Fabio Piano Associate Professor of Biology; Director, Center for Genomics and Systems Biology; Provost, NYU Abu Dhabi Ph.D. 1995 (Biology), New York University; M.A. 1991 (Biology), New York University; B.S. 1988 (Biology), New York University. Office Address: New York University Department of Biology Center for Genomics and Systems Biology 12 Waverly Place, Room 708 New York, NY 10003 Email: Phone: (212) 998-3737 Fax: (212) 995-4015 List of Publications from Pubmed

Research

We study the genetic and evolutionary mechanisms underlying early embryonic development using a combination of molecular genetic and functional genomics approaches in the animal model C. elegans and related nematodes. One of our major goals is to use RNA interference (RNAi) of ovary-expressed genes followed by time-lapse microscopy to work toward a comprehensive molecular description of early embryogenesis in C. elegans. RNAi offers a powerful way to obtain information about the loss-of-function phenotype of the genes tested, while the early embryo offers a system in which basic cellular and developmental processes can be easily studied. We currently have tested over 1,000 genes and identified about 300 genes required for embryogenesis. Although most of these genes are highly conserved, fewer than 10% have been identified in previous genetic screens. We use the data obtained from the RNAi tests to build gene clusters based on phenotypic analysis. The clusters are then used to guide two broad lines of investigation: (1) functional analysis of the genome, and (2) molecular dissection of specific cellular processes.

From the initial clustering studies, we have found groups of genes required for basic processes such as nuclear movements, mitotic spindle formation, cytokinesis, cell cycle progression, and proper asymmetric cell division. In many cases, these clusters contain genes that are conserved in humans. However, their function in humans is not yet known. Therefore, our data can be used not only to analyze the C. elegans genome but also to guide the functional examination of the human genome. In our current dataset we have already found genes for which the human homolog is associated with a genetic disease, including some that have been previously targeted for anti-cancer drug development.

In a related project we are using the early nematode embryo as a model to study the evolution of developmental mechanisms. Comparisons across species have revealed fundamental differences during early embryogenesis. Significantly, in some species the wild-type patterns of early cleavages resemble those produced by various C. elegans mutants. We are examining these phenotypic differences in conjunction with molecular analyses to identify mechanisms underlying the phenotypic diversity seen in nature.

Areas of Research/Interest

Genomics, genetics and evolution of early C. elegans development.

Fellowships/Honors

Post-doctoral fellowship from the Damon Runyon-Walter Winchell Foundation for Cancer Research; the Gladys Mateyko Award for Excellence in Biology; the James Arthur Fellowship.

Publications

RNAi methods and screening: RNAi based high-throughput genetic interaction screening. Methods Cell Biol   (2011) Cipriani PG, Piano F

A model of cytoplasmically driven microtubule-based motion in the single-celled Caenorhabditis elegans embryo. Proc Natl Acad Sci U S A   (2011 Jun 28) Shinar T, Mana M, Piano F, Shelley MJ

A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue. Cell   (2011 Apr 29) Green RA, Kao HL, Audhya A, Arur S, Mayers JR, Fridolfsson HN, Schulman M, Schloissnig S, Niessen S, Laband K, Wang S, Starr DA, Hyman AA, Schedl T, Desai A, Piano F, Gunsalus KC, Oegema K

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science   (2010 Dec 24) Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dose AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Ratsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Ahringer J, 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

Rapid and accurate developmental stage recognition of C. elegans from high-throughput image data. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit   (2010 Aug 5) White AG, Cipriani PG, Kao HL, Lees B, Geiger D, Sontag E, Gunsalus KC, Piano F

The landscape of C. elegans 3'UTRs. Science   (2010 Jul 23) Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak SD, 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

Automated sorting of live C. elegans using laFACS. Nat Methods   (2010 Jun) Fernandez AG, Mis EK, Bargmann BO, Birnbaum KD, Piano F

EGG-4 and EGG-5 Link Events of the Oocyte-to-Embryo Transition with Meiotic Progression in C. elegans. Curr Biol   (2009 Nov 3) Parry JM, Velarde NV, Lefkovith AJ, Zegarek MH, Hang JS, Ohm J, Klancer R, Maruyama R, Druzhinina MK, Grant BD, Piano F, Singson A

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat Methods   (2009 Oct) Stoeckius M, Maaskola J, Colombo T, Rahn HP, Friedlander MR, Li N, Chen W, Piano F, Rajewsky N

Evolution of early embryogenesis in rhabditid nematodes. Dev Biol   (2009 Nov 1) Brauchle M, Kiontke K, MacMenamin P, Fitch DH, Piano F

Unlocking the secrets of the genome. Nature   (2009 Jun 18) 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

A protein domain-based interactome network for C. elegans early embryogenesis. Cell   (2008 Aug 8) 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

Diverse roles of actin in C. elegans early embryogenesis. BMC Dev Biol   (2007) Velarde N, Gunsalus KC, Piano F

