Kris Gunsalus

Kris Gunsalus

Associate Professor of Biology; Faculty Director of Bioinformatics

Ph.D. 1997 (Genetics and Development), Cornell; B.A. 1984 (Chemistry/Biology), Cornell.

Office Address: 

New York University
Department of Biology
Center for Genomics and Systems Biology
12 Waverly Place, Room 603
New York, NY 10003

Phone: 

(212) 998-8236

Fax: 

(212) 995-4015

Areas of Research/Interest: 

Developmental systems biology.

List of Publications from Pubmed

Research:

Our laboratory is interested in the integrative analysis of diverse functional genomics data to identify groups of genes that work in specific cellular and developmental processes. A major challenge in systems biology is how to extract meaningful biological insights from large heterogeneous data sets that probe different aspects of gene function. Several ongoing projects in the lab use integrative approaches to analyze and interpret large-scale datasets and to generate testable hypotheses on gene function in different biological systems. These projects all involve close collaborative interaction between experimental and computational scientists.

Molecular networks in C. elegans early embryogenesis
We have used an integrative approach to characterize gene networks that function in the very early C. elegans embryo, based on data from different kinds of functional genomics data that we and others have collected, such as protein-protein interactions, gene expression profiles, and phenotypic maps (Fig. 1). We are currently extending this work in collaboration with the laboratory of Dr. Fabio Piano to systematically define genetic interactions in C. elegans early embryogenesis. Genetic interactions tell us about logical relationships between different cellular components, and we are analyzing how these functional dependencies complement other functional data that we already have in hand. The long-term goal of this work is to develop a global map of the molecular architecture underlying early development in C. elegans.


Figure 1. C. elegans gene networks in early embryogenesis. (a) A composite view of around 30,000 functional linkages between 661 C. elegans genes with phenotypes in the early embryo, based on protein-protein interactions (Int), phenotypic similarity based on a signature of 45 early embryonic phenotypic characters (Ph), and gene co-expression in a compendium of gene expression data (Tr). (b) When the network is filtered for high-confidence functional links between genes (supported by two or more types of functional genomic data, e.g. phenotypic correlation and protein-protein interaction), a modular organization of molecular machinery is revealed, in which groups of highly interconnected genes are linked to each other via a small number of functional interactions. Adapted from Gunsalus et al., Nature 2005.


Genetic requirements for mouse early embryogenesis
We are collaborating with Dr. Nicole Noyes of the NYU School of Medicine to predict and analyze RNAi phenotypes in early mouse embryos using time-lapse microscopy. For this work, we are leveraging functional genomic data from several model organisms to identify candidate genes for RNAi that will help us define the spectrum of phenotypic defects that can occur in early mammalian embryos, similar to our previous work in C. elegans. One of the goals of this translational project is to develop a more sophisticated and non-invasive way to determine the developmental potential of human embryos for patients who seek reproductive assistance for infertility.

Post-transcriptional gene regulation in C. elegans
Regulation of mRNA localization, translation, and stability is increasingly recognized as in important layer in the regulation of gene activity in diverse biological systems. The modENCODE Consortium is an NIH/NHGRI initiative to identify and analyze functional elements in model organism genomes. As part of modENCODE, we are involved in the annotation of C. elegans 3’UTRs and functional sequence elements contained in these regions. The goal of this work is to identify and test putative post-transcriptional regulatory networks in development. This project is a collaboration with Fabio Piano (PI), John Kim (U. Michigan, Co-PI), and Nikolaus Rajewsky (Center for Medical Systems Biology, Max Delbruck Center, Berlin, Co-PI).

Interactive tools for functional genomic data
As part of these projects, we develop web-based tools and graphical interfaces to provide the research community at large with enhanced access to and mining capabilities for large-scale functional genomic data. To facilitate a systems-level view of gene networks, we have developed a web-based network visualization tool called "N-Browse" (http://www.gnetbrowse.org) that allows researchers to browse gene neighborhoods and heterogeneous functional relationships in a modular way based on these integrated data. We have also developed a web-accessible database of RNA interference (RNAi) phenotypes in C. elegans, "RNAiDB" (http://www.rnai.org), which we use both to distribute data from large-scale RNAi studies and as an online notebook for ongoing high-content phenotypic analysis. In conjunction, we are developing strategies to make phenotypic data more amenable to computational analysis and tools to mine these data.

