Design of 240,000 orthogonal 25mer DNA barcode probes

EMBOSS: the European molecular biology open software suite.

Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466 · see citing works

Functional profiling of the Saccharomyces cerevisiae genome

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316 · see citing works

Functional Characterization of the <i>S. cerevisiae</i> Genome by Gene Deletion and Parallel Analysis

Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) · Science · doi:10.1126/science.285.5429.901 · Cited by 3,953 · see citing works

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.95.4.1460 · Cited by 2,791 · see citing works

UNAFold

Markham, N. R., & Zuker, M. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-429-6_1 · Cited by 1,026 · see citing works

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

Hillenmeyer, M. E., Fung, E., Wildenhain, J., Pierce, S. E., Hoon, S. S., Lee, W., Proctor, M. J., St.Onge, R. P., Tyers, M., Koller, D., et al. (2008) · Science · doi:10.1126/science.1150021 · Cited by 978 · see citing works

Second-generation shRNA libraries covering the mouse and human genomes

Silva, J. M., Li, M. Z., Chang, K. C. N., Ge, W., Golding, M. C., Rickles, R. J., Siolas, D., Hu, G., Paddison, P. J., Schlabach, M. R., et al. (2005) · Nature Genetics · doi:10.1038/ng1650 · Cited by 624 · see citing works

Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays

Kane, M. D. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.22.4552 · Cited by 618 · see citing works

Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar–coding strategy

Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittmann, M., & Davis, R. W. (1996) · Nature Genetics · doi:10.1038/ng1296-450 · Cited by 569 · see citing works

OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach

Rouillard, J. M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg426 · Cited by 419 · see citing works

Human ORFeome Version 1.1: A Platform for Reverse ProteomicsPreprint

Rual, J.-F. M., Hirozane-Kishikawa, T., Hao, T., Bertin, N., Li, S., Dricot, A., Li, N., Rosenberg, J., Lamesch, P., Vidalain, P., et al. (2004) · Genome Research · doi:10.1101/gr.2973604 · Cited by 242 · see citing works

Empirical Establishment of Oligonucleotide Probe Design Criteria

He, Z., Wu, L.-Y., Li, X., Fields, M., & Zhou, J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.7.3753-3760.2005 · Cited by 179 · see citing works

Oxidative stress is the new stress

Gingrich, J. A. (2005) · Nature Medicine · doi:10.1038/nm1205-1281 · Cited by 163 · see citing works

Selection of oligonucleotide probes for protein coding sequences

Wang, X., & Seed, B. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg086 · Cited by 153 · see citing works

A unique and universal molecular barcode array

Pierce, S. E., Fung, E., Jaramillo, D. F., Chu, A. M., Davis, R. W., Nislow, C., & Giaever, G. N. (2006) · Nature Methods · doi:10.1038/nmeth905 · Cited by 115 · see citing works

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

Nielsen, H. B. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg622 · Cited by 113 · see citing works

Oligonucleotide microarrays: widely applied poorly understood

Pozhitkov, A. E., Tautz, D., & Noble, P. A. (2007) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elm014 · Cited by 69 · see citing works

Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

Hu, G., Llinás, M., Li, J., Preiser, P. R., & Bozdech, Z. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-350 · Cited by 59 · see citing works

Orientation of DNA on a surface from simulation

Wong, K., & Pettitt, B. M. (2004) · Biopolymers · doi:10.1002/bip.20004 · Cited by 59 · see citing works

A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets

Wei, H., Kuan, P. F., Tian, S., Yang, C., Nie, J., Sengupta, S., Ruotti, V., Jónsdóttir, G. A., Keleş, S., Thomson, J. A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn133 · Cited by 40 · see citing works

Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips

Wang, Y., Miao, Z., Pommier, Y. G., Kawasaki, E. S., & Player, A. N. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm306 · Cited by 28 · see citing works

Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays

Wu, C., Zhao, H., Baggerly, K., Carta, R., & Zhang, L. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm271 · Cited by 26 · see citing works

RNA-Guided Human Genome Engineering via Cas9

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210 · see citing works

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969 · see citing works

Random access in large-scale DNA data storage

Organick, L., Ang, S. D., Chen, Y.-J., Lopez, R., Yekhanin, S., Makarychev, K., Racz, M. Z., Kamath, G., Gopalan, P., Nguyen, B., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4079 · Cited by 775 · see citing works

