Journal papers

High capacity clinical SARS-CoV-2 molecular testing using combinatorial pooling
Shosh Zismanov, Bar Shalem, Yulia Margolin-Miller, Dalia Rosin-Grunewald, Roy Adar, Ayelet Keren-Naus, Doron Amichay, Anat Ben-Dor, Yonat Shemer-Avni, Angel Porgador, Noam Shental^, Tomer Hertz^, Communications Medicine, 4, 121, June 2024
^ Corresponding author

Cytonuclear interactions modulate the plasticity of photosynthetic rhythmicity and growth in wild barley
Lalit Dev Tiwari, Eyal Bdolach, Manas Ranjan Prusty, Schewach Bodenheimer, Avital Be'ery, Adi Faigenboim-Doron, Eiji Yamamoto, Klára Panzarová, Khalil Kashkush, Noam Shental, Eyal Fridman, Physiologia Plantarum, 176(1), e14192, Feb 2024

Achieving pan-microbiome biological insights via the dbBact knowledge base
Amnon Amir^, Eitan Ozel, Yael Haberman, Noam Shental^, Nucleic Acids Research, Volume 51, Issue 13, 21 July 2023, Pages 6593–6608
^ Corresponding author

Sex, strain, and lateral differences in brain cytoarchitecture across a large mouse population
David Elkind, Hannah Hochgerner, Etay Aloni, Noam Shental^, Amit Zeisel^, eLife, May 2023, 12:e82376.
^ Corresponding author

Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water
Ashraf Al-Ashhab, Rivka Alexander-Shani, Yosef Avrahami, Roberto Ehrlich, Rosa Ines Strem, Shiri Meshner, Noam Shental and Galit Sharon, Animal microbiome 4, 42 (2022). https://doi.org/10.1186/s42523-022-00191-y

Biogeographic landscape of the human face skin microbiome viewed in high definition
Michael Brandwein, Garold Fuks, Avigail Israel, Emmilia Hodak, Fareed Sabbah, Doron Steinberg, Zvi Bentwich, Noam Shental^ and Shiri Meshner^
Acta Dermato-Venereologica Sep 2021, doi: 10.2340/00015555-3929. 
^ Corresponding author

Microbial exposure during early human development primes fetal immune cells

Archita Mishra, Ghee Chuan Lai, Leong Jing Yao, Thet Tun Aung, Noam Shental, Aviva Rotter-Maskowitz, Edwin Shepherdson, Gurmit Singh Naranjan Singh, Rhea Pai, Adhika Shanti, Regina Men Men Wong, Andrea Lee, Costerwell Khyriem, Charles Antoine Dutertre, Svetoslav Chakarov, K G Srinivasan, Nurhidaya Binte Shadan, Xiao-Meng Zhang, Shabnam Khalilnezhad, Fabien Cottier, Alrina Shin Min Tan, Gillian Low, Phyllis Chen, Yiping Fan, Pei Xiang Hor, Avery Khoo May Lee, Mahesh Choolani, David Vermijlen, Ankur Sharma, Garold Fuks, Ravid Straussman, Norman Pavelka, Benoit Malleret, Naomi McGovern, Salvatore Albani, Jerry Kok Yen Chan, Florent Ginhoux, Cell, May 2021, S0092-8674(21)00574-2. doi: 10.1016/j.cell.2021.04.039. Epub ahead of print. PMID: 34077752.

Identification of bacteria-derived HLA-bound peptides in melanoma

Shelly Kalaora, Adi Nagler, Deborah Nejman, Michal Alon, Chaya Barbolin, Eilon Barnea, Steven L. C. Ketelaars, Kuoyuan Cheng, Kevin Vervier, Noam Shental, Yuval Bussi, Ron Rotkopf, Ronen Levy, Gil Benedek, Sophie Trabish, Tali Dadosh, Smadar Levin-Zaidman, Leore T. Geller, Kun Wang, Polina Greenberg, Gal Yagel, Aviyah Peri, Garold Fuks, Neerupma Bhardwaj, Alexandre Reuben, Leandro Hermida, Sarah B. Johnson, Jessica R. Galloway-Peña, William C. Shropshire, Chantale Bernatchez, Cara Haymaker, Reetakshi Arora, Lior Roitman, Raya Eilam, Adina Weinberger, Maya Lotan-Pompan, Michal Lotem, Arie Admon, Yishai Levin, Trevor D. Lawley, David J. Adams, Mitchell P. Levesque, Michal J. Besser, Jacob Schachter, Ofra Golani, Eran Segal, Naama Geva-Zatorsky, Eytan Ruppin, Pia Kvistborg, Scott N. Peterson, Jennifer A. Wargo, Ravid Straussman & Yardena Samuels, Nature,  Apr 2021, 592, 138–143 (2021). https://doi.org/10.1038/s41586-021-03368-8

