| Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm X Li, S MacArthur, R Bourgon, D Nix, DA Pollard, VN Iyer, A Hechmer, ... PLoS biology 6 (2), e27, 2008 | 595 | 2008 |
| Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic … S MacArthur, XY Li, J Li, JB Brown, HC Chu, L Zeng, BP Grondona, ... Genome biology 10, 1-26, 2009 | 400 | 2009 |
| A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm CC Fowlkes, CLL Hendriks, SVE Keränen, GH Weber, O Rübel, ... Cell 133 (2), 364-374, 2008 | 324 | 2008 |
| Three-dimensional morphology and gene expression in the Drosophilablastoderm at cellular resolution I: data acquisition pipeline CL Luengo Hendriks, SVE Keränen, CC Fowlkes, L Simirenko, GH Weber, ... Genome biology 7, 1-21, 2006 | 168 | 2006 |
| PointCloudXplore: Visual analysis of 3D gene expression data using physical views and parallel coordinates. O Rübel, GH Weber, SVE Keränen, CC Fowlkes, CLL Hendriks, ... EuroVis, 203-210, 2006 | 85 | 2006 |
| A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila CC Fowlkes, KB Eckenrode, MD Bragdon, M Meyer, Z Wunderlich, ... PLoS Genetics 7 (10), e1002346, 2011 | 58 | 2011 |
| Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm L Xy, S MacArthur, R Bourgon, D Nix, DA Pollard, VN Iyer, A Hechmer, ... PLoS Biol 6 (2), e27, 2008 | 25 | 2008 |
| An integrated computer-aided design and manufacturing workflow for synthetic biology E Oberortner, R Evans, X Meng, S Nath, H Plahar, L Simirenko, A Tarver, ... DNA cloning and assembly: methods and protocols, 3-18, 2020 | 4 | 2020 |
| Correction: transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm X Li, S MacArthur, R Bourgon, D Nix, DA Pollard, VN Iyer, A Hechmer, ... PLoS Biology 6 (7), e190, 2008 | 4 | 2008 |
| gRNA-SeqRET: a universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes L Simirenko, JF Cheng, I Blaby Frontiers in Bioengineering and Biotechnology 11, 1217811, 2023 | 2 | 2023 |
| The Joint Genome Institute's synthetic biology internal review process L Simirenko, M Harmon-Smith, A Visel, EM Rubin, NJ Hillson Journal of Responsible Innovation 2 (1), 133-136, 2015 | 2 | 2015 |
| Constructing a quantitative spatio-temporal atlas of gene expression in Drosophila blastoderm CC Fowlkes, CLL Hendriks, SVE Keränen, GH Weber, O Rübel, ... Cell (Accepted January 2008), 0 | 1 | |
| SynBio QC Dual Barcode QC (DBC) v1. 0 L Simirenko, D Scott Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States), 2024 | | 2024 |
| Synthetic Biology PacBio/JAWS QC Analysis (PBJ) v3. 0 L Simirenko, D Scott Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States), 2024 | | 2024 |
| SynBio QC-Library QC (LibQC) v2. 0.0 L Simirenko, D Scott Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States), 2022 | | 2022 |
| gRNA-Seqret Version 2: Genome Wide Guide RNA Design and Sequence Extraction Tool for Any Genome L Simirenko, I Blaby, JF Cheng 2022 Synthetic Biology: Engineering, Evolution & Design (SEED), 2022 | | 2022 |
| guideRna and Sequence Region Extraction Tool (gRNA-SeqRET) v1. 0 L Simirenko Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States), 2020 | | 2020 |
| SynTrack: DNA Assembly Workflow Management (SynTrack) v2. 0.1 X MENG, L SIMIRENKO Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States), 2016 | | 2016 |
| Virtual embryos as tools for 3d gene expression analyses SVE Keranen, CLL Hendriks, CC Fowlkes, L Simirenko, GH Weber, ... | | 2007 |
| Virtual embryos as tools for 3D gene expression analyses CLL Hendriks, CC Fowlkes, SVE Keränen, L Simirenko, GH Weber, ... | | 2007 |
