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Publications

* Equal contribution # Corresponding author

Selected Publications

  1. Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer#. BioRxiv (2024). Optimizing Sequence Design Strategies for Perturbation MPRAs: A Computational Evaluation Framework. 

  2. Jiayi Liu, Anat Kreimer#, Wei Vivian Li#. Briefings in Bioinformatics (2023). Differential variability analysis of single-cell gene expression data. https://doi.org/10.1093/bib/bbad294

  3. Justin Koesterich, Joon-Yong An, Fumitaka Inoue, Ajuni Sohota, Nadav Ahituv, Stephan J. Sanders#, Anat Kreimer#. International Journal of Molecular Sciences (2023). Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. https://doi.org/10.3390/ijms24043509

  4. Anat Kreimer*#, Tal Ashuach*, Fumitaka Inoue*, Alex Khodaverdian, Chengyu Deng, Nir Yosef# , Nadav Ahituv#. Nature Communications (2022). Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Volume: 13, Article number: 1504. https://doi.org/10.1038/s41467-022-28659-0

  5. Fumitaka Inoue*, Anat Kreimer*, Tal Ashuach, Nadav Ahituv, Nir Yosef. Cell Stem Cell (2019). Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.  doi:https://doi.org/10.1016/j.stem.2019.09.010

  6. Anat Kreimer*#, Zhongxia Yan*, Nadav Ahituv, Nir Yosef#. Human Mutation (2019). Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types. doi: https://doi.org/10.1002/humu.23820 Top preforming method for predicting functional variants in disease associated regulatory elements in the Critical Assessment of Genome Interpretation (CAGI5) challenge.

  7. Anat Kreimer#, Haoyang Zeng, Matthew D Edwards, Yuchun Guo, Kevin Tian, Sunyoung Shin, Rene Welch, Michael Wainberg, Rahul Mohan, Nicholas A Sinnott-Armstrong, Yue Li, Gökcen Eraslan, Talal Bin AMIN, Jonathan Goke, Nikola S Mueller, Manolis Kellis, Anshul Kundaje, Michael A Beer, Sunduz Keles, David K Gifford, Nir Yosef#. Human Mutation (2017). Predicting gene expression in massively parallel reporter assays: a comparative study. doi:10.1002/humu.23197

  8. Tal Ashuach*, David Sebastian Fischer*, Anat Kreimer, Nadav Ahituv, Fabian J Theis, Nir Yosef. Genome Biology (2019). MPRAnalyze -A statistical framework for Massively Parallel Reporter Assays. Volume 20, Article number: 183. doi:10.1186/s13059-019-1787-z

  9. Dustin Shigaki, Orit Adato, Aashish Adhikar, Shengcheng Dong, Alex Hawkins-Hooker, Fumitaka Inoue, Henry Kenlay, Beth Martin, Ayoti Patra, Dmitry Penzar, Max Schubach, Chenling Xiong, Zhongxia Yan, Alan Boyle, Anat Kreimer, Ivan Kulakovskiy, John Reid, Ron Unger, Nir Yosef, Jay Shendure, Nadav Ahituv, Martin Kircher, Michael A Beer. Human Mutation (2019). Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay. doi: https://doi.org/10.1002/humu.23797

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  1. Anat Kreimer and Nir Yosef. Evaluation of Davis et al.: Exploring Sequence of Determinants of Transcriptional Regulation - The Case of c-AMP Response Element. Cell Systems. (2020) https://doi.org/10.1016/j.cels.2020.07.001

  2. Gracie Gordon, Fumitaka Inoue , Beth Martin , Max Schubach , Vikram Agarwal , Sean Whalen , Shiyun Feng , Jingjing Zhao , Tal Ashuach , Ryan Ziffra , Anat Kreimer , Ilias Georgakopoulos-Soares , Nir Yosef , Chun Ye , Katherine Pollard , Martin Kircher , Jay Shendure, Nadav Ahituv. Nature Protocols (2020). lentiMPRA & MPRAflow for high-throughput functional characterization of gene regulatory elements. Doi: 10.1038/s41596-020-0333-5

  3. Ryan S Ziffra, Chang N Kim, Amy Wilfert, Tychele N Turner, Maximilian Haeussler, Alex M Casella, Pawel F Przytycki, Anat Kreimer, Katherine S Pollard, Seth A Ament, Evan E Eichler, Nadav Ahituv, Tomasz J Nowakowski. Nature (2020). Single cell epigenomic atlas of the developing human brain and organoids.

  4. Ann H Ryu, Walter L Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv. Scientific Reports (2017). Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Volume 7, Article number: 7533. doi:10.1038/s41598-017-07757-w

  5. Jonathan M Carlson, Victor Y Du, Nico Pfeifer, Anju Bansal, Vincent Y F Tan, Karen Power, Chanson J Brumme, Anat Kreimer, Charles E DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A Brockman, Jill Gilmour, Matt A Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M Allen, Philip J R Goulder, Zabrina L Brumme, Eric Hunter and Paul A Goepfert. Nature Medicine (2016). Impact of pre-adapted HIV transmission. 22 (6):606–613. doi:10.1038/nm.4100

  6. Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich and Elhanan Borenstein. BMC Bioinformatics (2015). NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. 16:164 doi:10.1186/s12859-015-0588-y.

  7. Anat Kreimer# and Itsik Pe’er. PLOS Genetics (2014). Co-regulated transcripts associated to cooperating eSNPs define bi-fan motifs in human gene networks. doi: 10.1371/journal.pgen.1004587.

  8. Anat Kreimer# and Itsik Pe’er. Variants in exons and in transcription factors affect gene expression in trans. Genome Biology (2013), 14:R71. doi:10.1186/gb-2013-14-7-r71

  9. Anat Kreimer*#, Adi Doron-Faigenboim*, Elhanan Borenstein and Shiri Freilich#. Bioinformatics, (2012). NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species. 28 (16):2195-2197. doi:10.1093/bioinformatics/bts323

  10. Anat Kreimer#, Oren Litvin, Ke Hao, Cliona Molony, Dana Pe’er and Itsik Pe’er. Nucleic Acids Research (2012). Inference of modules associated to eQTLs. doi: 10.1093/nar/gks269

  11. Shiri Freilich, Anat Kreimer, Isacc Meilijson, Uri Gophna, Roded Sharan & Eytan Ruppin. Nucleic Acids Research (2010). The large scale organization of the bacterial ecological-interaction network. doi:10.1093/nar/gkq118

  12. Shiri Freilich*, Anat Kreimer*, Elhanan Borenstein, Uri Gophna, Roded Sharan, and Eytan Ruppin. PLOS Computational biology (2010). Decoupling Environment-Dependant and Independent Genetic Robustness across Bacterial Species. Volume: 6, Issue:

  13. Shiri Freilich*, Anat Kreimer*, Elhanan Borenstein, Nir Yosef, Uri Gophna, Roded Sharan, and Eytan Ruppin. Genome Biology (2009). Metabolic-network driven analysis of bacterial ecological strategies. 10(6):R61.

  14. Anat Kreimer*, Elhanan Borenstein*, Uri Gophna and Eytan Ruppin. Proceedings of the National Academy of Sciences (2008). The Evolution of Modularity in Bacterial Metabolic Networks. Volume: 105, No. 19, Pages: 6976–6981.

All Publications

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