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

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^, Science Advances,  Sep 2020, Vol. 6, no. 37, eabc5961, DOI: 10.1126/sciadv.abc5961

^ Corresponding author
The paper was featured by the New York Times on August 21st 2020

Characterization of the human tumor microbiome reveals tumor-type specific intra-cellular bacteria
Ilana Livyatan, Deborah Nejman, Noam Shental and Ravid Straussman, OncoImmunology, 9(1), July 2020, DOI 10.1080/2162402X.2020.1800957 

The human tumor microbiome is composed of tumor type–specific intracellular bacteria

Deborah Nejman, Ilana Livyatan, Garold Fuks, Nancy Gavert, Yaara Zwang, Leore T. Geller, Aviva Rotter-Maskowitz, Roi Weiser,Giuseppe Mallel, Elinor Gigi, Arnon Meltser, Gavin M. Douglas, Iris Kamer, Vancheswaran Gopalakrishnan, Tali Dadosh,Smadar Levin-Zaidman, Sofia Avnet, Tehila Atlan, Zachary A. Cooper, Reetakshi Arora, Alexandria P. Cogdill, Md Abdul Wadud Khan, Gabriel Ologun, Yuval Bussi, Adina Weinberger, Maya Lotan-Pompan, Ofra Golani, Gili Perry, Merav Rokah, Keren Bahar-Shany, Elisa A. Rozeman, Christian U. Blank,  Anat Ronai, Ron Shaoul, Amnon Amit, Tatiana Dorfman, Ran Kremer, Zvi R. Cohen, Sagi Harnof,  Tali Siegal, Einav Yehuda-Shnaidman , Einav Nili Gal-Yam, Hagit Shapira, Nicola Baldini, Morgan GI. Langille, Alon Ben-Nun,  Bella Kaufman, Aviram Nissan, Talia Golan, Maya Dadiani, Keren Levanon, Jair Bar, Shlomit Yust-Katz, Iris Barshack, Daniel S Peeper, Dan J. Raz, Eran Segal, Jennifer A. Wargo,  Judith Sandbank, Noam Shental^ and Ravid Straussman^, Science, May 2020, vol. 368 no. 6494 973-980.

^ Equal contribution

A Perspective in Science regarding our paper

 
The Role of Sweat in the Composition of Skin Microbiome: Lessons Learned from Patients with Congenital Insensitivity to Pain with Anhidrosis

Michael Brandwein, Amir Horev, Ben Bogen, Garold Fuks, Avigail Israel, Guy Shalom, Vered Pinsk, Zvi Bentwich, Noam Shental^ and Shiri Meshner^, Journal of the European Academy of Dermatology & Venereology. Dec 2019, doi: 10.1111/jdv.16170.

^ Corresponding author

Skin microbiome compositional changes in atopic dermatitis patients accompany Dead Sea climatotherapy
Michael Brandwein, Garold Fuks, Avigail Israel, Fareed Sabbah, Emmillia Hodak, Amir Szitenberg, Marco Harari, Zvi Bentwich, Noam Shental^ and Shiri Meshner^, Photochemistry and Photobiology. May 2019, doi: 10.1111/php.13119.
^ Corresponding author

Identification of a unique Staphylococcus aureus ribosomal signature in severe atopic dermatitis
Michael Brandwein, Garold Fuks, Avigail Israel, Deborah Nejman, Ravid Straussman, Emmilia Hodak, Marco Harari, Doron Steinberg, Zvi Bentwich,, Noam Shental^ and Shiri Meshner^, British Journal of Dermatology, doi: 10.1111/bjd.16936. [Epub ahead of print], July 2018.
^ Corresponding author

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling
Garold Fuks, Michael Elgart, Amnon Amir, Amit Zeisel, Peter J. Turnbaugh, Yoav Soen and Noam Shental^, Microbiome, 26;6(1):17. doi: 10.1186/s40168-017-0396-x, Jan 2018.
^ Corresponding author

