@inproceedings{landau2024competition,
  title={A competition-best drug prioritization algorithm},
  author={Landau, Ohad and Rubin, Eitan},
  booktitle={EUROPEAN JOURNAL OF HUMAN GENETICS},
  volume={32},
  pages={698--698},
  year={2024},
  organization={SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND}
}

@article{valiya2024transcription,
  title={Transcription Factor HNF4A is Involved in Breast Cancer Recurrence},
  author={Valiya Veettil, Rahul and Eyal Altman, Noah and Hashkes, Ruth and Rubin, Eitan},
  journal={bioRxiv},
  pages={2024--03},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

@article{veettil2024transcription,
  title={Transcription Factor HNF4A is Involved in Breast Cancer Recurrence},
  author={Veettil, Valiya and Altman, Eyal and Hashkes, R and Rubin, E},
  year={2024}
}

@article{ravkin2024machine,
  title={Machine-learning-based risk assessment tool to rule out empirical use of ESBL-targeted therapy in endemic areas},
  author={Ravkin, HD and Ravkin, RM and Rubin, E and Nesher, L},
  journal={Journal of Hospital Infection},
  volume={149},
  pages={90--97},
  year={2024},
  publisher={WB Saunders}
}

@article{miyashita2024transcriptomic,
  title={The transcriptomic expression pattern of immune checkpoints shows heterogeneity between and within cancer types},
  author={Miyashita, Hirotaka and Bevins, Nicholas J and Thangathurai, Kartheeswaran and Lee, Suzanna and Pabla, Sarabjot and Nesline, Mary K and Glenn, Sean T and Conroy, Jeffrey M and DePietro, Paul and Rubin, Eitan and others},
  journal={American Journal of Cancer Research},
  volume={14},
  number={5},
  pages={2240},
  year={2024},
  publisher={e-Century Publishing Corporation}
}

@article{moscona2023boris,
  title={BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells},
  author={Moscona, Roy and Janssen, Sanne Marlijn and Elchebly, Mounib and Papadakis, Andreas Ioannis and Rubin, Eitan and Spatz, Alan},
  journal={Pigment Cell \& Melanoma Research},
  volume={36},
  number={3-4},
  pages={299--313},
  year={2023}
}

@article{gesundheit2023autism,
  title={Autism spectrum disorder diagnosis using a new panel of immune-and inflammatory-related serum biomarkers: A case-control multicenter study},
  author={Gesundheit, Benjamin and Zisman, Philip David and Hochbaum, Leah and Posen, Yehudit and Steinberg, Avraham and Friedman, Gerald and Ravkin, Hersh D and Rubin, Eitan and Faktor, Ouriel and Ellis, Ronald},
  journal={Frontiers in Pediatrics},
  volume={11},
  pages={967954},
  year={2023},
  publisher={Frontiers Media SA}
}

@article{lazar2023transcriptomics,
  title={A transcriptomics approach to expand therapeutic options and optimize clinical trials in oncology},
  author={Lazar, Vladimir and Zhang, Baolin and Magidi, Shai and Le Tourneau, Christophe and Raymond, Eric and Ducreux, Michel and Bresson, Catherine and Raynaud, Jacques and Wunder, Fanny and Onn, Amir and others},
  journal={Therapeutic Advances in Medical Oncology},
  volume={15},
  pages={17588359231156382},
  year={2023},
  publisher={SAGE Publications Sage UK: London, England}
}

@article{elkoshi2023binary,
  title={Binary classification machine-learning Unveils Sex-Dependent mutated gene Signatures in Melanoma},
  author={Elkoshi, Nadav and Parikh, Shivang and Mahameed, Sajeda and Meidan, Abraham and Rubin, Eitan and Levy, Carmit},
  journal={bioRxiv},
  pages={2023--04},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

@article{miyashita2023t,
  title={T-cell priming transcriptomic markers: implications of immunome heterogeneity for precision immunotherapy},
  author={Miyashita, Hirotaka and Kurzrock, Razelle and Bevins, Nicholas J and Thangathurai, Kartheeswaran and Lee, Suzanna and Pabla, Sarabjot and Nesline, Mary and Glenn, Sean T and Conroy, Jeffrey M and DePietro, Paul and others},
  journal={NPJ Genomic Medicine},
  volume={8},
  number={1},
  pages={19},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{lender2023immune,
  title={Immune clustering reveals molecularly distinct subtypes of lung adenocarcinoma},
  author={Lender, Yan and Givton, Ofer and Bornshten, Ruth and Azar, Meitar and Moscona, Roy and Yarden, Yosef and Rubin, Eitan},
  journal={bioRxiv},
  pages={2023--04},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

@article{solomon2022win,
  title={A WIN Consortium phase I study exploring avelumab, palbociclib, and axitinib in advanced non-small cell lung cancer},
  author={Solomon, Benjamin and Callejo, Ana and Bar, Jair and Berchem, Guy and Bazhenova, Lyudmila and Saintigny, Pierre and Wunder, Fanny and Raynaud, Jacques and Girard, Nicolas and Lee, J Jack and others},
  journal={Cancer medicine},
  volume={11},
  number={14},
  pages={2790--2800},
  year={2022}
}

