance Functions for Image Retrieval,

,Conf. on Computer Vision and Pattern Recognition (CVPR), 2004.

Tomer Hertz, Aharon Bar-Hillel and Daphna Weinshall.

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Pairwise clustering and graphical models. 

Advances in Neural Information Processing Systems (NIPS), 2004.

Noam Shental, Assaf Zomet, Tomer Hertz and Yair Weiss.

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Computing Gaussian mixture models with EM using equivalence constraints.

Advances in Neural Information Processing Systems (NIPS), 2004.

Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.

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Enhancing image and video retrieval: learning via equivalence constraints.

Conf. on Computer Vision and Pattern Recognition (CVPR), 2003.

Tomer Hertz, Noam Shental, Aharon Bar-Hillel and Daphna Weinshall.

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Learning distance functions using equivalence relations.

International Conference on Machine Learning (ICML), 2003.

Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall.

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Learning and inferring image segmentations using the GBP Typical Cut. 

International Conference on Computer Vision (ICCV), 2003.

Noam Shental, Aassaf Zomet, Tomer Hertz and Yair Weiss.

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Adjustment learning and relevant component analysis. 

European Conf. on Computer Vision (ECCV), 2002.

Noam Shental, Tomer Hertz, Daphna Weinshall and Misha Pavel.

Contact

Contact us

Hertz Lab
Faculty of Health Sciences
Dept. of Microbiology, Immunology and Genetics
National Institute for Biotechnology in the Negev
Bldg. 41, Room 105
Ben-Gurion University of the Negev,
P.O.B. 653, Be'er-Sheva 84105, Israel
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Email: hertzlabbgu@gmail.com
Office: +972-8-642-8856
Cell: +972-58-44-90-888
US: +1-206-388-6320
Fax: +972-8-6477626
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