{"id":331,"date":"2021-05-05T09:45:43","date_gmt":"2021-05-05T13:45:43","guid":{"rendered":"https:\/\/dev-gunsaluspiano.bio.nyu.edu\/?page_id=331"},"modified":"2025-04-29T14:03:15","modified_gmt":"2025-04-29T18:03:15","slug":"publications","status":"publish","type":"page","link":"https:\/\/gunsaluspiano.bio.nyu.edu\/?page_id=331","title":{"rendered":"Publications"},"content":{"rendered":"\t\t
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Papers<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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View publications on PubMed<\/a>.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2025<\/span><\/strong><\/h4>

  1. Chung G, Piano F, Gunsalus KC. TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads,\u00a0G3 Genes|Genomes|Genetics<\/strong>, 2025; https:\/\/doi.org\/10.1093\/g3journal\/jkaf062<\/a><\/p><\/li>

  2. Das AK, Saj A, Gan HH, Gunsalus KC, Shubeita GT. BPS2025 – Enzyme-free, amplification-free, ultrasensitive optical detection of target nucleic acids. Biophysical Journal<\/strong> 2025; doi: 10.1016\/j.bpj.2024.11.2643<\/a>.<\/p><\/li><\/ol>

    1. Menon A, Elkhoury K, Zahraa A, Sapudom J, Rahic Z, Gunsalus KC, Teo J, Gupta N, Vijayavenkataraman S. Digital light processing 3D printing of dual crosslinked meniscal scaffolds with enhanced physical and biological properties. Advanced Composites and Hybrid Materials<\/strong> 2025; https:\/\/doi.org\/10.1007\/s42114-024-01196-8<\/a>.<\/p><\/li><\/ol>

      1. Das AK, Saj A, Gan HH, Gunsalus KC, Shubeita GT. Seek-a-Seq: Optical detection of target nucleic acids with attomolar sensitivity bioRxiv<\/strong> 2025; doi: https:\/\/doi.org\/10.1101\/2025.02.18.638747<\/a>.<\/p><\/li><\/ol>

        1. Fahs HZ, Refai FS, Gopinadhan S, Moussa Y, Gan HH, Hunashal Y, Battaglia G, Cipriani PG, Ciancia C, Rahiman N, Kremb S, Xie X, Pearson YE, Butterfoss GL, Maizels RM, Esposito G, Page AP, Gunsalus KC, Piano F. A new class of natural anthelmintics targeting lipid metabolism. Nature Communications<\/strong> 2025; doi: 10.1038\/s41467-024-54965-w<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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          2024<\/span><\/strong><\/h4>

          1. Guerin MN, Ellis TS, Ware MJ, Manning A, Coley AA, Amini A, Igboanugo AG, Rothrock AP, Chung G, Gunsalus KC, Bracht JR. Evolution of a biological thermocouple by adaptation of cytochrome c oxidase in a subterrestrial metazoan, Halicephalobus mephisto. Commun Biol<\/strong> 2024; doi: 10.1038\/s42003-024-06886-z<\/a>.<\/p><\/li>

          2. Bevilacqua A, Franco F, Lu YT, Rahiman N, Kao KC, Chuang YM, Zhu Y, Held W, Xie X, Gunsalus KC, Xiao Z, Chen SY, Ho PC. PPAR\u03b2\/\u03b4-orchestrated metabolic reprogramming supports the formation and maintenance of memory CD8+ T cells. Sci Immunol<\/strong> 2024; doi: 10.1126\/sciimmunol.adn2717<\/a>.<\/p><\/li>

          3. Vall\u00e8s Y, Arshad M, Abdalbaqi M, Inman CK, Ahmad A, Drou N, Gunsalus KC, Ali R, Tahlak M, Abdulle A. The infants’ gut microbiome: setting the stage for the early onset of obesity. Front Microbiol<\/strong>\u00a02024; doi: 10.3389\/fmicb.2024.1371292<\/a>.<\/p><\/li>

          4. Esposito G, Hunashal Y, Percipalle M, Fogolari F, Venit T, Leonchiks A, Gunsalus KC, Piano F, Percipalle P. Assessing nanobody interaction with SARS-CoV-2 Nsp9. PLoS One<\/strong>\u00a02024; doi: 10.1371\/journal.pone.0303839<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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            2023<\/span><\/strong><\/h4>

