Publications

2021

• Gussow AB, Koonin EV*, Auslander N. Identification of combinations of somatic mutations that predict cancer survival and immunotherapy benefit. NAR Cancer

• Patkar S*, Heselmeyer-Haddad K*, Auslander N*, Hirsch D, Camps J, Bronder D, Brown M, Chen WD, Lokanga R, Wangsa D, Wangsa D, Hu Y, Lischka A, Braun R, Emons G, Ghadimi BM, Gaedcke J, Grade M, Montagna C, Lazebnik Y, Difilippantonio MJ, Habermann J, Auer G, Ruppin E*, Ried T. Hard-wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer-type-specific aneuploidies. Genome Medicine

• Auslander N, Gussow AB, Koonin EV. Incorporating machine learning into established bioinformatics frameworks. International Journal of Molecular Sciences

2020

• Auslander M#, Ramos DM#, Zelaya I, Karathia H, Crawford TO, Schäffer AA, Sumner CJ, Ruppin E*. The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases. Molecular Systems Biology

• Gussow AB#, Auslander N#, Wolf YI, Koonin EV*. Prediction of the incubation period for COVID-19 and future virus disease outbreaks. BMC Biology

• Auslander N*, Gussow AB*, Benler S, Wolf YI, Koonin EV*. Seeker: Alignment-free identification of bacteriophage genomes by deep learning. Nucleic Acid Research

• Dattilo R, Mottini C, Camera E, Lamolinara A, Auslander N, Doglioni G, Muscolini M, Tang W, Planque M, Ercolani C, Buglioni S, Manni I, Trisciuoglio D, Boe A, Grande S, Luciani AM, Iezzi M, Ciliberto G, Ambs S, De Maria R, Fendt S-M, Ruppin E*, Cardone L. Pyrvinium pamoate induces death of triple-negative breast cancer stem-like cells and reduces metastases through effects on lipid anabolism. Cancer Research

• Gussow AB#, Auslander N#, Faure G, Wolf YI, Zhang F, Koonin EV*. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proceedings of the National Academy of Sciences

• Braun R, Anthuber L, Hirsch D, Wangsa D, Lack J, McNeil NE, Heselmeyer-Haddad K, Torres I, Wangsa D, Brown M, Tubbs A, Auslander N, Gertz EM, Brauer PR, Cam MC, Sackett DL, Habermann JK, Nussenzweig A, Ruppin E*, Zhang Z, Rosenberg DW, Ried T. Single-cell-derived primary rectal carcinoma cell lines reflect intratumor heterogeneity associated with treatment response. Clinical Cancer Research

• Auslander N#, Wolf YI, Koonin EV*. Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability. Nature Communications

2019

• Kwon SM, Budhu A, Woo HG, Chaisaingmongkol J, Dang H, Forgues M, Harris CC, Zhang G, Auslander N, Ruppin E*, Mahidol C, Ruchirawat M, Wang XW. Functional genomic complexity defines intratumor heterogeneity and tumor aggressiveness in liver cancer. Scientific Reports

• Auslander N#, Wolf YI,Shabalina SA, Koonin EV*. A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk. F1000Research

• Auslander N, Wolf YI, Koonin EV*. In silico learning of tumor evolution through mutational time series.Proceedings of the National Academy of Sciences

• Gal O, Auslander N, Fan Y, Meerzaman D. Predicting complete remission of acute myeloid leukemia: Machine learning applied to gene expression. Cancer Informatics

2018

• Auslander N, Zhang G, Lee JS, Frederick DT, Miao B, Moll T, Tian T, Wei Z, Sullivan RJ, Madan S, Boland G, Flaherty K, Herlyn M, Ruppin E*. Robust prediction of therapeutic response to immune checkpoint blockade therapy i­n metastatic melanoma. Nature Medicine

•  Lee JS, Adler L, Karathia H, Carmel N, Rabinovich S, Auslander N, Keshet R, Stettner N, Silberman A, Agemy L, Helbling D, Eilam R, Sun Q, Brandis A, Malitsky S, Itkin M, Weiss H, Pinto S, Kalaora S, Levy R, Barnea E, Admon A,  Dimmock D, Stern Ginossar N, Scherz A, Nagamani SCS, Unda M, Elhasid R, Carracedo A, Samuels Y, Hannenhalli S, Ruppin E*, Erez A. Urea cycle dysregulation in cancer results in a pyrimidine rich mutation bias associated with enhanced response to immune checkpoint therapies. Cell

• Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, McGarry L, James D, Amzallag A, Park SG, Cheng K, Robinson W, Atias D, Stossel C, Buzhor E, Stein G, Waterfall JJ, Meltzer PS, Golan T, Hannenhalli S, Gottlieb E, Benes CH, Samuels Y, Shanks E, Ruppin E*. ­­Harnessing synthetic lethality to predict the response to cancer treatment. Nature Communications

2017

• Auslander N, Cunningham CE, Toosi BM, McEwen E, Yizhak K, Vizeacoumar FS, Parameswaran S, Gonen N, Freywald A, Vizeacoumar FJ, Ruppin E*. An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer. Molecular Systems Biology

• Ferber S, Tiram G, Sousa-Herves A, Eldar-Boock A, Krivitsky A, Scomparin A, Yeini E, Ofek P, Ben-Shushan D, Vossen LI, Licha K, Grossman R, Ram Z, Henkin J, Ruppin E*, Auslander N, Haag R, Calderón M, Satchi-Fainaro R. Co-targeting the tumor endothelium and P-selectin-expressing glioblastoma cells leads to a remarkable therapeutic outcome. eLIFE

• Emons G, Spitzner M, Reineke S, Möller J, Auslander N, Kramer F, Beissbarth T, Wolff HA, Rave-Fränk M, Heßmann E, Gaedcke J, Ghadimi BM, Johnsen SA, Ried T, Grade M. Chemoradiotherapy resistance in colorectal cancer cells in mediated Wnt/β-catenin signaling. Molecular Cancer Research

2016

• Auslander N#, Wagner A, Oberhardt M, Ruppin E*. Data-driven metabolic pathway compositions enhance cancer survival prediction. PLOS Computational Biology

• Auslander N#, Yizhak K#, Weinstock A#, Budhu A, Tang W, Wang XW, Ambs S, Ruppin E*. A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer. Scientific Reports

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