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612826113 · Cited by 557 · see citing works

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

Kishi, J. Y., Lapan, S. W., Beliveau, B. J., West, E. R., Zhu, A., Sasaki, H. M., Saka, S. K., Wang, Y., Cepko, C. L., & Yin, P. (2019) · Nature Methods · doi:10.1038/s41592-019-0404-0 · Cited by 440 · see citing works

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

Tsanov, N., Samacoïts, A., Chouaib, R., Traboulsi, A.-M., Gostan, T., Weber, C., Zimmer, C., Zibara, K., Walter, T., Peter, M., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw784 · Cited by 432 · see citing works

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Alon, S., Goodwin, D., Sinha, A., Wassie, A. T., Chen, F., Daugharthy, E. R., Bando, Y., Kajita, A., Xue, A. G., Marrett, K., et al. (2021) · Science · doi:10.1126/science.aax2656 · Cited by 413 · see citing works

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

Chari, R., Mali, P., Moosburner, M., & Church, G. M. (2015) · Nature Methods · doi:10.1038/nmeth.3473 · Cited by 394 · see citing works

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

Beliveau, B. J., Boettiger, A. N., Avendaño, M. S., Jungmann, R., McCole, R. B., Joyce, E. F., Kim-Kiselak, C., Bantignies, F., Fonseka, C. Y., Erceg, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms8147 · Cited by 384 · see citing works

Programmable molecular recognition based on the geometry of DNA nanostructures

Woo, S., & Rothemund, P. W. K. (2011) · Nature Chemistry · doi:10.1038/nchem.1070 · Cited by 375 · see citing works

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes

Bentzen, A. K., Marquard, A. M., Lyngaa, R., Saini, S. K., Ramskov, S., Donia, M., Such, L., Furness, A. J. S., McGranahan, N., Rosenthal, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3662 · Cited by 332 · see citing works

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

Hafner, M., Renwick, N. M., Brown, M., Mihailović, A., Holoch, D., Lin, C. P., Pena, J., Nusbaum, J. D., Morozov, P. S., Ludwig, J., et al. (2011) · RNA · doi:10.1261/rna.2799511 · Cited by 329 · see citing works

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

LeProust, E. M., Peck, B. J., Spirin, K., McCuen, H. B., Moore, B., Namsaraev, E., & Caruthers, M. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq163 · Cited by 326 · see citing works

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

Kosuri, S., Eroshenko, N., LeProust, E. M., Super, M., Way, J. C., Li, J. B., & Church, G. M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1716 · Cited by 266 · see citing works

Spatial atlas of the mouse central nervous system at molecular resolution

Shi, H., He, Y., Zhou, Y., Huang, J., Maher, K., Wang, B., Tang, Z., Luo, S., Tan, P., Wu, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06569-5 · Cited by 244 · see citing works

RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)

Moffitt, J. R., & Zhuang, X. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.03.020 · Cited by 219 · see citing works

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

Smith, A. M., Heisler, L. E., St.Onge, R. P., Farias‐Hesson, E., Wallace, I. M., Bodeau, J. P., Harris, A. N., Perry, K. M., Giaever, G. N., Pourmand, N., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq368 · Cited by 207 · see citing works

A transcriptomic axis predicts state modulation of cortical interneurons

Bugeon, S., Duffield, J. A. M., Dipoppa, M., Ritoux, A., Prankerd, I., Nicoloutsopoulos, D., Orme, D., Shinn, M., Peng, H., Forrest, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04915-7 · Cited by 177 · see citing works

Spatial organization shapes the turnover of a bacterial transcriptome

Moffitt, J. R., Pandey, S., Boettiger, A. N., Wang, S. S., & Zhuang, X. (2016) · eLife · doi:10.7554/elife.13065 · Cited by 164 · see citing works

Multiplexed detection of RNA using MERFISH and branched DNA amplification

Xia, C., Babcock, H. P., Moffitt, J. R., & Zhuang, X. (2019) · Scientific Reports · doi:10.1038/s41598-019-43943-8 · Cited by 160 · see citing works

Spatial proteomics in neurons at single-protein resolution

Unterauer, E. M., Boushehri, S. S., Jevdokimenko, K., Masullo, L. A., Ganji, M., Sograte‐Idrissi, S., Kowalewski, R., Strauss, S., Reinhardt, S., Perovic, A., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.045 · Cited by 152 · see citing works