            1. Gjorgjieva T, Chaloemtoem A, Shahin T, Bayaraa O, Dieng MM, Alshaikh M, Abdalbaqi M, Del Monte J, Begum G, Leonor C, Manikandan V, Drou N, Arshad M, Arnoux M, Kumar N, Jabari A, Abdulle A, ElGhazali G, Ali R, Shaheen SY, Abdalla J, Piano F, Gunsalus KC, Daggag H, Al Nahdi H, Abuzeid H, Idaghdour Y. Systems genetics identifies miRNA-mediated regulation of host response in COVID-19. Hum Genomics<\/strong>\u00a02023; doi: 10.1186\/s40246-023-00494-4<\/a>.<\/p><\/li>

            2. Mahmood SR, Said NHE, Gunsalus KC, Percipalle P. \u03b2-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation. Genome Biol<\/strong> 2023; doi: 10.1186\/s13059-023-02853-9<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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              2022<\/span><\/strong><\/h4>

              1. Pearson YE, Kremb S, Butterfoss GL, Xie X, Fahs H, Gunsalus KC. A statistical framework for high-content phenotypic profiling using cellular feature distributions. Communications Biology<\/strong> 2022; doi: 1038\/s42003-022-04343-3<\/a><\/p><\/li>

              2. Gan HH, Zinno J, Piano F, Gunsalus KC. Omicron Spike Protein Has a Positive Electrostatic Surface That Promotes ACE2 Recognition and Antibody Escape. Frontiers in Virology<\/b><\/em> 2022; doi: 10.3389\/fviro.2022.894531<\/a>.<\/p><\/li>

              3. Marnik EA, Almeida MV, Cipriani PG, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF, Gunsalus KC, Updike DL. The Caenorhabditis elegans<\/em> TDRD5\/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLOS Genetics<\/b><\/em> 2022; doi: 10.1371\/journal.pgen.1010245<\/a>.<\/span><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                2021<\/strong><\/span><\/h4>

                1. Esposito G, Hunashal Y, Percipalle M, Venit T, Dieng MM, Fogolari F, Hassanzadeh G, Piano F, Gunsalus KC, Idaghdour Y, Percipalle P. NMR-Based Analysis of Nanobodies to SARS-CoV-2 Nsp9 Reveals a Possible Antiviral Strategy Against COVID-19. Advanced Biology<\/b><\/em> 2021; doi: 10.1002\/adbi.202101113<\/a>.<\/p><\/li>

                2. Mahmood SR, Xie X, El Said NH, Venit T, Gunsalus KC, Percipalle P. \u03b2-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture. Nature Communications <\/em><\/strong>2021; doi:\u00a010.1038\/s41467-021-25596-2.<\/a><\/span><\/p><\/li>

                3. Cipriani PG, Bay O, Zinno J, Gutwein M, Gan HH, Mayya VK, Chung G, Chen JX, Fahs H, Guan Y, Duchaine TF, Selbach M, Piano F,\u00a0Gunsalus KC. <\/strong>Novel LOTUS-domain proteins are organizational hubs that recruit elegans <\/em>Vasa to germ granules. Elife<\/em><\/strong> 2021; doi: 10.7554\/eLife.60833<\/a>.<\/p><\/li>

                4. Galanti L, Shasha D,\u00a0Gunsalus KC. <\/strong>Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing. BMC Bioinformatics<\/em><\/strong> 2021; doi: 10.1186\/s12859-021-04267-5<\/a>.<\/p><\/li>

                5. Murade CU, Chaudhuri S, Nabti I, Fahs H, Refai FSM, Xie X, Pearson YE,\u00a0Gunsalus KC, Shubeita GT. FRET-Based Probe for High-Throughput DNA Intercalator Drug Discovery and In Vivo<\/em> ACS Sens <\/em><\/strong>2021; doi: 10.1021\/acssensors.1c00167<\/a>.<\/p><\/li>

                6. Gan HH, Twaddle A, Marchand B,\u00a0Gunsalus KC. <\/strong>Structural Modeling of the SARS-CoV-2 Spike\/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. J Mol Biol<\/em><\/strong> 2021; doi: 10.1016\/j.jmb.2021.167051<\/a>.<\/p><\/li>

