School of Computer Science

Research output

Research output per year 2011 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2024

• 256410 Citations
• 212 h-index
• 1438 Conference contribution
• 1034 Article
• 210 Conference article
• 82 Paper
• 137 More
  • 35 Editorial
  • 34 Chapter
  • 27 Review article
  • 17 Book
  • 14 Comment/debate
  • 4 Letter
  • 2 Entry for encyclopedia/dictionary
  • 1 Report
  • 1 Meeting Abstract
  • 1 Short survey
  • 1 Discussion paper

Research output per year

Research output per year

Search results

• 2024

  Current and future directions in network biology

  Zitnik, M., Li, M. M., Wells, A., Glass, K., Gysi, D. M., Krishnan, A., Murali, T. M., Radivojac, P., Roy, S., Baudot, A., Bozdag, S., Chen, D. Z., Cowen, L., Devkota, K., Gitter, A., Gosline, S. J. C., Gu, P., Guzzi, P. H., Huang, H., Jiang, M., & 17 othersKesimoglu, Z. N., Koyuturk, M., Ma, J., Pico, A. R., Przulj, N., Przytycka, T. M., Raphael, B. J., Ritz, A., Sharan, R., Shen, Y., Singh, M., Slonim, D. K., Tong, H., Yang, X. H., Yoon, B. J., Yu, H. & Milenkovic, T., 2024, In: Bioinformatics Advances. 4, 1, vbae099.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access
• 2023

  Banking on a new understanding: translational opportunities from veterinary biobanks

  Jun 2023, In: GeroScience. 45, 3, p. 1439-1450 12 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • banking 100%
  • dogs 54%
  • biomarkers 43%
  • Dogs 38%
  • human physiology 37%

• Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies

  Malbranke, C., Bikard, D., Cocco, S., Monasson, R. & Tubiana, J., Jun 2023, In: Current Opinion in Structural Biology. 80, 102571.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Physics 100%
  • Machine Learning 92%
  • Entropy 32%
  • Proteins 30%

• Toward next-generation endoscopes integrating biomimetic video systems, nonlinear optical microscopy, and deep learning

  Stanciu, S. G., König, K., Song, Y. M., Wolf, L., Charitidis, C. A., Bianchini, P. & Goetz, M., 1 Jun 2023, In: Biophysics Reviews. 4, 2, 021307.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Nonlinear Optical Microscopy 100%
  • Deep Learning 80%
  • Biomimetics 73%
  • Endoscopy 71%
  • Endoscopes 66%
• 2022

  An open science study of ageing in companion dogs

  3 Feb 2022, In: Nature. 602, 7895, p. 51-57 7 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Dogs 100%
  • Environment 78%
  • Plasma 42%
  • Data Science 32%
  • Electronic Health Records 23%

• Big-data approaches lead to an increased understanding of the ecology of animal movement

  Nathan, R., Monk, C. T., Arlinghaus, R., Adam, T., Alós, J., Assaf, M., Baktoft, H., Beardsworth, C. E., Bertram, M. G., Bijleveld, A. I., Brodin, T., Brooks, J. L., Campos-Candela, A., Cooke, S. J., Gjelland, K., Gupte, P. R., Harel, R., Hellström, G., Jeltsch, F., Killen, S. S., & 17 othersKlefoth, T., Langrock, R., Lennox, R. J., Lourie, E., Madden, J. R., Orchan, Y., Pauwels, I. S., Říha, M., Roeleke, M., Schlägel, U. E., Shohami, D., Signer, J., Toledo, S., Vilk, O., Westrelin, S., Whiteside, M. A. & Jarić, I., 18 Feb 2022, In: Science. 375, 6582, eabg1780.

  The Hebrew University of Jerusalem, Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • ecology 100%
  • Big Data 96%
  • Ecology 94%
  • animals 68%
  • Animals 68%

• The Seattle report on database research

  Abadi, D., Ailamaki, A., Andersen, D., Bailis, P., Balazinska, M., Bernstein, P. A., Boncz, P., Chaudhuri, S., Cheung, A., Doan, A., Dong, L., Franklin, M. J., Freire, J., Halevy, A., Hellerstein, J. M., Idreos, S., Kossmann, D., Kraska, T., Krishnamurthy, S., Markl, V., & 13 othersMelnik, S., Milo, T., Mohan, C., Neumann, T., Ooi, B. C., Ozcan, F., Patel, J., Pavlo, A., Popa, R., Ramakrishnan, R., Re, C., Stonebraker, M. & Suciu, D., Aug 2022, In: Communications of the ACM. 65, 8, p. 72-79 8 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Data Science 100%
  • Cleaning 69%
  • Pipelines 56%
  • Engines 47%
• 2021