T cell antigen discovery

Joglekar, A. V., & Li, G. (2020) · Nature Methods · doi:10.1038/s41592-020-0867-z · Cited by 150 · see citing works

Random access DNA memory using Boolean search in an archival file storage system

Banal, J. L., Shepherd, T. R., Berleant, J., Huang, H., Reyes, M., Ackerman, C. M., Blainey, P. C., & Bathe, M. (2021) · Nature Materials · doi:10.1038/s41563-021-01021-3 · Cited by 143 · see citing works

Neoantigen-reactive CD8+ T cells affect clinical outcome of adoptive cell therapy with tumor-infiltrating lymphocytes in melanoma

Kristensen, N. P., Heeke, C., Tvingsholm, S. A., Borch, A., Draghi, A., Crowther, M. D., Carri, I., Munk, K. K., Holm, J. S., Bjerregaard, A.-M., et al. (2021) · Journal of Clinical Investigation · doi:10.1172/jci150535 · Cited by 140 · see citing works

Probing the physical limits of reliable DNA data retrieval.

Organick, L., Chen, Y.-J., Dumas Ang, S., Lopez, R., Liu, X., Strauss, K., & Ceze, L. (2020) · Nature Communications · doi:10.1038/s41467-020-14319-8 · Cited by 135 · see citing works

Progress and Opportunities in Soft Photonics and Biologically Inspired Optics

Kolle, M., & Lee, S. (2017) · Advanced Materials · doi:10.1002/adma.201702669 · Cited by 131 · see citing works

CD8+ T cells from patients with narcolepsy and healthy controls recognize hypocretin neuron-specific antigens

Pedersen, N. W., Holm, A., Kristensen, N. P., Bjerregaard, A.-M., Bentzen, A. K., Marquard, A. M., Tamhane, T., Burgdorf, K. S., Ullum, H., Jennum, P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08774-1 · Cited by 117 · see citing works

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing

Hafner, M., Renwick, N. M., Farazi, T. A., Mihailović, A., Pena, J., & Tuschl, T. (2012) · Methods · doi:10.1016/j.ymeth.2012.07.030 · Cited by 114 · see citing works

One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

Casini, A., MacDonald, J. T., Jonghe, J. D., Christodoulou, G., Freemont, P. S., Baldwin, G. S., & Ellis, T. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt915 · Cited by 111 · see citing works

T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes

Bentzen, A. K., Such, L., Jensen, K. K., Marquard, A. M., Jessen, L. E., Miller, N. J., Church, C. D., Lyngaa, R., Koelle, D. M., Becker, J. C., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4303 · Cited by 94 · see citing works

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology

Zhou, W., Emery, S. B., Flasch, D. A., Wang, Y., Kwan, K. Y., Kidd, J. M., Moran, J. V., & Mills, R. E. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1173 · Cited by 93 · see citing works

Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes

Guo, S.-M., Veneziano, R., Gordonov, S., Li, L., Danielson, E., de Arce, K. P., Park, D., Kulesa, A. B., Wamhoff, E., Blainey, P. C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12372-6 · Cited by 80 · see citing works

A brief review of DNA and RNA chemical synthesis

Caruthers, M. H. (2011) · Biochemical Society Transactions · doi:10.1042/bst0390575 · Cited by 79 · see citing works

The COMET toolkit for composing customizable genetic programs in mammalian cells

Donahue, P. S., Draut, J. W., Muldoon, J. J., Edelstein, H. I., Bagheri, N., & Leonard, J. N. (2020) · Nature Communications · doi:10.1038/s41467-019-14147-5 · Cited by 78 · see citing works

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

Vu, T., Vallmitjana, A., Gu, J., La, K., Xu, Q., Flores, J., Zimak, J., Shiu, J., Hosohama, L., Wu, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27798-0 · Cited by 78 · see citing works

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., Schweitzer, M., Ferenc, K., Li, X., Mirzazadeh, R., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09616-w · Cited by 70 · see citing works

Evolution of MHC-based technologies used for detection of antigen-responsive T cells

Bentzen, A. K., & Hadrup, S. R. (2017) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-017-1971-5 · Cited by 69 · see citing works