                7. Khoury E, Abou Fayad A, Karam Sarkis D, Fahs H, Gunsalus KC, Kallassy Awad M. The Microbiome of the Lebanese Wild Apple, Malus trilobata, is a Rich Source of Potential Biocontrol Agents for Fungal Post-harvest Pathogens of Apples. Curr Microbiol<\/em><\/strong> 2021; doi: 10.1007\/s00284-021-02397-w<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                  2020<\/span><\/strong><\/h4>

                  1. Xie X, Gjorgjieva T, Attieh Z, Dieng M, Arnoux M, Khair M, Moussa Y, Al Jallaf F, Rahiman N, Jackson C, Messery LE, Pamplona K, Victoria Z, Zafar M, Ali R, Piano F, Gunsalus KC*,<\/strong> and Idaghdour Y*. Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2. Processes<\/em><\/strong> 2020, 8:1425; doi: 10.3390\/pr8111425<\/a>. (* co-corresponding authors)<\/p><\/li>

                  2. Shibl AA, Isaac A, Ochsenk\u00fchn MA, C\u00e1rdenas A, Fei C, Behringer G, Arnoux M, Drou N, Santos MP, Gunsalus KC, Voolstra CR, Amin SA. Diatom modulation of select bacteria through use of two unique secondary metabolites. Proc Natl Acad Sci U S A<\/em><\/strong> 2020, 117:27445-27455. doi: 10.1073\/pnas.2012088117<\/a><\/p><\/li>

                  3. Gjorgjieva T, Xie X, Commins P, Pasricha R, Mahmood SR, Gunsalus KC, Naumov P, Percipalle P. Loss of \u03b2-Actin Leads to Accelerated Mineralization and Dysregulation of Osteoblast-Differentiation Genes during Osteogenic Reprogramming. Adv Sci<\/em><\/strong> 2020, 7:2002261; doi: 10.1002\/advs.202002261<\/a>.<\/p><\/li>

                  4. Yousif A, Drou N, Rowe J, Khalfan M, Gunsalus KC.\u00a0NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization.\u00a0BMC Bioinf <\/em><\/strong>2020, 21:267; doi: 10.1186\/s12859-020-03577<\/a><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                    2019<\/strong><\/span><\/h4>

                    1. Sofela S, Sahloul S, Stubbs C, Orozaliev A, Refai FS, Esmaeel AM, Fahs H, Abdelgawad MO,\u00a0Gunsalus KC, Song YA. Phenotyping of the thrashing forces exerted by partially immobilized elegans<\/em> using elastomeric micropillar arrays. Lab Chip<\/em><\/strong> 2019; doi: 10.1039\/c9lc00660e<\/a>.<\/p><\/li>

                    2. Solntsev KM, Schramm S, Kremb S,\u00a0Gunsalus KC, Amin SA. Isolation of biologically active compounds from mangrove sediments. Bioanalyt. Chem<\/em><\/strong>.<\/em> 2019; doi: 10.1007\/s00216-019-02001-y<\/a>.<\/p><\/li>

                    3. Chahal J, Gebert LFR, Gan HH, Camacho E,\u00a0Gunsalus KC, MacRae IJ, Sagan SM. miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5′ terminus. Nucleic Acids Res.<\/em><\/strong> 2019; doi: 10.1093\/nar\/gkz194<\/a>.<\/p><\/li>

                    4. Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Sch\u00fctz F, G\u00f6nczy P, Piano F,\u00a0Gunsalus K, Miska EA, Keller L. Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment. PLoS Genetics<\/em><\/strong> 2019; doi: 10.1371\/journal.pgen.1007905<\/a>.<\/p><\/li>

                    5. Beltran T, Barroso C, Birkle TY, Stevens L, Schwartz HT, Sternberg PW, Fradin H,\u00a0Gunsalus K, Piano F, Sharma G, Cerrato C, Ahringer J, Mart\u00ednez-P\u00e9rez E, Blaxter M, Sarkies P. Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis. Developmental Cell<\/em><\/strong> 2019; doi: 10.1016\/j.devcel.2018.12.026<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                      2018<\/span><\/strong><\/h4>

                      1. West SM, Mecenas D, Gutwein M, Aristizabal-Corrales D, Piano F, Gunsalus KC. Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis<\/em> elegans<\/em> Genome Biology<\/em><\/strong> 2018; doi: 10.1186\/s13059-017-1369-x<\/a>.<\/p><\/li>