  Mutational Signatures: From Methods to Mechanisms

  Kim, Y. A., Leiserson, M. D. M., Moorjani, P., Sharan, R., Wojtowicz, D. & Przytycka, T. M., 11 May 2021, In: Annual Review of Biomedical Data Science. 4, p. 189-206 18 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • DNA 100%
  • Error 72%
  • Deamination 64%
  • DNA Repair 44%
  • DNA Damage 42%
• 2020

  Shape analysis

  Chang, B. Y. E., Drăgoi, C., Manevich, R., Rinetzky, N. & Rival, X., 5 Oct 2020, In: Foundations and Trends in Programming Languages. 6, 1-2, p. 1-158 158 p.

  Tel Aviv University, Ben-Gurion University of the Negev

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Shape Analysis 100%
  • Data storage equipment 44%
  • Data structures 43%
  • Data Structures 41%
  • Abstraction 35%
• 2019

  Microbial community design: methods, applications, and opportunities

  Eng, A. & Borenstein, E., Aug 2019, In: Current Opinion in Biotechnology. 58, p. 117-128 12 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Microbiota 100%
  • Computational methods 35%
  • Application 31%
  • Social Planning 24%
  • Reduction 22%

• Rexpansions of nondeterministic matrices and their applications in nonclassical logics

  Avron, A. & Zohar, Y., 1 Mar 2019, In: Review of Symbolic Logic. 12, 1, p. 173-200 28 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Non-classical Logics 100%
  • Conservative Extension 41%
  • Logic 22%
  • Consequence Relation 19%
  • Many valued 19%

• To embed or not: Network embedding as a paradigm in computational biology

  Nelson, W., Zitnik, M., Wang, B., Leskovec, J., Goldenberg, A. & Sharan, R., 2019, In: Frontiers in Genetics. 10, MAY, 381.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Computational Biology 100%
  • Proteins 39%
  • Technology 34%
• 2017

  Network propagation: A universal amplifier of genetic associations

  Cowen, L., Ideker, T., Raphael, B. J. & Sharan, R., 1 Sep 2017, In: Nature Reviews Genetics. 18, 9, p. 551-562 12 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Gene Regulatory Networks 100%
  • Genetic Research 58%
  • Electric Impedance 46%
  • Computational Biology 43%
  • Inborn Genetic Diseases 42%
• 2016

  Telemedicine: a novel service in pediatric emergency care

  Nevet, A., Bitton, Y., Wolf, L. & Waisman, Y., 1 Jul 2016, In: Harefuah. 155, 7, p. 410-413 4 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Telemedicine 100%
  • Emergency Medical Services 94%
  • Pediatricians 78%
  • Referral and Consultation 66%
  • Pediatrics 58%

• The beckman report on database research

  Abadi, D., Agrawal, R., Ailamaki, A., Balazinska, M., Bernstein, P. A., Carey, M. J., Chaudhuri, S., Dean, J., Doan, A., Franklin, M. J., Gehrke, J., Haas, L. M., Halevy, A. Y., Hellerstein, J. M., Ioannidis, Y. E., Jagadish, H. V., Kossmann, D., Madden, S., Mehrotra, S., Milo, T., & 10 othersNaughton, J. F., Ramakrishnan, R., Markl, V., Olston, C., Ooi, B. C., Re, C., Suciu, D., Stonebraker, M., Walter, T. & Widom, J., Feb 2016, In: Communications of the ACM. 59, 2, p. 92-99 8 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review
• 2015

  Modeling cancer metabolism on a genome scale

  Yizhak, K., Chaneton, B., Gottlieb, E. & Ruppin, E., 1 Jun 2015, In: Molecular Systems Biology. 11, 6, 817.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Metabolism 100%
  • Genome 81%
  • Genomics 77%
  • Cancer 76%
  • Pharmacological Metabolism 57%
• 2014