R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences

Casini, A., Christodoulou, G., Freemont, P. S., Baldwin, G. S., Ellis, T., & MacDonald, J. T. (2014) · ACS Synthetic Biology · doi:10.1021/sb4001323 · Cited by 59 · see citing works

Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation

Viets, K., Sauria, M. E. G., Chernoff, C., Viales, R. R., Echterling, M., Anderson, C., Tran, S., Dove, A., Goyal, R., Voortman, L., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.09.007 · Cited by 58 · see citing works

HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging

Safieddine, A., Coleno, E., Lionneton, F., Traboulsi, A.-M., Salloum, S., Lecellier, C., Gostan, T., Georget, V., Hassen‐Khodja, C., Imbert, A., et al. (2022) · Nature Protocols · doi:10.1038/s41596-022-00750-2 · Cited by 56 · see citing works

A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosis

Hundley, F. V., Sanvisens, N., Marin, H. C., Carr, K. L., Tian, R., & Toczyski, D. P. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.01.014 · Cited by 55 · see citing works

Multiplexed, high-throughput analysis of 3D microtissue suspensions

Chen, A. A., Underhill, G. H., & Bhatia, S. N. (2010) · Integrative Biology · doi:10.1039/c0ib00054j · Cited by 49 · see citing works

Machine Learning-Guided Systematic Search of DNA Sequences for Sorting Carbon Nanotubes

Lin, Z., Yang, Y., Jagota, A., & Zheng, M. (2022) · ACS Nano · doi:10.1021/acsnano.1c11448 · Cited by 44 · see citing works

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

Costea, P. I., Lundeberg, J., & Akan, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057521 · Cited by 44 · see citing works

Tracking Multiple Genomic Elements Using Correlative CRISPR Imaging and Sequential DNA FISH

Guan, J., Liu, H., Shi, X., Feng, S., & Huang, B. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.01.032 · Cited by 44 · see citing works

Transcriptionally inactive hepatitis B virus episome DNA preferentially resides in the vicinity of chromosome 19 in 3D host genome upon infection

Tang, D., Zhao, H., Wu, Y., Peng, X., Gao, Z., Sun, Y., Duan, J., Qi, Y., Li, Y., Zhou, Z., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109288 · Cited by 44 · see citing works

High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer

Koblan, L. W., Yost, K. E., Zheng, P., Colgan, W. N., Jones, M. G., Yang, D., Kumar, A., Sandhu, J., Schnell, A., Sun, D., et al. (2025) · Science · doi:10.1126/science.adx3800 · Cited by 43 · see citing works

Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes

Gresham, D., Curry, B., Ward, A., Gordon, D. B., Brizuela, L., Kruglyak, L., & Botstein, D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913883107 · Cited by 43 · see citing works

Clonal Analysis of Cells with Cellular Barcoding: When Numbers and Sizes Matter

Bystrykh, L. V., & Belderbos, M. E. (2016) · Methods in molecular biology · doi:10.1007/7651_2016_343 · Cited by 43 · see citing works

Highly Efficient Single-Pot Scarless Golden Gate Assembly

HamediRad, M., Weisberg, S., Chao, R., Lian, J., & Zhao, H. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00480 · Cited by 43 · see citing works

Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens

Strezoska, Ž., Licon, A., Haimes, J. D., Spayd, K. J., Patel, K. M., Sullivan, K., Jastrzebski, K., Simpson, K. J., Leake, D., Smith, A. V. B., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042341 · Cited by 37 · see citing works

Genome oligopaint via local denaturation fluorescence in situ hybridization

Wang, Y., Cottle, W. T., Wang, H., Feng, X. A., Mallon, J. P., Gavrilov, M. M., Bailey, S., & Ha, T. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.02.011 · Cited by 36 · see citing works

Targeted insertional mutagenesis libraries for deep domain insertion profiling

Coyote‐Maestas, W., Nedrud, D. M., Okorafor, S., He, Y., & Schmidt, D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1110 · Cited by 34 · see citing works

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

Marshall, J. L., Doughty, B. R., Subramanian, V., Guckelberger, P., Wang, Q. S., Chen, L. M., Rodriques, S. G., Zhang, K., Fulco, C. P., Nasser, J., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2010738117 · Cited by 34 · see citing works

Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures

Xin, L., Duan, X., & Liu, N. (2021) · Nature Communications · doi:10.1038/s41467-021-23532-y · Cited by 32 · see citing works

A primer on using pooled shRNA libraries for functional genomic screens

Hu, G., & Luo, J. (2012) · Acta Biochimica et Biophysica Sinica · doi:10.1093/abbs/gmr116 · Cited by 32 · see citing works

Perturb-tracing enables high-content screening of multi-scale 3D genome regulators

Cheng, Y., Hu, M., Yang, B., Jensen, T. B., Zhang, Y., Yang, T., Yu, R., Ma, Z., Radda, J. S. D., Jin, S., et al. (2025) · Nature Methods · doi:10.1038/s41592-025-02652-z · Cited by 31 · see citing works

Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

Rensen, E., Pietropaoli, S., Mueller, F., Weber, C., Souquère, S., Sommer, S., Isnard, P., Rabant, M., Gibier, J., Terzi, F., et al. (2022) · Life Science Alliance · doi:10.26508/lsa.202101124 · Cited by 31 · see citing works

Cell type–specific 3D-genome organization and transcription regulation in the brain

Liu, S., Wang, C. Y., Zheng, P., Jia, B. B., Zemke, N. R., Ren, P., Park, H. L., Ren, B., & Zhuang, X. (2025) · Science Advances · doi:10.1126/sciadv.adv2067 · Cited by 30 · see citing works

Engineering genomes in multiplex

Woodruff, L. B. A., & Gill, R. T. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.04.019 · Cited by 29 · see citing works

Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy

Tan, X., Lu, Z. J., Gao, G., Xu, Q., Hu, L., Fellmann, C., Li, M. Z., Qu, H., Lowe, S. W., Hannon, G. J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119873109 · Cited by 29 · see citing works

Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention

McIntyre, A. B. R., Tschan, A. B., Meyer, K., Walser, S., Rai, A. K., Fujita, K., & Pelkmans, L. (2025) · Nature Communications · doi:10.1038/s41467-024-55469-3 · Cited by 27 · see citing works

In the fast lane: Large-scale bacterial genome engineering

Fehér, T., Burland, V., & Pósfai, G. (2012) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2012.02.012 · Cited by 25 · see citing works

DNA Structural Barcode Copying and Random Access

Bošković, F., Ohmann, A., Keyser, U. F., & Chen, K. (2021) · Small Structures · doi:10.1002/sstr.202000144 · Cited by 24 · see citing works

Gene Assembly from Chip‐Synthesized Oligonucleotides

Eroshenko, N., Kosuri, S., Marblestone, A. H., Conway, N., & Church, G. M. (2012) · Current Protocols in Chemical Biology · doi:10.1002/9780470559277.ch110190 · Cited by 24 · see citing works

Thermodynamic Post-Processing versus GC-Content Pre-Processing for DNA Codes Satisfying the Hamming Distance and Reverse-Complement Constraints

Tulpan, D., Smith, D. H., & Montemanni, R. (2014) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2014.2299815 · Cited by 24 · see citing works

Integrated analysis of receptor activation and downstream signaling with EXTassays

Botvinnik, A., Wichert, S. P., Fischer, T. M., & Rossner, M. J. (2009) · Nature Methods · doi:10.1038/nmeth.1407 · Cited by 24 · see citing works

RNA structure-wide discovery of functional interactions with multiplexed RNA motif library

Komatsu, K. R., Taya, T., Matsumoto, S., Miyashita, E., Kashida, S., & Saito, H. (2020) · Nature Communications · doi:10.1038/s41467-020-19699-5 · Cited by 23 · see citing works

High-multiplex tissue imaging in routine pathology—are we there yet?

Einhaus, J. F., Rochwarger, A., Mattern, S., Gaudilliere, B. L., & Schürch, C. M. (2023) · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin · doi:10.1007/s00428-023-03509-6 · Cited by 22 · see citing works

Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens

Lyons, E., Sheridan, P. J., Tremmel, G., Miyano, S., & Sugano, S. (2017) · Scientific Reports · doi:10.1038/s41598-017-12825-2 · Cited by 22 · see citing works

A comparative analysis of DNA barcode microarray feature size

Ammar, R., Smith, A. M., Heisler, L. E., Giaever, G. N., & Nislow, C. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-471 · Cited by 21 · see citing works