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine
Leore T. Geller, Michal Barzily-Rokni, Tal Danino, Oliver H. Jonas, Noam Shental, Deborah Nejman, Nancy Gavert, Yaara Zwang, Zachary A. Cooper, Kevin Shee, Christoph A. Thaiss, Alexandre Reuben, Jonathan Livny, Roi Avraham, Dennie T. Frederick, Matteo Ligorio, Kelly Chatman, Stephen E. Johnston, Carrie M. Mosher, Alexander Brandis, Garold Fuks, Candice Gurbatri, Vancheswaran Gopalakrishnan, Michael Kim, Mark W. Hurd, Matthew Katz, Jason Fleming, Anirban Maitra, David A. Smith, Matt Skalak, Jeffrey Bu, Monia Michaud, Sunia A. Trauger, Iris Barshack, Talia Golan, Judith Sandbank, Keith T. Flaherty, Anna Mandinova, Wendy S. Garrett, Sarah P. Thayer, Cristina R. Ferrone, Curtis Huttenhower, Sangeeta N. Bhatia, Dirk Gevers, Jennifer A. Wargo, Todd R. Golub and Ravid Straussman, Science, 357, Issue 6356, pp. 1156-1160, 15 Sept, 2017.
 

Ants regulate colony spatial organization using multiple chemical road-signs
Yael Heyman, Noam Shental, Alexander Brandis, Abraham Hefetz and Ofer Feinerman, Nature Communications. 8, 15414 doi:10.1038/ncomms15414T, 2017

Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy
Michael Brandwein, Garold Fuks, Avigail Israel, Ashraf Al-Ashhab, Deborah Nejman, Ravid Straussman, Emmilia Hodak,  Marco Harari, Doron Steinberg, Zvi Bentwich, Noam Shental^ and Shiri Meshner^, Acta Derm Venereol. 2017 Aug 17. doi: 10.2340/00015555-2769.
^ Corresponding author

Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach
Habte Nida, Shula Blum, Dina Zielinski, Dhruv A. Srivastava, Rivka Elbaum, Zhanguo Xin, Yaniv Erlich, Eyal Fridman^ and Noam Shental^, The Plant Journal, DOI: 10.1111/tpj.13161, 2016.
^ Corresponding author

Guanine polynucleotides are self-antigens for human natural autoantibodies and are significantly reduced in the human genome
Ittai Fattal*, Noam Shental*, Shifra Ben-Dor, Yair Molad, Armando Gabrielli, Elisheva Pokroy-Shapira, Shirly Oren, Avi Livneh, Pnina Langevitz,  Gisele Zandman-Goddard, Ofer Sarig, Raanan Margalit, Uzi Gafter, Eytan Domany, Irun R. Cohen, Immunology, DOI: 10.1111/imm.12514, 2015.
* Equal contribution

Pemphigus Vulgaris is characterized by low IgG reactivities to specific self-antigens along with high IgG reactivity to Desmoglein 3
Ittai Fattal*, Jacob Rimer*, Noam Shental*, Yair Molad, Armando Gabrielli, Avi Livneh, Ofer Sarig, Ilan Goldberg, Uzi Gafter, Eytan Domany and Irun R. Cohen, Immunology, DOI: 10.1111/imm. 12316, 2014.
* Equal contribution

Delayed development induced by toxicity to the host can be inherited by a bacterial-dependent, transgenerational effect
Yael Fridmann-Sirkis, Shay Stern, Michael Elgart, Matana Galili, Amit Zeisel, Noam Shental and Yoav Soen, Frontiers in Genetics 5:27, DOI: 10.3389/fgene.2014.00027, 2014.

EBV Antibodies Mark SLE and Scleroderma Patients Negative for Anti-DNA
Ittai Fattal*, Noam Shental*, Yair Molad, Armando Gabrielli, Elisheva Pokroy-Shapira, Shirly Oren, Avi Livneh, Pnina Langevitz, Rachel Pauzner, Ofer Sarig, Uzi Gafter, Eytan Domany, Irun R. Cohen, Immunology, DOI: 10.1111/imm.12200, 2013.
* Equal contribution

High resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions
Amnon Amir., Amit Zeisel, Or Zuk, Michael Elgart, Shay Stern, Ohad Shamir, Peter J. Turnbaugh, Yoav Soen and Noam Shental^.
Nucleic Acids Research 2013; doi: 10.1093/nar/gkt1070, Nov 2013
^ Corresponding author
COMPASS code (at GitHub)
         
Identification of rare alleles and their carriers using compressed se(que)nsing
Noam Shental^, Amnon Amir and Or Zuk.
Nucleic Acids Research, 38(19):e179, 1-22, Aug 2010
^ Corresponding author
ComSeq code (matlab)