C. elegans network biology: a beginning. WormBook   (2006) Piano F, Gunsalus KC, Hill DE, Vidal M

UTRome.org: a platform for 3'UTR biology in C. elegans. Nucleic Acids Res   (2008 Jan) Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC

EGG-3 regulates cell-surface and cortex rearrangements during egg activation in Caenorhabditis elegans. Curr Biol   (2007 Sep 18) Maruyama R, Velarde NV, Klancer R, Gordon S, Kadandale P, Parry JM, Hang JS, Rubin J, Stewart-Michaelis A, Schweinsberg P, Grant BD, Piano F, Sugimoto A, Singson A

Forward chemical genetic approach identifies new role for GAPDH in insulin signaling. Nat Chem Biol   (2007 Jan) 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

MEL-28 is downstream of the Ran cycle and is required for nuclear-envelope function and chromatin maintenance. Curr Biol   (2006 Sep 5) Fernandez AG, Piano F

A peptidomimetic siRNA transfection reagent for highly effective gene silencing. Mol Biosyst   (2006 Jun) Utku Y, Dehan E, Ouerfelli O, Piano F, Zuckermann RN, Pagano M, Kirshenbaum K

Two phases of astral microtubule activity during cytokinesis in C. elegans embryos. Dev Cell   (2006 Apr) Motegi F, Velarde NV, Piano F, Sugimoto A

A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol   (2006 Mar 7) 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

Nucleoporins NPP-1, NPP-3, NPP-4, NPP-11 and NPP-13 are required for proper spindle orientation in C. elegans. Dev Biol   (2006 Jan 15) Schetter A, Askjaer P, Piano F, Mattaj I, Kemphues K

Caenorhabditis elegans decapping proteins: localization and functional analysis of Dcp1, Dcp2, and DcpS during embryogenesis. Mol Biol Cell   (2005 Dec) Lall S, Piano F, Davis RE

Toward automatic phenotyping of developing embryos from videos. IEEE Trans Image Process   (2005 Sep) Ning F, Delhomme D, LeCun Y, Piano F, Bottou L, Barbano PE

Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature   (2005 Aug 11) Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F

Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature   (2005 Mar 24) Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, 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, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ

New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res   (2005 Feb) Fernandez AG, Gunsalus KC, Huang J, Chuang LS, Ying N, Liang HL, Tang C, Schetter AJ, Zegar C, Rual JF, Hill DE, Reinke V, Vidal M, Piano F

RNAi as a tool to study cell biology: building the genome-phenome bridge. Curr Opin Cell Biol   (2005 Feb) Gunsalus KC, Piano F

Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sci U S A   (2004 Jun 15) Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DH

A map of the interactome network of the metazoan C. elegans. Science   (2004 Jan 23) 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

RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res   (2004 Jan 1) Gunsalus KC, Yueh WC, MacMenamin P, Piano F

mRNA capping enzyme requirement for Caenorhabditis elegans viability. J Biol Chem   (2003 Apr 18) Srinivasan P, Piano F, Shatkin AJ

Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol   (2002 Nov 19) Piano F, Schetter AJ, Morton DG, Gunsalus KC, Reinke V, Kim SK, Kemphues KJ

Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol   (2002 Nov 19) Walhout AJ, Reboul J, Shtanko O, Bertin N, Vaglio P, Ge H, Lee H, Doucette-Stamm L, Gunsalus KC, Schetter AJ, Morton DG, Kemphues KJ, Reinke V, Kim SK, Piano F, Vidal M

The ZW10 and Rough Deal checkpoint proteins function together in a large, evolutionarily conserved complex targeted to the kinetochore. J Cell Sci   (2001 Sep) Scaerou F, Starr DA, Piano F, Papoulas O, Karess RE, Goldberg ML

RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Curr Biol   (2000 Dec 14-28) Piano F, Schetter AJ, Mangone M, Stein L, Kemphues KJ

A Drosophila melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis formation. Nat Cell Biol   (2000 Jul) Tomancak P, Piano F, Riechmann V, Gunsalus KC, Kemphues KJ, Ephrussi A

Evidence for redundancy but not trans factor-cis element coevolution in the regulation of Drosophila Yp genes. Genetics   (1999 Jun) Piano F, Parisi MJ, Karess R, Kambysellis MP

Atypical protein kinase C cooperates with PAR-3 to establish embryonic polarity in Caenorhabditis elegans. Development   (1998 Sep) Tabuse Y, Izumi Y, Piano F, Kemphues KJ, Miwa J, Ohno S

Phylogeny of the island populations of the Hawaiian Drosophila grimshawi complex: evidence from combined data. Mol Phylogenet Evol   (1997 Apr) Piano F, Craddock EM, Kambysellis MP

Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiian Drosophila yolk protein gene Yp2. J Mol Evol   (1996 Aug) Ho KF, Craddock EM, Piano F, Kambysellis MP

Pattern of ecological shifts in the diversification of Hawaiian Drosophila inferred from a molecular phylogeny. Curr Biol   (1995 Oct 1) Kambysellis MP, Ho KF, Craddock EM, Piano F, Parisi M, Cohen J