Accelerating protein design by scaling experimental characterization

Qian, J., Milles, L. F., Wicky, B. I. M., Ragotte, R. J., Motmaen, A., Borst, A. J., Skotheim, R., Ols, S., Coventry, B., Li, X., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-76740-9 · Cited by 20 · see citing works

Advances and Challenges in Random Access Techniques for In Vitro DNA Data Storage

Zhou, Y., Bi, K., Ge, Q., & Lu, Z. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c07235 · Cited by 20 · see citing works

An Effective DNA‐Based File Storage System for Practical Archiving and Retrieval of Medical MRI Data

Rasool, A., Hong, J., Hong, Z., Li, Y., Zou, C., Chen, H., Qu, Q., Wang, Y., Jiang, Q., Huang, X., et al. (2024) · Small Methods · doi:10.1002/smtd.202301585 · Cited by 19 · see citing works

A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains

Nedrud, D. M., Coyote‐Maestas, W., & Schmidt, D. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26067 · Cited by 19 · see citing works

Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies

Voortman, L., Anderson, C., Urban, E., Yuan, L., Tran, S., Neuhaus‐Follini, A., Derrick, J., Gregor, T., & Johnston, R. J. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.06.016 · Cited by 19 · see citing works

CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays

Barber, K. W., Shrock, E. L., & Elledge, S. J. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.027 · Cited by 18 · see citing works

A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR

Xu, M., Mehl, L. C., Zhang, T., Thakur, R., Sowards, H., Myers, T. A., Jessop, L., Chesi, A., Johnson, M. E., Wells, A. D., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.07.002 · Cited by 17 · see citing works

Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules

Banal, J. L., & Bathe, M. (2021) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.1c14985 · Cited by 17 · see citing works

Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set

Kristensen, N. P., Dionisio, E., Bentzen, A. K., Tamhane, T., Kemming, J. S., Nos, G., Voss, L. F., Hansen, U. K., Lauer, G. M., & Hadrup, S. R. (2024) · Science Advances · doi:10.1126/sciadv.adm8951 · Cited by 17 · see citing works

Rapid identification of bacterial isolates using microfluidic adaptive channels and multiplexed fluorescence microscopy

Chatzimichail, S., Turner, P., Feehily, C., Farrar, A., Crook, D. W., Andersson, M. I., Oakley, S. J., Barrett, L. K., Sayyed, H. E., Kyropoulos, J., et al. (2024) · Lab on a Chip · doi:10.1039/d4lc00325j · Cited by 17 · see citing works

Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion

Thompson, M. K., Kiourlappou, M., & Davis, I. (2020) · RNA · doi:10.1261/rna.076562.120 · Cited by 17 · see citing works

Scalable and cost-efficient custom gene library assembly from oligopools

Freschlin, C. R., Yang, K. K., & Romero, P. A. (2026) · Science Advances · doi:10.1126/sciadv.ady2279 · Cited by 16 · see citing works

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

Poisson, W., Prunier, J., Carrier, A., Gilbert, I., Mastromonaco, G. F., Albert, V., Taillon, J., Bourret, V., Droit, A., Côté, S. D., et al. (2023) · BMC Genomics · doi:10.1186/s12864-023-09189-5 · Cited by 15 · see citing works

Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging

Tomov, M. L., O’Neil, A., Abbasi, H. S., Cimini, B. A., Carpenter, A. E., Rubin, L. L., & Bathe, M. (2021) · Communications Biology · doi:10.1038/s42003-021-02276-x · Cited by 15 · see citing works

Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design

Imburgia, C. E., Organick, L., Zhang, K. H., Cardozo, N., McBride, J., Bee, C., Wilde, D., Roote, G., Jorgensen, S., Ward, D., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61264-5 · Cited by 14 · see citing works

Scalable design of orthogonal DNA barcode libraries

Gowri, G., Sheng, K., & Yin, P. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00646-z · Cited by 14 · see citing works

Computational Sequence Design with R2oDNA Designer

MacDonald, J. T., & Siciliano, V. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7223-4_18 · Cited by 14 · see citing works

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics

Gelali, E., Custodio, J., Girelli, G., Wernersson, E., Crosetto, N., & Bienko, M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7768-0_17 · Cited by 14 · see citing works