@misc{miyashita2022comprehensive,
  title={Comprehensive transcriptomic analysis of immune checkpoint markers in a pancancer cohort: Implications for response and resistance.},
  author={Miyashita, Hirotaka and Bevins, Nicholas J and Thangathurai, Kartheeswaran and Lee, Suzanna and Pabla, Sarabjot and Nesline, Mary and Glenn, Sean and Conroy, Jeffrey M and DePietro, Paul and Rubin, Eitan and others},
  year={2022},
  publisher={American Society of Clinical Oncology}
}

@article{lazar2022transcriptomics,
  title={Transcriptomics in Tumor and Normal Lung Tissues Identify Patients With Early-Stage Non--Small-Cell Lung Cancer With High Risk of Postsurgery Recurrence Who May Benefit From Adjuvant Therapies},
  author={Lazar, Vladimir and Girard, Nicolas and Raymond, Eric and Martini, Jean-Fran{\c{c}}ois and Galbraith, Susan and Raynaud, Jacques and Bresson, Catherine and Solomon, Benjamin and Magidi, Shai and Nechushtan, Hovav and others},
  journal={JCO Precision Oncology},
  volume={6},
  pages={e2200072},
  year={2022},
  publisher={Wolters Kluwer Health}
}

@article{bornshten2022projection,
  title={Projection of Expression Profiles to Transcription Factor Activity Space Provides Added Information},
  author={Bornshten, Rut and Danilenko, Michael and Rubin, Eitan},
  journal={Genes},
  volume={13},
  number={10},
  pages={1819},
  year={2022},
  publisher={MDPI}
}

@article{huleihel2022rnaseq,
  title={RNASEQ ANALYSIS OF FACS SORTED SPERMATOGONIAL CELLS USED TO IDENTIFY MELANOCORTIN RECEPTOR 2 AS A NOVEL AND FUNCTIONAL MEMBRANE-ASSOCIATED SPERMATOGONIAL STEM CELL MARKER},
  author={Huleihel, Mahmoud and Abumadeghem, Ali and Rubin, Eitan and Lunenfeld, Eitan},
  journal={Fertility and Sterility},
  volume={118},
  number={4},
  pages={e240},
  year={2022},
  publisher={Elsevier}
}

@article{lazar2022comorbidity,
  title={Comorbidity between lung cancer and COVID-19 pneumonia: role of immunoregulatory gene transcripts in high ACE2-expressing normal lung},
  author={Lazar, Vladimir and Raynaud, Jacques and Magidi, Shai and Bresson, Catherine and Martini, Jean-Fran{\c{c}}ois and Galbraith, Susan and Wunder, Fanny and Onn, Amir and Batist, Gerald and Girard, Nicolas and others},
  journal={Therapeutic advances in medical oncology},
  volume={14},
  pages={17588359221133893},
  year={2022},
  publisher={SAGE Publications Sage UK: London, England}
}

@article{ahuja2021high,
  title={High levels of LINE-1 transposable elements expressed in Kaposi’s sarcoma-associated herpesvirus-related primary effusion lymphoma},
  author={Ahuja, Anuj and Journo, Guy and Eitan, Ron and Rubin, Eitan and Shamay, Meir},
  journal={Oncogene},
  volume={40},
  number={3},
  pages={536--550},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{mizrahi2021results,
  title={Results of an early second PCR test performed on SARS-CoV-2 positive patients may indicate risk for severe COVID-19},
  author={Mizrahi, Barak and Bivas-Benita, Maytal and Kalkstein, Nir and Akiva, Pinchas and Yanover, Chen and Yehezkelli, Yoav and Kessler, Yoav and Alon, Sharon Hermoni and Rubin, Eitan and Chodick, Gabriel},
  journal={medRxiv},
  pages={2021--02},
  year={2021},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{lee2021synthetic,
  title={Synthetic lethality-mediated precision oncology via the tumor transcriptome},
  author={Lee, Joo Sang and Nair, Nishanth Ulhas and Dinstag, Gal and Chapman, Lesley and Chung, Youngmin and Wang, Kun and Sinha, Sanju and Cha, Hongui and Kim, Dasol and Schperberg, Alexander V and others},
  journal={Cell},
  volume={184},
  number={9},
  pages={2487--2502},
  year={2021},
  publisher={Elsevier}
}