                      2. Xie X, Almuzzaini B, Drou N, Kremb S, Yousif A, Farrants AO, Gunsalus KC, Percipalle P. \u03b2-Actin-dependent global chromatin organization and gene expression programs control cellular identity. FASEB Journal <\/em><\/strong>2018; doi: 10.1096\/fj.201700753R<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                        2017<\/span><\/strong><\/h4>

                        1. Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F,\u00a0Gunsalus KC. Genome Architecture and Evolution of a Unichromosomal Asexual Nematode. Current Biology <\/em><\/strong>2017; doi: 10.1016\/j.cub.2017.08.038<\/a>.<\/p><\/li>

                        2. Nelson DR, Khraiwesh B, Fu W, Alseekh S, Jaiswal AK, Chaiboonchoe A, Hazzouri KM, O\u2019Connor MJ, Butterfoss GL, Drou N, Rowe JD, Harb J, Fernie AR, Gunsalus KC, Salehi-Ashtiani K. The genome and phenome of the green alga Chloroidium sp.<\/em> UTEX 3007 reveal adaptive traits for desert acclimatization. Elife<\/em><\/strong> 2017; pii: e25783. doi: 10.7554\/eLife.25783<\/a>.<\/p><\/li>

                        3. Flamand MN, Gan HH, Mayya VK, Gunsalus KC, Duchaine TF. A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing. Nucleic Acids Research<\/em><\/strong> 2017; 45:7212-25. doi: 10.1093\/nar\/gkx340<\/a>.<\/p><\/li>

                        4. Benyettou F, Fahs H, Elkharrag R, Bilbeisi RA, Asma B, Rezgui R, Motte L, Magzoub M, Brandel J, Olsen J-C, Piano F, Gunsalus KC, Platas-Iglesias C, Trabolsi A. Selective growth inhibition of cancer cells with doxorubicin-loaded CB[7]-modified iron-oxide nanoparticles. RSC Advances<\/em><\/strong> 2017; 7, 23827. doi: 10.1039\/C7RA02693E<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                          2016<\/strong><\/span><\/h4>

                          1. Weicksel SE, Mahadav A, Moyle M, Cipriani PG, Kudron M, Pincus Z, Bahmanyar S, Abriola L, Merkel J, Gutwein M, Fernandez AG, Piano F, Gunsalus KC, Reinke V. A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in elegans<\/em>. Development<\/em><\/strong> 2016; 143(19):3540-3548. doi: 10.1242\/dev.140046<\/a>.<\/p><\/li>

                          2. Desta IT, Al-Sharif A, AlGharibeh N, Mustafa N, Orozaliev A, Giakoumidis N, Gunsalus KC, Song Ya. Detecting and Trapping of a Single elegans<\/em> Worm in a Microfluidic Chip for Automated Microplate Dispensing. J Lab Automation<\/em><\/strong> 2016; doi: 10.1177\/2211068216669688<\/a>.<\/p><\/li>

                          3. Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M. In Vivo Interaction Proteomics in Caenorhabditis elegans<\/em> Embryos Provides New Insights into P Granule Dynamics. Mol Cell Proteomics<\/em><\/strong> 2016; 15(5):1642-57. doi: 10.1074\/mcp.M115.053975<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                            2015<\/strong><\/span><\/h4>

                            1. Gan HH & Gunsalus KC. Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition. Nucleic Acids Res<\/em><\/strong> 2015;43:9613-25. doi: 10.1093\/nar\/gkv990<\/a>. PMCID: PMC4787751.<\/p><\/li>

                            2. Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F and Rockman MV. Wild worm embryogenesis harbors ubiquitous polygenic modifier variation. eLife<\/em><\/strong> 2015; doi: 10.7554\/eLife.09178<\/a>. PMCID: PMC4569889<\/a>.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                              2014<\/span><\/strong><\/h4>

                              1. Cicconet M, Gutwein M, Gunsalus KC, and Geiger D. Label Free Cell-Tracking and Division Detection Based on 2D Time-Lapse Images For Lineage Analysis of Early Embryo Development. Computers in Biology and Medicine<\/em><\/strong> 2014, 51: 24-34.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                2013<\/span><\/strong><\/h4>

                                1. White A, Lees B, Kao H-L, Cipriani G, Munarriz E, Paaby AL, Erickson K, Guzman S, Rattanakorn K, Sontag E, Geiger D, Gunsalus KC, Piano F. DevStaR: high-throughput quantification of developmental stages. IEEE Transactions on Biomedical Imaging <\/em><\/strong>IEEE Trans Med Imaging<\/em><\/strong> 2013; 32(10):1791-803.<\/p><\/li>