A highly parallel strategy for storage of digital information in living cells

Akhmetov, A., Ellington, A. D., & Marcotte, E. M. (2018) · BMC Biotechnology · doi:10.1186/s12896-018-0476-4 · Cited by 14 · see citing works

Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ

Beckwith, K. S., Ødegård-Fougner, Ø., Morero, N. R., Barton, C., Schueder, F., Tang, W., Alexander, S., Peters, J. M., Jungmann, R., Birney, E., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61689-y · Cited by 13 · see citing works

A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components

Subramanian, S. K., Russ, W. P., & Ranganathan, R. (2018) · Synthetic Biology · doi:10.1093/synbio/ysx008 · Cited by 13 · see citing works

Design of character‐based DNA barcode motif for species identification: A computational approach and its validation in fishes

Choudhury, M. C., Dhar, B., & Ghosh, S. K. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12671 · Cited by 13 · see citing works

A DNA-assisted immunoassay for enzyme activity via a DNA-linked, activity-based probe

Kim, D., Jetson, R. R., & Krusemark, C. J. (2017) · Chemical Communications · doi:10.1039/c7cc05236g · Cited by 13 · see citing works

Roadmap for network-based biocomputation

van Delft, F. C. M. J. M., Månsson, A., Kugler, H., Korten, T., Reuther, C., Zhu, J., Lyttleton, R. W., Blaudeck, T., Meinecke, C., Reuter, D., et al. (2022) · Nano Futures · doi:10.1088/2399-1984/ac7d81 · Cited by 13 · see citing works

Determining T-cell specificity to understand and treat disease

Hadrup, S. R., & Newell, E. W. (2017) · Nature Biomedical Engineering · doi:10.1038/s41551-017-0143-4 · Cited by 13 · see citing works

Hybridization-encoded DNA tags with paper-based readout for anti-forgery raw material tracking

Li, J., Crown, A., Ney, P., Yekhanin, S., Partap, A., Shirole, A., Jiang, H., Russ, S. G., Gordon, M., Aroh, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60282-7 · Cited by 11 · see citing works

Conversion of natural cytokine receptors into orthogonal synthetic biosensors

Edelstein, H. I., Cosio, A., Ezekiel, M. L., Corcoran, W. K., Morris, A. H., & Leonard, J. N. (2025) · Nature Chemical Biology · doi:10.1038/s41589-025-01986-1 · Cited by 11 · see citing works

LUMI-PCR: an Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites

Dawes, J., Webster, P., Iadarola, B., Garcia-Diaz, C., Dore, M. H., Bolt, B. J., Dewchand, H., Dharmalingam, G., McLatchie, A. P., Kaczor, J., et al. (2020) · Mobile DNA · doi:10.1186/s13100-020-0201-4 · Cited by 11 · see citing works

A Method for Multiplex Gene Synthesis Employing Error Correction Based on Expression

Hsiau, T. H.-C., Sukovich, D. J., Elms, P., Prince, R. N., Strittmatter, T., Ruan, P., Curry, B., Anderson, P., Sampson, J., & Anderson, J. C. (2015) · PLoS ONE · doi:10.1371/journal.pone.0119927 · Cited by 11 · see citing works

A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization

Talla, E., Tekaia, F., Brino, L., & Dujon, B. (2003) · BMC Genomics · doi:10.1186/1471-2164-4-38 · Cited by 35 · see citing works

Designing DNA Barcodes Orthogonal in Melting Temperature by Simulated Annealing Optimization

Elmas, A., Jajamovich, G. H., Wang, X., & Samoilov, M. S. (2013) · Nucleic Acid Therapeutics · doi:10.1089/nat.2012.0394 · Cited by 1 · see citing works

Group testing with DNA chips: generating designs and decoding experiments

Schliep, A., Torney, D. C., & Rahmann, S. (2004) · IEEE Computational Systems Bioinformatics Conference (CSB) · doi:10.1109/csb.2003.1227307 · Cited by 67 · see citing works

Optimization of a Microarray Probe Design Focusing on the Minimization of Cross-hybridization

Horn, F., Nützmann, H. W., Schroeckh, V., Guthke, R., & Hummert, C. (2012)

Model-based probe set optimization for high-performance microarrays

Leparc, G., Tüchler, T., Striedner, G., Bayer, K., Sykacek, P., Hofacker, I. L., & Kreil, D. P. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn1001 · Cited by 23 · see citing works