@article{lazar2021digital,
  title={Digital Display Precision Predictor: the prototype of a global biomarker model to guide treatments with targeted therapy and predict progression-free survival},
  author={Lazar, Vladimir and Magidi, Shai and Girard, Nicolas and Savignoni, Alexia and Martini, Jean-Fran{\c{c}}ois and Massimini, Giorgio and Bresson, Catherine and Berger, Raanan and Onn, Amir and Raynaud, Jacques and others},
  journal={npj Precision Oncology},
  volume={5},
  number={1},
  pages={33},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{mizrahi2021results,
  title={Results of an early second PCR test performed on SARS-CoV-2 positive patients may support risk assessment for severe COVID-19},
  author={Mizrahi, Barak and Bivas-Benita, Maytal and Kalkstein, Nir and Akiva, Pinchas and Yanover, Chen and Yehezkelli, Yoav and Kessler, Yoav and Alon, Sharon Hermoni and Rubin, Eitan and Chodick, Gabriel},
  journal={Scientific Reports},
  volume={11},
  number={1},
  pages={20463},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{janssen2020boris,
  title={BORIS/CTCFL promotes a switch from a proliferative towards an invasive phenotype in melanoma cells},
  author={Janssen, Sanne Marlijn and Moscona, Roy and Elchebly, Mounib and Papadakis, Andreas Ioannis and Redpath, Margaret and Wang, Hangjun and Rubin, Eitan and van Kempen, L{\'e}on Cornelis and Spatz, Alan},
  journal={Cell death discovery},
  volume={6},
  number={1},
  pages={1},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{toren2020gray,
  title={Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination},
  author={Toren, Dmitri and Kulaga, Anton and Jethva, Mineshbhai and Rubin, Eitan and Snezhkina, Anastasia V and Kudryavtseva, Anna V and Nowicki, Dmitry and Tacutu, Robi and Moskalev, Alexey A and Fraifeld, Vadim E},
  journal={Aging Cell},
  volume={19},
  number={7},
  pages={e13158},
  year={2020}
}

@article{lee2020whole,
  title={Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome},
  author={Lee, Joo Sang and Nair, Nishanth Ulhas and Chapman, Lesley and Sinha, Sanju and Wang, Kun and Cha, Houngui and Rubin, Eitan and Berger, Raanan and Lazar, Vladimir and Kurzrock, Razelle and others},
  journal={bioRxiv},
  pages={2020--02},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}

@article{ravkin2020direct,
  title={Direct comparison shows that mRNA-based diagnostics incorporate information which cannot be learned directly from genomic mutations},
  author={Ravkin, Hersh D and Givton, Ofer and Geffen, David B and Rubin, Eitan},
  journal={BMC bioinformatics},
  volume={21},
  pages={1--10},
  year={2020},
  publisher={BioMed Central}
}

@misc{solomon2020spring,
  title={SPRING: A Worldwide Innovative Network (WIN) Consortium phase I study of triple therapy (avelumab, axitinib, and palbociclib) in advanced non-small cell lung cancer (NSCLC) with genomic and transcriptomic correlates.},
  author={Solomon, Benjamin Maurice and Callejo, Ana and Bar, Jair and Berchem, Guy J and Bazhenova, Lyudmila and Saintigny, Pierre and Raymond, Eric and Girard, Nicolas and Sulaiman, Raed and Prouse, Bruce and others},
  year={2020},
  publisher={American Society of Clinical Oncology}
}

@article{rijensky2020identification,
  title={Identification of tumor antigens in the HLA peptidome of patient-derived xenograft tumors in mouse},
  author={Rijensky, Nataly Mancette and Shraga, Netta R Blondheim and Barnea, Eilon and Peled, Nir and Rosenbaum, Eli and Popovtzer, Aron and Stemmer, Solomon M and Livoff, Alejandro and Shlapobersky, Mark and Moskovits, Neta and others},
  journal={Molecular \& Cellular Proteomics},
  volume={19},
  number={8},
  pages={1360--1374},
  year={2020},
  publisher={Elsevier}
}

@article{brana2020961p,
  title={961P Genomic and transcriptomic profiling in head and neck tumours to identify treatment options: The WINTHER trial experience},
  author={Brana, I and Loriot, Y and Berger, Raanan and Rubin, Eitan and Rodon, Jordi and Miller, WH and Tsimberidou, AM and Saintigny, P and Dienstmann, R and Nuciforo, P and others},
  journal={Annals of Oncology},
  volume={31},
  pages={S679},
  year={2020},
  publisher={Elsevier}
}

@article{rodon2019genomic,
  title={Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial},
  author={Rodon, Jordi and Soria, Jean-Charles and Berger, Raanan and Miller, Wilson H and Rubin, Eitan and Kugel, Aleksandra and Tsimberidou, Apostolia and Saintigny, Pierre and Ackerstein, Aliza and Bra{\~n}a, Irene and others},
  journal={Nature medicine},
  volume={25},
  number={5},
  pages={751--758},
  year={2019},
  publisher={Nature Publishing Group US New York}
}

@article{solomon2019abstract,
  title={Abstract CT223: Survival Prolongation by Rationale INnovative Genomics (SPRING): An international WIN Consortium Phase I/II proof-of-concept study to explore the safety and efficacy of a tri-therapy approach using avelumab, palbociclib and axitinib in advanced/metastatic non-small cell lung cancer (NSCLC) with integrated genomic and transcriptomic correlates},
  author={Solomon, Benjamin and Felip, Enriqueta and Bar, Jair and Berchem, Guy and Bazhenova, Lyudmila and Saintigny, Pierre and Girard, Nicolas and Sulaiman, Raed and Bresson, Catherine and Wunder, Fanny and others},
  journal={Cancer Research},
  volume={79},
  number={13\_Supplement},
  pages={CT223--CT223},
  year={2019},
  publisher={The American Association for Cancer Research}
}