                                2. Gan HH & Gunsalus KC. Tertiary structure-based analysis of microRNA-target interactions. RNA<\/em><\/strong> 2013;19:539-51.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                  2012<\/span><\/strong><\/h4>

                                  1. Mizrak D, Ruben M, Myers GN, Rhrissorrakrai K, Gunsalus KC, Blau J. Electrical Activity Can Impose Time of Day on the Circadian Transcriptome of Pacemaker Neurons. Curr Biol <\/em><\/strong>2012; 22:1-10.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                    2011<\/span><\/strong><\/h4>

                                    1. Rhrissorrakrai K, Gunsalus KC. MINE: a tool to identify Modules In Networks. BMC Bioinf<\/em><\/strong> 2011; 12:192.<\/p><\/li>

                                    2. Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha D, Bonneau R. Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction. PLoS ONE<\/em><\/strong> 2011; 6:e23947. doi:10.1371\/journal.pone.0023947<\/a><\/p><\/li>

                                    3. Green R, Kao H-L, Audhya A, Arur S, Schulman M, Schloissnig S, Niessen S, Laband K, Wang S, Hyman A, Desai A, Schedl T, Piano F, Gunsalus KC*, Oegema K*. High-Resolution Phenotypic Profiling Based on the Complex Architecture of the elegans<\/em> Gonad Syncytium. Cell<\/strong><\/em> 2011; 145\u00a0:470-82. <\/em>(*Corresponding authors) (selected for video abstract)<\/em><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                      2010<\/span><\/strong><\/h4>
                                      1. Gerstein M\u2026(115 other authors)\u2026 Strome S*, Gunsalus KC*, Micklem G*, Liu XS*, Reinke V*, Kim SK*, Hillier LW*, Henikoff S*, Piano F*, Snyder M*, Stein L*, Lieb JD*, Waterston RH*. Integrative Analysis of Functional Elements in the

                                        Caenorhabditis elegans<\/em> Genome by the modENCODE Project. Science<\/em><\/strong> 2010; 330:1775-87.<\/em> (*corresponding authors)<\/p><\/li>

                                      2. Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak S, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F*, Gunsalus KC*, Kim JK*. The landscape of elegans<\/em> 3’UTRs. Science<\/em><\/strong> 2010; 329:432-5. (*Corresponding authors)<\/p><\/li>

                                      3. Dreij K, Rhrissorrakrai K, Gunsalus KC, Geacintov NE, Scicchitano DA. Benzo[a]pyrene diol epoxide stimulates an inflammatory response in normal human lung fibroblasts through a p53 and JNK mediated pathway. Carcinogenesis<\/em><\/strong> 2010; 31:1149-57.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                        2009<\/span><\/strong><\/h4>

                                        1. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium. Unlocking the secrets of the genome. Nature<\/em><\/strong> 2009; 459:927-30.<\/p><\/li>

                                        2. Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M. Empirically controlled mapping of the Caenorhabditis elegans<\/em> protein-protein interactome network. Nature Methods<\/em><\/strong> 2009; 6:47-54.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                          2008<\/span><\/strong><\/h4>

                                          1. Kapelnikov A, Zelinger E, Gottlieb Y, Rhrissorrakrai K, Gunsalus KC, Heifetz Y. Mating induces an immune response and developmental switch in the Drosophila <\/em> Proc Natl Acad Sci USA<\/em><\/strong> 2008; 105:13912-7.<\/p><\/li>

                                          2. Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M. A protein domain-based interactome network for elegans <\/em>early embryogenesis. Cell<\/em><\/strong> 2008; 134:534-45.<\/p><\/li>

                                          3. Structural Genomics Consortium; China Structural Genomics Consortium; Northeast Structural Genomics Consortium (83 authors \u2026 Gunsalus KC). Protein production and purification. Nature Methods<\/em><\/strong> 2008 5:135-46.<\/p><\/li>

                                          4. Mangone M, MacMenamin P, Zegar C, Piano F, Gunsalus KC. UTRome.org: a platform for 3’UTR biology in elegans<\/em>. Nucl Acids Res<\/em><\/strong> (Database issue 2008) 36:D57-62.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                            2007<\/span><\/strong><\/h4>