Web Resources:

 

Employment Opportunities:

The Center for Genomics and Systems Biology at NYU Abu Dhabi is currently inviting applications for multiple Bioinformatics Software Engineer positions. These personnel will form the nucleus of a new bioinformatics core group to support multiple large-scale projects in the new NYU Abu Dhabi Center for Genomics and Systems Biology as part of a larger NYUAD Research Institute initiative. These position are NOT located in the United States. You must be willing to RELOCATE TO ABU DHABI, UNITED ARAB EMIRATES. NYU Abu Dhabi is an Equal Oppurtunity/Affirmative Action Employer.

Fellowships/Honors:

National Academies Education Fellow in the Life Sciences, NSF ADVANCE Fellows Award, W.M. Keck Foundation Fellowship in Biology

Selected Works:

PubMed Search Results:

In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics.
Mol Cell Proteomics   (2016 May);  PMC4858945 free full-text archive
Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M
 
Erratum to: MINE: Module Identification in Networks.
BMC Bioinformatics   (2016);  PMC4756399 free full-text archive
Rhrissorrakrai K, Gunsalus KC
 
Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition.
Nucleic Acids Res   (2015 Nov 16);  PMC4787751 free full-text archive
Gan HH, Gunsalus KC
 
Wild worm embryogenesis harbors ubiquitous polygenic modifier variation.
Elife   (2015);  PMC4569889 free full-text archive
Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F, Rockman MV
 
Label free cell-tracking and division detection based on 2D time-lapse images for lineage analysis of early embryo development.
Comput Biol Med   (2014 Aug);  PMC4096606 free full-text archive
Cicconet M, Gutwein M, Gunsalus KC, Geiger D
 
DevStaR: high-throughput quantification of C. elegans developmental stages.
IEEE Trans Med Imaging   (2013 Oct);   PMID: 23722463
White AG, Lees B, Kao HL, Cipriani PG, Munarriz E, Paaby AB, Erickson K, Guzman S, Rattanakorn K, Sontag E, Geiger D, Gunsalus KC, Piano F
 
Tertiary structure-based analysis of microRNA-target interactions.
RNA   (2013 Apr);  PMC3677264 free full-text archive
Gan HH, Gunsalus KC
 
Electrical activity can impose time of day on the circadian transcriptome of pacemaker neurons.
Curr Biol   (2012 Oct 23);  PMC3562355 free full-text archive
Mizrak D, Ruben M, Myers GN, Rhrissorrakrai K, Gunsalus KC, Blau J
 
Networks in Caenorhabditis elegans.
Curr Opin Genet Dev   (2011 Dec);   PMID: 22054717
Gunsalus KC, Rhrissorrakrai K
 
Rational design of temperature-sensitive alleles using computational structure prediction.
PLoS One   (2011);  PMC3166291 free full-text archive
Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R
 
MINE: Module Identification in Networks.
BMC Bioinformatics   (2011);  PMC3123237 free full-text archive
Rhrissorrakrai K, Gunsalus KC
 
A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue.
Cell   (2011 Apr 29);  PMC3086541 free full-text archive
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);  PMC3142569 free full-text archive
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);  PMC3205469 free full-text archive
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);  PMC3142571 free full-text archive
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
 
Benzo[a]pyrene diol epoxide stimulates an inflammatory response in normal human lung fibroblasts through a p53 and JNK mediated pathway.
Carcinogenesis   (2010 Jun);  PMC2878364 free full-text archive
Dreij K, Rhrissorrakrai K, Gunsalus KC, Geacintov NE, Scicchitano DA
 
Unlocking the secrets of the genome.
Nature   (2009 Jun 18);  PMC2843545 free full-text archive
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
 
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.
Nat Methods   (2009 Jan);  PMC3057923 free full-text archive
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
 
Browsing multidimensional molecular networks with the generic network browser (N-Browse).
Curr Protoc Bioinformatics   (2008 Sep);  PMC3217184 free full-text archive
Kao HL, Gunsalus KC
 
Mating induces an immune response and developmental switch in the Drosophila oviduct.
Proc Natl Acad Sci U S A   (2008 Sep 16);  PMC2544553 free full-text archive
Kapelnikov A, Zelinger E, Gottlieb Y, Rhrissorrakrai K, Gunsalus KC, Heifetz Y
 
A protein domain-based interactome network for C. elegans early embryogenesis.
Cell   (2008 Aug 8);  PMC2596478 free full-text archive
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 Caenorhabditis elegans genetic-interaction map wiggles into view.
J Biol   (2008);  PMC2323036 free full-text archive
Gunsalus KC
 
Protein production and purification.
Nat Methods   (2008 Feb);  PMC3178102 free full-text archive
Graslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schutz A, Heinemann U, Yokoyama S, Bussow K, Gunsalus KC
 
Diverse roles of actin in C. elegans early embryogenesis.
BMC Dev Biol   (2007);  PMC2323969 free full-text archive
Velarde N, Gunsalus KC, Piano F
 