@article{pandya2019picot,
  title={PICOT binding to chromatin-associated EED negatively regulates cyclin D2 expression by increasing H3K27me3 at the CCND2 gene promoter},
  author={Pandya, Pinakin and Jethva, Minesh and Rubin, Eitan and Birnbaum, Ramon Y and Braiman, Alex and Isakov, Noah},
  journal={Cell Death \& Disease},
  volume={10},
  number={10},
  pages={685},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@article{solomon2019survival,
  title={Survival prolongation by rationale innovative genomics (SPRING): An international WIN consortium phase I study exploring safety and efficacy of avelumab, palbociclib, and axitinib in advanced non-small cell lung cancer (NSCLC) with integrated genomic and transcriptomic correlates},
  author={Solomon, B and Callejo, A and Bar, J and Berchem, G and Bazhenova, L and Saintigny, P and Raymond, E and Girard, N and Sulaiman, R and Bresson, C and others},
  journal={Annals of Oncology},
  volume={30},
  pages={v648},
  year={2019},
  publisher={Elsevier}
}

@inproceedings{solomon2019survival,
  title={Survival Prolongation by Rationale INnovative Genomics (SPRING): An international WIN Consortium Phase I/II proof-of-concept study to explore the safety and efficacy of a tri-therapy approach using avelumab, palbociclib and axitinib in advanced/metastatic non-small cell lung cancer (NSCLC) with integrated genomic and transcriptomic correlates},
  author={Solomon, Benjamin and Felip, Enriqueta and Bar, Jair and Berchem, Guy and Bazhenova, Lyudmila and Saintigny, Pierre and Girard, Nicolas and Sulaiman, Raed and Bresson, Catherine and Wunder, Fanny and others},
  booktitle={CANCER RESEARCH},
  volume={79},
  number={13},
  year={2019},
  organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}
}

@article{toren2019gray,
  title={Gray whale transcriptome reveals longevity adaptations associated with DNA repair, autophagy and ubiquitination},
  author={Toren, D and Kulaga, A and Jethva, M and Rubin, E and Snezhkina, AV and Kudryavtseva, AV and Nowicki, D and Tacutu, R and Moskalev, AA and Fraifeld, VE},
  journal={bioRxiv},
  pages={754218},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@misc{rodon2018winther,
  title={WINTHER: An international WIN Consortium precision medicine trial using genomic and transcriptomic analysis in patients with advanced malignancies.},
  author={Rodon, Jordi and Soria, Jean-Charles and Berger, Raanan and Miller, Wilson H and Lazar, Vladimir and Rubin, Eitan and Tsimberidou, Apostolia Maria and Saintigny, Pierre and Ackerstein, Aliza and Brana, Irene and others},
  year={2018},
  publisher={American Society of Clinical Oncology}
}

@article{spatz2018ma21,
  title={MA21. 09 Differential Gene Expression in Tumor and Normal Tissue Reveals New Insights in the Biology of Non-Small Cell Lung Carcinoma.},
  author={Spatz, A and Lazar, V and Rubin, E and Lach, K and Wang, H and Papadakis, A and Moscona, R and Jimenez, P and Kasymjanova, G and Cohen, V and others},
  journal={Journal of Thoracic Oncology},
  volume={13},
  number={10},
  pages={S432},
  year={2018},
  publisher={Elsevier}
}

@article{eyal2017pcm,
  title={PCM-SABRE: a platform for benchmarking and comparing outcome prediction methods in precision cancer medicine},
  author={Eyal-Altman, Noah and Last, Mark and Rubin, Eitan},
  journal={BMC bioinformatics},
  volume={18},
  pages={1--7},
  year={2017},
  publisher={BioMed Central}
}

@misc{soria2017winther,
  title={WINTHER: An international study to select rational therapeutics based on the analysis of matched tumor and normal biopsies in subjects with advanced malignancies.},
  author={Soria, Jean-Charles and Rodon Ahnert, Jordi and Berger, Raanan and Miller, Wilson H and Brana, Irene and Loriot, Yohann and Mughal, Tariq I and Lazar, Vladimir and Wunder, Fanny and Bresson, Catherine and others},
  year={2017},
  publisher={American Society of Clinical Oncology}
}

@article{shemesh2016survival,
  title={Survival in acute myeloid leukemia is associated with NKp44 splice variants},
  author={Shemesh, Avishai and Brusilovsky, Michael and Hadad, Uzi and Teltsh, Omri and Edri, Avishay and Rubin, Eitan and Campbell, Kerry S and Rosental, Benyamin and Porgador, Angel},
  journal={Oncotarget},
  volume={7},
  number={22},
  pages={32933},
  year={2016},
  publisher={Impact Journals, LLC}
}

@article{shemesh2016nkp44,
  title={NKp44 and NKp30 splice variant profiles in decidua and tumor tissues: a comparative viewpoint},
  author={Shemesh, Avishai and Kugel, Aleksandra and Steiner, Naama and Yezersky, Michal and Tirosh, Dan and Edri, Avishay and Teltsh, Omri and Rosental, Benyamin and Sheiner, Eyal and Rubin, Eitan and others},
  journal={Oncotarget},
  volume={7},
  number={43},
  pages={70912},
  year={2016},
  publisher={Impact Journals, LLC}
}