                                            1. Velarde N, Gunsalus KC, Piano F. Actin roles in elegans <\/em>early embryogenesis. BMC Dev Biol<\/em><\/strong> 2007 7:142.<\/p><\/li>

                                            2. Pujana MA, Han J-DJ, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, ElShamy WM, Rual J-F, Levine D, Rozek LS, Gelman RS, Gunsalus KC, Greenberg RA, Sobhian B, Bertin N, Venkatesan K, Ayivi-Guedehoussou N, Sol\u00e9 X, Hern\u00e1ndez P, L\u00e1zaro C, Nathanson KL, Weber BL, Cusick ME, Hill DE, Offit K, Livingston DM, Gruber SB, Parvin JD & Vidal M. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nature Genetics<\/em><\/strong> 2007; 39:1338-49.<\/p><\/li>

                                            3. Min J, Kyung Kim Y, Cipriani PG, Kang M, Khersonsky SM, Walsh DP, Lee JY, Niessen S, Yates JR 3rd, Gunsalus K, Piano F, Chang YT. Forward chemical genetic approach identifies new role for GAPDH in insulin signaling. Nat Chem Biol<\/em><\/strong> 2007; 3:55-9.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                              2006<\/span><\/strong><\/h4>

                                              1. Blair A, Tomlinson A, Pham H, Gunsalus KC, Goldberg ML, Laski FA. Twinstar, the Drosophila <\/em>homologue of Cofilin\/ADF, is required for planar cell polarity patterning. Development<\/em><\/strong> 2006 133:1789-97.<\/p><\/li>

                                              2. Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, MacMenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N. A Genome-Wide Map of Conserved MicroRNA Targets in elegans<\/em>. Current Biology<\/em><\/strong> 2006; 16: 460-71. (Most downloaded article and Featured Article online for March 7, 2006 issue)<\/em><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                2005<\/span><\/strong><\/h4>

                                                1. Gunsalus KC*, Ge H*, Schetter A*, Goldberg DS*, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, S\u00f6nnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F. Predictive models of molecular machines involved in early elegans<\/em> embryogenesis. Nature<\/em><\/strong> 2005; 436:861-865. [*Co-1st authors] (Featured online at NSF.gov, NPR radio series “Imagine That”, and radio interview for WPUR, Boston; highlighted in Developmental Cell; selected as “Must Read” by Faculty of 1000 Biology)<\/em><\/em><\/em><\/em><\/p><\/li>

                                                2. Gr\u00fcn D, Wang Y-L, Langenberger D, Gunsalus KC, Rajewsky N. microRNA target predictions across seven Drosophila<\/em> species and comparison to mammalian targets. PLoS Comput Biol<\/em><\/strong> 2005; 1(1):e13.<\/p><\/li>

                                                3. S\u00f6nnichsen B, Koski L, Walsh A, Marshall P, Neumann F, Brehm M, Alleaume A-M, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, R\u00f6der M, Finell J, H\u00e4ntsch H, Jones S, Jones M, Piano F, Gunsalus KC, Oegema K, G\u00f6nczy P, Coulson A, Hyman AA, Echeverri CJ. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans<\/em>. Nature<\/em><\/strong> 2005; 434:462-469. <\/em>(“Must Read” selection by Faculty of 1000 Biology)<\/em><\/p><\/li>

                                                4. Krek A, Gr\u00fcn D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat Genet<\/em><\/strong> 2005; 37:495-500. (highlighted on issue cover; “Recommended” selection by Faculty of 1000 Biology)<\/em><\/em><\/em><\/p><\/li>

                                                5. Maciejowski J, Ahn JH, Cipriani PG, Killian DJ, Chaudhary AL, Lee JI, Voutev R, Johnsen RC, Baillie DL, Gunsalus KC, Fitch DHA, Hubbard EJA. Autosomal genes of autosomal\/X-linked duplicated gene pairs and germline proliferation in elegans<\/em>. Genetics<\/em><\/strong> 2005; 169:1997-2011.<\/p><\/li>

                                                6. Fernandez AG*, Gunsalus KC*, Huang J, Chuang LS, Ying N, Liang H-L, Tang CT, Schetter A, Zegar C, Rual J, Hill DE, Reinke V, Vidal M, and Piano F. Novel gene function in elegans<\/em> embryogenesis revealed using RNAi of ovary-enriched ORFeome clones. Genome Res <\/em><\/strong>2005; 15:250-259.<\/em> [*Co-first authors] (cover artwork for the issue)<\/em><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                  2004<\/span><\/strong><\/h4>