  An EEG Finger-Print of fMRI deep regional activation

  Meir-Hasson, Y., Kinreich, S., Podlipsky, I., Hendler, T. & Intrator, N., 5 Nov 2014, In: NeuroImage. 102, P1, p. 128-141 14 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Fingers 100%
  • Electroencephalography 92%
  • Magnetic Resonance Imaging 72%
  • Amygdala 54%
  • Electrodes 31%

• Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation

  Rashi-Elkeles, S., Warnatz, H. J., Elkon, R., Kupershtein, A., Chobod, Y., Paz, A., Amstislavskiy, V., Sultan, M., Safer, H., Nietfeld, W., Lehrach, H., Shamir, R., Yaspo, M. L. & Shiloh, Y., 13 May 2014, In: Science Signaling. 7, 325, rs3.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Epigenome 100%
  • Ionizing Radiation 97%
  • Gene Expression Profiling 82%
  • DNA Damage 34%
  • Enhancer 31%
• 2013

  Metabolically re-modeling the drug pipeline

  Oberhardt, M. A., Yizhak, K. & Ruppin, E., Oct 2013, In: Current Opinion in Pharmacology. 13, 5, p. 778-785 8 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Pipeline 100%
  • Drug Design 99%
  • Metabolic 70%
  • Genome 58%
  • Drug 45%

• Network-based interpretation of genomic variation data

  Halldórsson, B. V. & Sharan, R., 1 Nov 2013, In: Journal of Molecular Biology. 425, 21, p. 3964-3969 6 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Protein Interaction Maps 100%
  • Information Services 97%
  • Genome-Wide Association Study 84%
  • Proteins 59%
  • Technology 52%

• Pathway-based analysis of genomic variation data

  Atias, N., Istrail, S. & Sharan, R., Dec 2013, In: Current Opinion in Genetics and Development. 23, 6, p. 622-626 5 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Phenotype 100%
  • Direction compound 40%
  • Genotype 39%
  • Technology 36%

• Phase-change memory: An architectural perspective

  Zilberberg, O., Weiss, S. & Toledo, S., Jun 2013, In: ACM Computing Surveys. 45, 3, 29.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Phase change memory 100%
  • Phase Change 96%
  • Architecture 78%
  • Dynamic random access storage 61%
  • Data storage equipment 43%
• 2012

  Comparative analysis of protein networks: Hard problems, practical solutions

  Atias, N. & Sharan, R., May 2012, In: Communications of the ACM. 55, 5, p. 88-97 10 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  • Proteins 100%
  • Color 78%
  • Electric network analysis 73%

• Foreword

  Arieli, O., Konikowska, B., Rabinovich, A. & Zamansky, A., 14 Oct 2012, In: Journal of Logic and Computation. 26, 1, p. 1-6 6 p.

  Tel Aviv University, University of Haifa

  Research output: Contribution to journal › Review article › peer-review

  • Tel Aviv 100%
  • Foreword 85%
  • Mathematics 62%
  • Logic 59%
  • Automated Reasoning 37%
• 2011

  ANAT: A tool for constructing and analyzing functional protein networks

  Yosef, N., Zalckvar, E., Rubinstein, A. D., Homilius, M., Atias, N., Vardi, L., Berman, I., Zur, H., Kimchi, A., Ruppin, E. & Sharan, R., 25 Oct 2011, In: Science Signaling. 4, 196, pl1.

  Tel Aviv University, Weizmann Institute of Science

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Software 100%
  • Protein 54%
  • Apoptotic 50%
  • Proteins 48%
  • Autophagic Cell Death 47%

• A survey on shape correspondence

  Van Kaick, O., Zhang, H., Hamarneh, G. & Cohen-Or, D., 2011, In: Computer Graphics Forum. 30, 6, p. 1681-1707 27 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Correspondence 100%
  • Semantic Analysis 32%
  • Pipelines 31%
  • Triangle Mesh 30%
  • Correspondence Problem 30%

• Transcriptional modulation induced by ionizing radiation: P53 remains a central player

  Rashi-Elkeles, S., Elkon, R., Shavit, S., Lerenthal, Y., Linhart, C., Kupershtein, A., Rechavi, G., Shamir, R. & Shiloh, Y., Aug 2011, In: Molecular Oncology. 5, 4, p. 336-348 13 p.

  Tel Aviv University

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Ionizing Radiation 100%
  • DNA Damage 84%
  • Datasets 57%
  • p53 Genes 53%
  • Genes 39%