@article{lazar2015simplified,
  title={A simplified interventional mapping system (SIMS) for the selection of combinations of targeted treatments in non-small cell lung cancer},
  author={Lazar, Vladimir and Rubin, Eitan and Depil, Stephane and Pawitan, Yudi and Martini, Jean-Fran{\c{c}}ois and Gomez-Navarro, Jesus and Yver, Antoine and Kan, Zhengyin and Dry, Jonathan R and Kehren, Jeanne and others},
  journal={Oncotarget},
  volume={6},
  number={16},
  pages={14139},
  year={2015},
  publisher={Impact Journals, LLC}
}

@article{teltsh2015extracting,
  title={Extracting tumor tissue immune status from expression profiles: correlating renal cancer prognosis with tumor-associated immunome},
  author={Teltsh, Omri and Porgador, Angel and Rubin, Eitan},
  journal={Oncotarget},
  volume={6},
  number={32},
  pages={33191},
  year={2015},
  publisher={Impact Journals, LLC}
}

@article{rodon2015challenges,
  title={Challenges in initiating and conducting personalized cancer therapy trials: perspectives from WINTHER, a Worldwide Innovative Network (WIN) Consortium trial},
  author={Rodon, Jordi and Soria, Jean-Charles and Berger, Raanan and Batist, G and Tsimberidou, A and Bresson, C and Lee, JJ and Rubin, E and Onn, Amir and Schilsky, RL and others},
  journal={Annals of Oncology},
  volume={26},
  number={8},
  pages={1791--1798},
  year={2015},
  publisher={Elsevier}
}

@inproceedings{eyal2015comparison,
  title={Comparison of three classifiers for breast cancer outcome prediction},
  author={Eyal, Noa and Last, Mark and Rubin, Eitan},
  booktitle={Proceedings of the 16th International Conference on Engineering Applications of Neural Networks (INNS)},
  pages={1--6},
  year={2015}
}

@misc{mendelsohn2015therapeutic,
  title={Therapeutic Interventional Mapping System (TIMS): A novel strategy for the selection of tri-targeted therapy combinations for non-small cell lung cancer (NSCLC).},
  author={Mendelsohn, John and Lazar, Vladimir and Rubin, Eitan and Pawitan, Yudi and Bresson, Catherine and Soria, Jean-Charles and Eggermont, Alexander and Wunder, Fanny and Scoazec, Jean-Yves and Hong, Waun Ki and others},
  year={2015},
  publisher={American Society of Clinical Oncology}
}

@article{lazar2015simplified,
  title={A simplified interventional mapping system (SIMS) for the selection of combinations of},
  author={Lazar, Vladimir and Rubin, Eitan and Depil, Stephane},
  journal={Oncotarget, 6 (16)},
  year={2015}
}

@article{geifman2014promoting,
  title={Promoting precision cancer medicine through a community-driven knowledgebase},
  author={Geifman, Nophar and Haviv, Izhak and Kurzrock, Razelle and Rubin, Eitan},
  journal={Journal of personalized medicine},
  volume={4},
  number={4},
  pages={475--488},
  year={2014},
  publisher={Multidisciplinary Digital Publishing Institute}
}

@article{geifman2014community,
  title={a Community-Driven Knowledgebase},
  author={Geifman, Nophar and Haviv, Izhak and Kurzrock, Razelle and Rubin, Eitan},
  year={2014}
}

@article{geifman2013redefining,
  title={Redefining meaningful age groups in the context of disease},
  author={Geifman, Nophar and Cohen, Raphael and Rubin, Eitan},
  journal={Age},
  volume={35},
  pages={2357--2366},
  year={2013},
  publisher={Springer Netherlands}
}

@article{ragolsky2013suicidal,
  title={Suicidal thoughts are associated with platelet counts in adolescent inpatients},
  author={Ragolsky, Micha and Shimon, Hady and Shalev, Hadar and Weizman, Abraham and Rubin, Eitan},
  journal={Journal of Child and Adolescent Psychopharmacology},
  volume={23},
  number={1},
  pages={49--53},
  year={2013},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@article{geifman2013mouse,
  title={The mouse age phenome knowledgebase and disease-specific inter-species age mapping},
  author={Geifman, Nophar and Rubin, Eitan},
  journal={PLoS One},
  volume={8},
  number={12},
  pages={e81114},
  year={2013},
  publisher={Public Library of Science San Francisco, USA}
}

@article{bluher2012two,
  title={Two patterns of adipokine and other biomarker dynamics in a long-term weight loss intervention},
  author={Bl{\"u}her, Matthias and Rudich, Assaf and Kl{\"o}ting, Nora and Golan, Rachel and Henkin, Yaakov and Rubin, Eitan and Schwarzfuchs, Dan and Gepner, Yftach and Stampfer, Meir J and Fiedler, Martin and others},
  journal={Diabetes care},
  volume={35},
  number={2},
  pages={342--349},
  year={2012},
  publisher={American Diabetes Association}
}

@article{zamir2012tight,
  title={Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility},
  author={Zamir, Lyad and Zaretsky, Marianna and Fridman, Yearit and Ner-Gaon, Hadas and Rubin, Eitan and Aharoni, Amir},
  journal={Proceedings of the National Academy of Sciences},
  volume={109},
  number={7},
  pages={E406--E414},
  year={2012},
  publisher={National Academy of Sciences}
}