An antibody core signature of Systemic Lupus Erythematosus detected by antigen microarray
Ittai Fattal*, Noam Shental*, Dror Mevorach , Juan-Manuel Anaya, Avi Livneh, Pnina Langevitz, Gisele Zandman-Goddard, Rachel Pauzner, Miriam Lerner, Miri Blank, Maria-Eugenia Hincapie, Uzi Gafter, Yaakov Naparstek, Yehuda Shoenfeld, Eytan Domany and Irun R. Cohen.
Immunology (130): 337-343, 2009.
* Equal contribution
   
Discrete-Input Two-Dimensional Gaussian Channels With Memory: Estimation and Information Rates via Graphical Models and Statistical Mechanics.
Ori Shental*, Noam Shental*, Shlomo Shamai (Shitz), Ido Kanter, Anthony Weiss, and Yair Weiss.
IEEE Transactions on Information Theory (TIT), 54(April): 1500-1513, 2008.
* Equal contribution
Awarded Best Student Paper of the Year 2008 in Signal Processing and Coding for Data Storage, by the IEEE Communications Society Data Storage Technical Committee.

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

Peer-Reviewed Conference Publications

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing Using Convex Optimization.
 Or Zuk, Amnon Amir, Amit Zeisel, Ohad Shamir and Noam Shental.
 String Processing and Information Retrieval Symposium (SPIRE), 2013, LNCS 8214, O. Kurland, M. Lewenstein, and E. Porat (Eds.), 279-297.

Semi-Supervised Learning - A Statistical Physics Approach.
Gad Getz*, Noam Shental* and Eytan Domany.
Workshop on "Learning with Partially Classified Training Data", 22nd International Conference on Machine Learning (ICML), 2005.
* Equal contribution

On the Achievable Information Rates of Finite-State Input Two-Dimensional Channels with Memory.
Ori Shental, Noam Shental and Shlomo Shamai (Shitz).
International Symposium For Information Theory (ISIT), 2005.

Generalized Belief Propagation Receiver for Near-Optimal Detection of Two-Dimensional Channels with Memory.
Ori Shental, Noam Shental, Anthony Weiss and Yair Weiss.
IEEE Information Theory Workshop (ITW), 2004.

Computing Gaussian Mixture Models with EM using Equivalence Constraints.
Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.
Neural Information Processing Systems (NIPS), 2003.

Pairwise Clustering and Graphical Models.
Noam Shental, A. Zomet, Tomer Hertz and Yair Weiss.
Neural Information Processing Systems (NIPS), 2003.

Learning and Inferring Image Segmentations using the GBP Typical Cut.
Noam Shental, Assaf Zomet, Tomer Hertz and Yair Weiss.
9th International Conference on Computer Vision (ICCV), 2003.

Computing Gaussian Mixture Models with EM using Side Information.
Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.
Workshop on "The Continuum from Labeled to Unlabeled Data in Machine Learning and Data Mining",
20th International Conference on Machine Learning (ICML), 2003.

Learning Distance Functions using Equivalence Relations.
Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall.
20th International Conference on Machine Learning (ICML), 2003.

Enhancing Image and Video Retrieval: Learning via Equivalence Constraints.
Tomer Hertz, Aharon Bar-Hillel, Noam Shental and Daphna Weinshall.
IEEE Conf. on Computer Vision and Pattern Recognition (CVPR), 2003.

Adjustment Learning and Relevant Component Analysis.
Noam Shental, Tomer Hertz, Daphna Weinshall and M. Pavel.
7th European conference of Computer Vision (ECCV), 2002.

Perceptual Grouping and Segmentation by Stochastic Clustering.
Yoram Gdalyahu, Noam Shental and Daphna Weinshall.
Conference on Computer Vision and Pattern Recognition (CVPR), 2000.

Book Chapters

Gaussian Mixture Models with Equivalence Constraints.  
Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall.
in "Constrained Clustering: Advances in Algorithms, Theory, and Applications", edited by S. Basu, I. Davidson, and K.L. Wagstaff, Chapman & Hall/CRC Data Mining Series, 2008. (for example in alibris.com)

Code

COMPASS code (at GitHub) - both matlab and stand alone application for Linux 64bit.
Compressed Sequencing (ComSeq)  – matlab implementation
Relevant Component Analysis (RCA)  - matlab implementation
Constrained EM algorithm  - stand-alone matlab implementation which includes the BNT package.
GBP for image segmentation - matlab implementation.