C. elegans network biology: a beginning.
WormBook   (2006);  PMC4781290 free full-text archive
Piano F, Gunsalus KC, Hill DE, Vidal M
 
UTRome.org: a platform for 3'UTR biology in C. elegans.
Nucleic Acids Res   (2008 Jan);  PMC2238901 free full-text archive
Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC
 
Network modeling links breast cancer susceptibility and centrosome dysfunction.
Nat Genet   (2007 Nov);   PMID: 17922014
Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, Elshamy WM, Rual JF, Levine D, Rozek LS, Gelman RS, Gunsalus KC, Greenberg RA, Sobhian B, Bertin N, Venkatesan K, Ayivi-Guedehoussou N, Sole X, Hernandez P, Lazaro C, Nathanson KL, Weber BL, Cusick ME, Hill DE, Offit K, Livingston DM, Gruber SB, Parvin JD, Vidal M
 
Forward chemical genetic approach identifies new role for GAPDH in insulin signaling.
Nat Chem Biol   (2007 Jan);   PMID: 17115034
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
 
Twinstar, the Drosophila homolog of cofilin/ADF, is required for planar cell polarity patterning.
Development   (2006 May);   PMID: 16571634
Blair A, Tomlinson A, Pham H, Gunsalus KC, Goldberg ML, Laski FA
 
A genome-wide map of conserved microRNA targets in C. elegans.
Curr Biol   (2006 Mar 7);   PMID: 16458514
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
 
microRNA target predictions across seven Drosophila species and comparison to mammalian targets.
PLoS Comput Biol   (2005 Jun);  PMC1183519 free full-text archive
Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N
 
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.
Nature   (2005 Aug 11);   PMID: 16094371
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
 
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.
Methods Enzymol   (2005);   PMID: 15808222
Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GV, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT
 
Combinatorial microRNA target predictions.
Nat Genet   (2005 May);   PMID: 15806104
Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N
 
Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.
Nature   (2005 Mar 24);   PMID: 15791247
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);  PMC546526 free full-text archive
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
 
Autosomal genes of autosomal/X-linked duplicated gene pairs and germ-line proliferation in Caenorhabditis elegans.
Genetics   (2005 Apr);  PMC1449572 free full-text archive
Maciejowski J, Ahn JH, Cipriani PG, Killian DJ, Chaudhary AL, Lee JI, Voutev R, Johnsen RC, Baillie DL, Gunsalus KC, Fitch DH, Hubbard EJ
 
RNAi as a tool to study cell biology: building the genome-phenome bridge.
Curr Opin Cell Biol   (2005 Feb);   PMID: 15661512
Gunsalus KC, Piano F
 
Feo, the Drosophila homolog of PRC1, is required for central-spindle formation and cytokinesis.
Curr Biol   (2004 Sep 7);   PMID: 15341744
Verni F, Somma MP, Gunsalus KC, Bonaccorsi S, Belloni G, Goldberg ML, Gatti M
 
Backbone 1H, 15N and 13C assignments for the 21 kDa Caenorhabditis elegans homologue of "brain-specific" protein.
J Biomol NMR   (2004 Jan);   PMID: 14739645
Monleon D, Chiang Y, Aramini JM, Swapna GV, Macapagal D, Gunsalus KC, Kim S, Szyperski T, Montelione GT
 
A map of the interactome network of the metazoan C. elegans.
Science   (2004 Jan 23);  PMC1698949 free full-text archive
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);  PMC308844 free full-text archive
Gunsalus KC, Yueh WC, MacMenamin P, Piano F
 
Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans.
Curr Biol   (2002 Nov 19);   PMID: 12445391
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);   PMID: 12445390
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
 
Cofilin/ADF is required for cell motility during Drosophila ovary development and oogenesis.
Nat Cell Biol   (2001 Feb);   PMID: 11175754
Chen J, Godt D, Gunsalus K, Kiss I, Goldberg M, Laski FA
 
Protein NMR spectroscopy in structural genomics.
Nat Struct Biol   (2000 Nov);   PMID: 11104006
Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski T
 
A Drosophila melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis formation.
Nat Cell Biol   (2000 Jul);   PMID: 10878812
Tomancak P, Piano F, Riechmann V, Gunsalus KC, Kemphues KJ, Ephrussi A
 
Mutations in twinstar, a Drosophila gene encoding a cofilin/ADF homologue, result in defects in centrosome migration and cytokinesis.
J Cell Biol   (1995 Dec);  PMC2120640 free full-text archive
Gunsalus KC, Bonaccorsi S, Williams E, Verni F, Gatti M, Goldberg ML
 
Updated on 06/22/2016