@article{kolusheva2012novel,
  title={A novel “reactomics” approach for cancer diagnostics},
  author={Kolusheva, Sofiya and Yossef, Rami and Kugel, Aleksandra and Hanin-Avraham, Nirit and Cohen, Meital and Rubin, Eitan and Porgador, Angel},
  journal={Sensors},
  volume={12},
  number={5},
  pages={5572--5585},
  year={2012},
  publisher={Molecular Diversity Preservation International (MDPI)}
}

@article{avital2012mitochondrial,
  title={Mitochondrial DNA heteroplasmy in diabetes and normal adults: role of acquired and inherited mutational patterns in twins},
  author={Avital, Gal and Buchshtav, Mor and Zhidkov, Ilia and Tuval, Jeanette and Dadon, Sarah and Rubin, Eitan and Glass, Dan and Spector, Timothy D and Mishmar, Dan},
  journal={Human molecular genetics},
  volume={21},
  number={19},
  pages={4214--4224},
  year={2012},
  publisher={Oxford University Press}
}

@article{markovich2012unsupervised,
  title={Unsupervised analysis of classical biomedical markers: robustness and medical relevance of patient clustering using bioinformatics tools},
  author={Markovich Gordon, Michal and Moser, Asher M and Rubin, Eitan},
  journal={PloS one},
  volume={7},
  number={3},
  pages={e29578},
  year={2012},
  publisher={Public Library of Science San Francisco, USA}
}

@article{geifman2012age,
  title={The age-phenome database},
  author={Geifman, Nophar and Rubin, Eitan},
  journal={SpringerPlus},
  volume={1},
  pages={1--8},
  year={2012},
  publisher={Springer International Publishing}
}

@article{kolusheva2012array,
  title={Array-based disease diagnostics using lipid/polydiacetylene vesicles encapsulated in a sol--gel matrix},
  author={Kolusheva, Sofiya and Yossef, Rami and Kugel, Aleksandra and Katz, Marina and Volinsky, Roman and Welt, M and Hadad, Uzi and Drory, Vivian and Kliger, Mark and Rubin, Eitan and others},
  journal={Analytical chemistry},
  volume={84},
  number={14},
  pages={5925--5931},
  year={2012},
  publisher={American Chemical Society}
}

@article{cohen2011serum,
  title={Serum apolipoproteins CI and C-III are reduced in stomach cancer patients: results from MALDI-based peptidome and immuno-based clinical assays},
  author={Cohen, Meital and Yossef, Rami and Erez, Tamir and Kugel, Aleksandra and Welt, Michael and Karpasas, Mark M and Bones, Jonathan and Rudd, Pauline M and Taieb, Julien and Boissin, Herve and others},
  journal={PloS one},
  volume={6},
  number={1},
  pages={e14540},
  year={2011},
  publisher={Public Library of Science}
}

@article{geifman2011towards,
  title={Towards an age-phenome knowledge-base},
  author={Geifman, Nophar and Rubin, Eitan},
  journal={BMC bioinformatics},
  volume={12},
  pages={1--9},
  year={2011},
  publisher={BioMed Central}
}

@article{zhidkov2011child,
  title={CHILD: a new tool for detecting low-abundance insertions and deletions in standard sequence traces},
  author={Zhidkov, Ilia and Cohen, Raphael and Geifman, Nophar and Mishmar, Dan and Rubin, Eitan},
  journal={Nucleic Acids Research},
  volume={39},
  number={7},
  pages={e47--e47},
  year={2011},
  publisher={Oxford University Press}
}

@article{rubin2011ethnic,
  title={Ethnic differences in age-related changes of postpartum hemoglobin levels},
  author={Rubin, Eitan and Gordon, Michal and Sergienko, Ruslan and Ragolsky, Micha and Lunenfeld, Eitan and Sheiner, Eyal},
  journal={Archives of gynecology and obstetrics},
  volume={283},
  pages={173--178},
  year={2011},
  publisher={Springer-Verlag}
}

@article{zhidkov2011mitobamannotator,
  title={MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences},
  author={Zhidkov, Ilia and Nagar, Tal and Mishmar, Dan and Rubin, Eitan},
  journal={Mitochondrion},
  volume={11},
  number={6},
  pages={924--928},
  year={2011},
  publisher={Elsevier}
}

@inproceedings{cohen2011informatics,
  title={An informatics approach to studying incidence and treatment of Epilepsy at Soroka Hospital},
  author={Cohen, R and Serlin, Y and Rubin, E and Elhadad, M and Shorer, Z and Afawi, Z},
  booktitle={JOURNAL OF MOLECULAR NEUROSCIENCE},
  volume={45},
  number={SUPPL 1},
  pages={S25--S26},
  year={2011},
  organization={HUMANA PRESS INC 999 RIVERVIEW DRIVE SUITE 208, TOTOWA, NJ 07512 USA}
}

@article{geifman2010neural,
  title={The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems},
  author={Geifman, Nophar and Monsonego, Alon and Rubin, Eitan},
  journal={BMC bioinformatics},
  volume={11},
  pages={1--14},
  year={2010},
  publisher={BioMed Central}
}