                                                  1. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. A map of the interactome network of the metazoan elegans<\/em>. Science<\/em><\/strong> 2004; 303:540-3. (“Recommended” selection by Faculty of 1000 Biology)<\/em><\/p><\/li>

                                                  2. Gunsalus KC, Yueh WC, MacMenamin P, Piano F. RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res<\/em><\/strong> 2004; 32:D406-10.<\/p><\/li>

                                                  3. Verni F, Somma MP, Gunsalus KC, Bonaccorsi S, Belloni G, Goldberg ML, and Gatti M. Feo, the Drosophila<\/em> homologue of PRC1, is required for central spindle formation and cytokinesis. Curr Biol<\/em><\/strong> 2004; 14:1569-75.<\/p><\/li>

                                                  4. Monleon D, Chiang Y, Aramini JM, Swapna GV, Macapagal D, Gunsalus KC, Kim S, Szyperski T, Montelione GT. Backbone 1H, 15N and 13C assignments for the 21 kDa Caenorhabditis elegans <\/em>homologue of “brain-specific” protein. J Biomolec NMR<\/em> <\/strong>2004; 28: 91-2.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                    2002<\/span><\/strong><\/h4>

                                                    1. Piano F, Schetter A, Morton D, Gunsalus KC, Reinke V, Kim SK, Kemphues KJ. Gene clustering based on 47 embryonic phenotypes derived from RNAi analysis of 751 ovary-enriched genes in elegans<\/em>. Current Biology<\/em><\/strong> 2002; 12: 1959-1964.<\/p><\/li>

                                                    2. Walhout AJM, Reboul J, Shtanko O, Bertin N, Vaglio P, Ge H, Lee H, Doucette-Stamm L, Schetter AJ, Morton DG, Gunsalus KC, Kemphues KJ, Reinke V, Kim SK, Piano F, Vidal M. Integration of interactome, phenome and transcriptome maps of the elegans <\/em>germline. Curr Biol<\/em><\/strong> 2002; 12: 1952-1959. (“Recommended” selection by Faculty of 1000 Biology)<\/em><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                      2001<\/span><\/strong><\/h4>

                                                      1. Chen J, Godt D, Gunsalus K, Kiss I, Goldberg M, and Laski FA. Cofilin\/ADF is required for cell motility during Drosophila<\/em> ovary development and oogenesis. Nat Cell Biol<\/em><\/strong> 2001; 3:204-9.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                        2000<\/span><\/strong><\/h4>

                                                        1. Montelione GT, Zheng D, Huang YJ, Gunsalus KC, and Szyperski T. Protein NMR spectroscopy in structural genomics. Nat Struct Biol<\/em><\/strong> 2000; 7 Suppl:982-5.<\/p><\/li>

                                                        2. Tomancak P, Piano F, Riechmann V, Gunsalus KC, Kemphues KJ, and Ephrussi A. A Drosophila<\/em> melanogaster homologue of Caenorhabditis elegans <\/em>par-1 acts at an early step in embryonic-axis formation. <\/span>Nat Cell Biol<\/em> <\/strong>2000; 2:458-60.<\/span><\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                          1995<\/span><\/strong><\/h4>

                                                          1. Gunsalus KC, Bonaccorsi S, Williams E, Verni F, Gatti M, and Goldberg ML. Mutations in twinstar<\/em>, a Drosophila<\/em> gene encoding a cofilin\/ADF homologue, result in defects in centrosome migration and cytokinesis. J Cell Biol<\/em><\/strong> 1995; 131:1243-59.<\/p><\/li><\/ol>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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                                                            Reviews and Book or Series Chapters<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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                                                              \n
                                                            1. Gan HH and Gunsalus KC<\/strong>. The role of tertiary structure in microRNA target recognition. In microRNA Target Identification, Methods in Molecular Biology<\/em><\/strong> Series<\/strong><\/em>. Ed. Alessandro Lagan\u00e0 2019; Springer pp. 43-64.

                                                              <\/li>\n
                                                            2. Gunsalus KC <\/strong>and Rhrissorrakrai K. Networks in elegans<\/em>. Curr Opin Genet Devel<\/em><\/strong> 2011;21:787-98.