@incollection{blueher2010two,
  title={Two major patterns of dynamics in adipokine serum concentrations over 2 years of dietary weight-loss intervention},
  author={Blueher, M and Rudich, A and Kloeting, N and Golan, R and Rubin, E and Schwarzfuchs, D and Fiedler, M and Gepner, Y and Tangi, O and Stampfer, M},
  booktitle={Diabetologia},
  pages={S367},
  year={2010}
}

@article{zhidkov2009mtdna,
  title={MtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints},
  author={Zhidkov, Ilia and Livneh, Erez A and Rubin, Eitan and Mishmar, Dan},
  journal={Genome research},
  volume={19},
  number={4},
  pages={576--580},
  year={2009},
  publisher={Cold Spring Harbor Lab}
}

@article{snir2009proteins,
  title={Proteins Length and their Phenotypic Potential},
  author={Snir, Tom and Rubin, Eitan},
  journal={International Journal of Biomedical and Biological Engineering},
  volume={3},
  number={6},
  pages={320--324},
  year={2009}
}

@article{fliss2008reverse,
  title={Reverse translational bioinformatics: a bioinformatics assay of age, gender and clinical biomarkers},
  author={Fliss, Amit and Ragolsky, Micha and Rubin, Eitan},
  journal={Summit on translational bioinformatics},
  volume={2008},
  pages={11},
  year={2008},
  publisher={American Medical Informatics Association}
}

@article{ner2007comparative,
  title={Comparative cross-species alternative splicing in plants},
  author={Ner-Gaon, Hadas and Leviatan, Noam and Rubin, Eitan and Fluhr, Robert},
  journal={Plant physiology},
  volume={144},
  number={3},
  pages={1632--1641},
  year={2007},
  publisher={American Society of Plant Biologists}
}

@misc{rubin2006circumventing,
  title={Circumventing the cut-off for enrichment analysis},
  author={Rubin, Eitan},
  year={2006},
  publisher={Oxford University Press}
}

@misc{rubin2006list,
  title={List mania: interpreting microarray results with the L2L server},
  author={Rubin, Eitan},
  year={2006},
  publisher={Oxford University Press}
}

@article{broderick2006modeling,
  title={Modeling of Biological Systems: A Workshop Synopsis},
  author={Broderick, Gordon and Rubin, Eitan},
  journal={ComPlexUs},
  volume={3},
  number={4},
  pages={217--230},
  year={2006},
  publisher={Kerger}
}

@article{shachak2005applying,
  title={Applying instructional design theories to bioinformatics education in microarray analysis and primer design workshops},
  author={Shachak, Aviv and Ophir, Ron and Rubin, Eitan},
  journal={Cell Biology Education},
  volume={4},
  number={3},
  pages={199--206},
  year={2005},
  publisher={American Society for Cell Biology}
}

@article{rubin2005lapis,
  title={LAPIS: A TEXT EDITOR AND A SMART PARSER COMBINED.},
  author={Rubin, Eitan},
  journal={Briefings in Bioinformatics},
  volume={6},
  number={2},
  year={2005}
}

@article{rubin2005news,
  title={News section},
  author={Rubin, Eitan and Biery, Nancy J and Will, Hans-Martin},
  journal={Briefings in Bioinformatics},
  volume={6},
  number={2},
  pages={205--207},
  year={2005},
  publisher={London: H. Stewart Publications,[2000-}
}

@article{seckbach2005new,
  title={The New Avenues in Bioinformatics (Cellular Origin, Life in Extreme Habitats and Astrobiology)},
  author={Seckbach, Joseph and Rubin, Eitan},
  year={2005}
}

@article{ner2004intron,
  title={Intron retention is a major phenomenon in alternative splicing in Arabidopsis},
  author={Ner-Gaon, Hadas and Halachmi, Ronit and Savaldi-Goldstein, Sigal and Rubin, Eitan and Ophir, Ron and Fluhr, Robert},
  journal={The Plant Journal},
  volume={39},
  number={6},
  pages={877--885},
  year={2004},
  publisher={Blackwell Science Ltd Oxford, UK}
}

@article{ben2004biases,
  title={Biases and complex patterns in the residues flanking protein N-glycosylation sites},
  author={Ben-Dor, Shifra and Esterman, Nir and Rubin, Eitan and Sharon, Nathan},
  journal={Glycobiology},
  volume={14},
  number={2},
  pages={95--101},
  year={2004},
  publisher={Soc Glycobiology}
}

@misc{seckbach2004new,
  title={The new avenues in bioinformatics},
  author={Seckbach, Joseph and Rubin, Eitan},
  year={2004},
  publisher={Springer Netherlands Dordrecht}
}

@misc{grosu2004news,
  title={News section},
  author={Grosu, Paul and Rubin, Eitan},
  year={2004},
  publisher={Henry Stewart Publications}
}

@misc{grosu2004microarray,
  title={Microarray image quantification},
  author={Grosu, P and Rubin, E},
  year={2004},
  publisher={HENRY STEWART PUBLICATIONS RUSSELL HOUSE, 28/30 LITTLE RUSSELL ST, LONDON~…}
}