                                                              <\/li>\n
                                                            3. Fernandez A, Gunsalus KC<\/strong>, Piano F. Toward a systems view of development in elegans <\/em>early embryogenesis. In Systems Biology<\/em>, Annual Plant Reviews, Blackwell Publishing. Edds. G.M. Coruzzi & R.A. Gutierrez 2009; pp. 137-165.

                                                              <\/li>\n
                                                            4. Kao HL and Gunsalus KC<\/strong>. Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr Protoc Bioinf<\/em><\/strong> 2008; Chapter 9:Unit 9.11.

                                                              <\/li>\n
                                                            5. Gunsalus KC.<\/strong> A Caenorhabditis elegans <\/em>genetic interaction map wiggles into view. J Biol<\/em><\/strong> 2008; 7:8.

                                                              <\/li>\n
                                                            6. Piano F, Gunsalus KC<\/strong>, Hill DA, Vidal M. elegans <\/em>network biology: a beginning. WormBook<\/em><\/strong>, ed. The C. elegans<\/em> Research Community, WormBook, doi\/10.1895\/wormbook.1.7.1, http:\/\/www.wormbook.org. (August 21, 2006)

                                                              <\/li>\n
                                                            7. Acton T, Gunsalus KC<\/strong>, Xiao R, Ma LC, Aramini J, Baron MC, Chiang Y-W, Climent T, Cooper B, Denissova N, Douglas SM, Everett JK, Palacios D, Paranji RK, Shastry R, Wu M, Ho CK, Shih L-Y, Swapna GVT, Wilson M, Gerstein M, Inouye M, Hunt JF, Montelione GT. Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. Methods Enzymol <\/em><\/strong>2005; 394:210-243.

                                                              <\/li>\n
                                                            8. Gunsalus KC<\/strong> and Piano F. RNAi as a tool to study cell biology: building the genome-phenome bridge. Curr Opin Cell Biol<\/em><\/strong> 2005; 17:3-8.

                                                              <\/em><\/li>\n
                                                            9. Piano F and Gunsalus KC<\/strong>. RNAi-based functional genomics in elegans<\/em>. Curr Genomics<\/em> 2002; 3:69-81.

                                                              <\/li>\n
                                                            10. Montelione GT, Zheng D, Huang YJ, Gunsalus KC<\/strong>, Szyperski T<\/a>. Protein NMR spectroscopy in structural genomics. Nat Struct Biol<\/em><\/strong> 2000; 7 Suppl: 982-5.

                                                              <\/li>\n
                                                            11. Goldberg, ML, Gunsalus KC<\/strong>, Karess R, and Chang F. New Insights into Cytokinesis.\u00a0 In Mechanisms of Cell Division<\/em><\/strong>: Frontiers in Molecular Biology<\/em>.\u00a0 S. Endow & D. Glover 1998; pp. 270-317. OUP, Oxford.

                                                              <\/li>\n
                                                            12. Giansanti MG, Bonaccorsi S, Williams BC, Gunsalus KC<\/strong>, and Goldberg ML. Genes controlling cytokinesis during meiosis in Drosophila<\/em> melanogaster<\/em>\u00a0 In Proceedings on Chromosome Segregation and Aneuploidy (April 24-29, 1995, Sorrento, Italy). <\/em>Eds. A. Abbondandolo, BK Vig, R Roi 1995; pp. 304-316.<\/li>\n<\/ol>\n

                                                              \u00a0<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

                                                              Publications Papers View publications on PubMed. 2025 Chung G, Piano F, Gunsalus KC. TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads,\u00a0G3 Genes|Genomes|Genetics, 2025; https:\/\/doi.org\/10.1093\/g3journal\/jkaf062 Das AK, Saj A, Gan HH, Gunsalus KC, Shubeita GT. BPS2025 – Enzyme-free, amplification-free, ultrasensitive optical detection of target nucleic acids. Biophysical Journal 2025; doi: 10.1016\/j.bpj.2024.11.2643. […]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":256,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-331","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/331","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=331"}],"version-history":[{"count":52,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/331\/revisions"}],"predecessor-version":[{"id":860,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/331\/revisions\/860"}],"up":[{"embeddable":true,"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=\/wp\/v2\/pages\/256"}],"wp:attachment":[{"href":"https:\/\/gunsaluspiano.bio.nyu.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=331"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}