@article{rubin2004new,
  title={The new avenues in bioinformatics},
  author={Rubin, Eitan and Seckbach, Joseph},
  year={2004},
  publisher={Kluwer Academic Publishers}
}

@misc{palyi2004biological,
  title={Biological Chirality: A Tool of Information in vivo and in vitro},
  author={P{\'a}lyi, G and Zucchi, C and Bencze, L and Caglioti, L},
  journal={New Avenues in Bioinformatics},
  pages={81--98},
  year={2004},
  publisher={Springer: Berlin, Germany}
}

@article{gruso2004news,
  title={News section.},
  author={Gruso, Paul and Rubin, Eitan and Prilusky, Jaime and Iyer, Lakshmanan},
  journal={Briefings in Bioinformatics},
  volume={5},
  number={1},
  year={2004}
}

@inproceedings{ben2003training,
  title={Training and support for bioinformatics: theoretical and practical aspects},
  author={Ben-Dor, S and Butcher, S and Iyer, KL and Kelso, J and Littlejohn, T and Shachak, A and Rubin, E},
  booktitle={Intelligent Systems for Molecular Biology (ISMB) conference, Brisbane, Australia},
  year={2003}
}

@article{pietrokovski2003advanced,
  title={Advanced topics in bioinformatics},
  author={Pietrokovski, Shmuel and Rubin, Eitan},
  year={2003}
}

@article{rubin2001structure,
  title={Structure and evolution of the hAT transposon superfamily},
  author={Rubin, Eitan and Lithwick, Gila and Levy, Avraham A},
  journal={Genetics},
  volume={158},
  number={3},
  pages={949--957},
  year={2001},
  publisher={Oxford University Press}
}

@phdthesis{rubin1999evolution,
  title={Evolution of the Ac-Ds transposable element family},
  author={Rubin, Eitan},
  year={1999},
  school={The Weizmann Institute of Science (Israel)}
}

@article{rubin1997abortive,
  title={Abortive gap repair: underlying mechanism for Ds element formation},
  author={Rubin, Eitan and Levy, Avraham A},
  journal={Molecular and Cellular Biology},
  year={1997},
  publisher={Taylor \& Francis}
}

@article{rubin1996mathematical,
  title={A mathematical model and a computerized simulation of PCR using complex templates},
  author={Rubin, Eitan and Levy, Avraham A},
  journal={Nucleic acids research},
  volume={24},
  number={18},
  pages={3538--3545},
  year={1996},
  publisher={Oxford Univ Press}
}

@article{levy1996binding,
  title={Binding of Nicotiana nuclear proteins to the subterminal regions of the Ac transposable element},
  author={Levy, Avraham A and Fridlender, Marcelo and Hanania, Uri and Rubin, Eitan and Sitrit, Yaron},
  journal={Molecular and General Genetics MGG},
  volume={251},
  pages={436--441},
  year={1996},
  publisher={Springer-Verlag}
}

@article{rubin1996evolution,
  title={Evolution of Ac/Ds transposable elements.},
  author={Rubin, E and Levy, AA},
  year={1996}
}

@article{altschulergene,
  title={A gene set repository for model organisms},
  author={Altschuler, Josiah and Rubin, Eitan and Regev, Aviv}
}

@article{rubinbiases,
  title={Biases and Complex Patterns in the Residues Flanking Protein N-glycosylation Sites},
  author={Rubin, E and Ben-Dor, S and Sharon, N}
}

@article{rubintraining,
  title={Training and Support for Bioinformatics: Theoretical and Practical Aspects},
  author={Rubin, Eitan and Ben-Dor, Shifra and Butcher, Sarah and Iyer, Lakshmanan K and Kelso, Janet and Littlejohn, Tim and Shachak, Aviv}
}

@article{lazartranscriptomics,
  title={Transcriptomics in Tumor and Normal Tissues and Precision Oncology Algorithms Identify Early-Stage NSCLC Patients with High Risk of Post-Surgery Recurrence Who May Benefit from Adjuvant Therapies},
  author={Lazar, Vladimir and Raymond, Eric and GIRARD, Nicolas and Martini, Jean-Fran{\c{c}}ois and Galbraith, Susan and Raynaud, Jacques and Bresson, Catherine and Solomon, Benjamin and Magidi, Shai and Nechushtan, Hovav and others}
}

@article{miyashitadiverse,
  title={Diverse RNA expression patterns of T cell priming markers in various solid tumors and their clinical implication},
  author={Miyashita, Hirotaka and Kurzrock, Razelle and Bevins, Nicholas and Thangathurai, Kartheeswaran and Lee, Suzanna and Pabla, Sarabjot and Nesline, Mary and Glenn, Sean and Conroy, Jeffrey M and DePietro, Paul and others}
}

@article{mosconaatac,
  title={ATAC-Seq and RNA-Seq combined analysis elucidates the impact of BORIS/CTCFL on melanoma progression, mediated by chromatin accessibility and gene expression alterations},
  author={Moscona, Roy and Janssen, Sanne Marlijn and Elchebly, Mounib and Papadakis, Andreas Ioannis and Spatz, Alan and Rubin, Eitan}
}