Calculated based on number of publications stored in Pure and citations from Scopus
20102022

Research activity per year

Search results

  • 2022

    BioSimulators: a central registry of simulation engines and services for recommending specific tools

    Shaikh, B., Smith, L. P., Vasilescu, D., Marupilla, G., Wilson, M., Agmon, E., Agnew, H., Andrews, S. S., Anwar, A., Beber, M. E., Bergmann, F. T., Brooks, D., Brusch, L., Calzone, L., Choi, K., Cooper, J., Detloff, J., Drawert, B., Dumontier, M., Ermentrout, G. B., & 55 othersFaeder, J. R., Freiburger, A. P., Fröhlich, F., Funahashi, A., Garny, A., Gennari, J. H., Gleeson, P., Goelzer, A., Haiman, Z., Hasenauer, J., Hellerstein, J. L., Hermjakob, H., Hoops, S., Ison, J. C., Jahn, D., Jakubowski, H. V., Jordan, R., Kalaš, M., König, M., Liebermeister, W., Sheriff, R. S. M., Mandal, S., McDougal, R., Medley, J. K., Mendes, P., Müller, R., Myers, C. J., Naldi, A., Nguyen, T. V. N., Nickerson, D. P., Olivier, B. G., Patoliya, D., Paulevé, L., Petzold, L. R., Priya, A., Rampadarath, A. K., Rohwer, J. M., Saglam, A. S., Singh, D., Sinha, A., Snoep, J., Sorby, H., Spangler, R., Starruß, J., Thomas, P. J., Van Niekerk, D., Weindl, D., Zhang, F., Zhukova, A., Goldberg, A. P., Schaff, J. C., Blinov, M. L., Sauro, H. M., Moraru, I. I. & Karr, J. R., 5 Jul 2022, In: Nucleic Acids Research. 50, W1, p. W108-W114

    Research output: Contribution to journalArticlepeer-review

    Open Access
    9 Scopus citations
  • 2021

    Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm

    Tourigny, D. S., Goldberg, A. P. & Karr, J. R., 7 Dec 2021, In: Biophysical Journal. 120, 23, p. 5231-5242 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    6 Scopus citations
  • 2020

    Best Practices for Making Reproducible Biochemical Models

    Porubsky, V. L., Goldberg, A. P., Rampadarath, A. K., Nickerson, D. P., Karr, J. R. & Sauro, H. M., 26 Aug 2020, In: Cell Systems. 11, 2, p. 109-120 12 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    21 Scopus citations
  • Open Access
  • 2018

    A blueprint for human whole-cell modeling

    Szigeti, B., Roth, Y. D., Sekar, J. A. P., Goldberg, A. P., Pochiraju, S. C. & Karr, J. R., 1 Feb 2018, In: Current Opinion in Systems Biology. 7, p. 8-15 8 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    49 Scopus citations
  • Emerging whole-cell modeling principles and methods

    Goldberg, A. P., Szigeti, B., Chew, Y. H., Sekar, J. AP., Roth, Y. D. & Karr, J. R., Jun 2018, In: Current Opinion in Biotechnology. 51, p. 97-102 6 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    49 Scopus citations
  • 2017

    Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

    Anney, R. J. L., Ripke, S., Anttila, V., Grove, J., Holmans, P., Huang, H., Klei, L., Lee, P. H., Medland, S. E., Neale, B., Robinson, E., Weiss, L. A., Zwaigenbaum, L., Yu, T. W., Wittemeyer, K., Willsey, A. J., Wijsman, E. M., Werge, T., Wassink, T. H., Waltes, R., & 143 othersWalsh, C. A., Wallace, S., Vorstman, J. A. S., Vieland, V. J., Vicente, A. M., Vanengeland, H., Tsang, K., Thompson, A. P., Szatmari, P., Svantesson, O., Steinberg, S., Stefansson, K., Stefansson, H., State, M. W., Soorya, L., Silagadze, T., Scherer, S. W., Schellenberg, G. D., Sandin, S., Sanders, S. J., Saemundsen, E., Rouleau, G. A., Rogé, B., Roeder, K., Roberts, W., Reichert, J., Reichenberg, A., Rehnström, K., Regan, R., Poustka, F., Poultney, C. S., Piven, J., Pinto, D., Pericak-Vance, M. A., Pejovic-Milovancevic, M., Pedersen, M. G., Pedersen, C. B., Paterson, A. D., Parr, J. R., Pagnamenta, A. T., Oliveira, G., Nurnberger, J. I., Nordentoft, M., Murtha, M. T., Mouga, S., Mortensen, P. B., Mors, O., Morrow, E. M., Moreno-De-Luca, D., Monaco, A. P., Minshew, N., Merikangas, A., McMahon, W. M., McGrew, S. G., Mattheisen, M., Martsenkovsky, I., Martin, D. M., Mane, S. M., Magnusson, P., Magalhaes, T., Maestrini, E., Lowe, J. K., Lord, C., Levitt, P., Martin, C. L., Ledbetter, D. H., Leboyer, M., Lecouteur, A. S., Ladd-Acosta, C., Kolevzon, A., Klauck, S. M., Jacob, S., Iliadou, B., Hultman, C. M., Hougaard, D. M., Hertz-Picciotto, I., Hendren, R., Hansen, C. S., Haines, J. L., Guter, S. J., Grice, D. E., Green, J. M., Green, A., Goldberg, A. P., Gillberg, C., Gilbert, J., Gallagher, L., Freitag, C. M., Fombonne, E., Folstein, S. E., Fernandez, B., Fallin, M. D., Ercan-Sencicek, A. G., Ennis, S., Duque, F., Duketis, E., Delorme, R., Derubeis, S., Dejonge, M. V., Dawson, G., Cuccaro, M. L., Correia, C. T., Conroy, J., Conceição, I. C., Chiocchetti, A. G., Celestino-Soper, P. B. S., Casey, J., Cantor, R. M., Café, C., Bybjerg-Grauholm, J., Brennan, S., Bourgeron, T., Bolton, P. F., Bölte, S., Bolshakova, N., Betancur, C., Bernier, R., Beaudet, A. L., Battaglia, A., Bal, V. H., Baird, G., Bailey, A. J., Bækvad-Hansen, M., Bader, J. S., Bacchelli, E., Anagnostou, E., Amaral, D., Almeida, J., Børglum, A. D., Buxbaum, J. D., Chakravarti, A., Cook, E. H., Coon, H., Geschwind, D. H., Gill, M., Hallmayer, J., Palotie, A., Santangelo, S., Sutcliffe, J. S., Arking, D. E., Devlin, B., Daly, M. J. & Hakonarson, H., 22 May 2017, In: Molecular Autism. 8, 1, 21.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    98 Scopus citations
  • Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

    Psychiatric Genomics Consortium Autism Group & iPSYCH-Broad Autism Group, 1 Jul 2017, In: Nature Genetics. 49, 7, p. 978-985 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    309 Scopus citations
  • Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

    Lim, E. T., Uddin, M., De Rubeis, S., Chan, Y., Kamumbu, A. S., Zhang, X., D'Gama, A. M., Kim, S. N., Hill, R. S., Goldberg, A. P., Poultney, C., Minshew, N. J., Kushima, I., Aleksic, B., Ozaki, N., Parellada, M., Arango, C., Penzol, M. J., Carracedo, A., Kolevzon, A., & 9 othersHultman, C. M., Weiss, L. A., Fromer, M., Chiocchetti, A. G., Freitag, C. M., Church, G. M., Scherer, S. W., Buxbaum, J. D. & Walsh, C. A., 1 Sep 2017, In: Nature Neuroscience. 20, 9, p. 1217-1224 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    192 Scopus citations
  • 2016

    Guidelines for Reproducibly Building and Simulating Systems Biology Models

    Medley, J. K., Goldberg, A. P. & Karr, J. R., Oct 2016, In: IEEE Transactions on Biomedical Engineering. 63, 10, p. 2015-2020 6 p., 7514982.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    19 Scopus citations
  • Toward Community Standards and Software for Whole-Cell Modeling

    Waltemath, D., Karr, J. R., Bergmann, F. T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C. J., Pir, P., Alaybeyoglu, B., Aranganathan, N. K., Baghalian, K., Bittig, A. T., Burke, P. E. P., Cantarelli, M., Chew, Y. H., Costa, R. S., Cursons, J., Czauderna, T., & 37 othersGoldberg, A. P., Gomez, H. F., Hahn, J., Hameri, T., Gardiol, D. F. H., Kazakiewicz, D., Kiselev, I., Knight-Schrijver, V., Knupfer, C., Konig, M., Lee, D., Lloret-Villas, A., Mandrik, N., Medley, J. K., Moreau, B., Naderi-Meshkin, H., Palaniappan, S. K., Priego-Espinosa, D., Scharm, M., Sharma, M., Smallbone, K., Stanford, N. J., Song, J. H., Theile, T., Tokic, M., Tomar, N., Toure, V., Uhlendorf, J., Varusai, T. M., Watanabe, L. H., Wendland, F., Wolfien, M., Yurkovich, J. T., Zhu, Y., Zardilis, A., Zhukova, A. & Schreiber, F., Oct 2016, In: IEEE Transactions on Biomedical Engineering. 63, 10, p. 2007-2014 8 p., 7489010.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    40 Scopus citations
  • Toward scalable whole-cell modeling of human cells

    Goldberg, A. P., Chew, Y. H. & Karr, J. R., 15 May 2016, SIGSIM-PADS 2016 - Proceedings of the 2016 Annual ACM Conference on Principles of Advanced Discrete Simulation. Association for Computing Machinery, Inc, p. 259-262 4 p. (SIGSIM-PADS 2016 - Proceedings of the 2016 Annual ACM Conference on Principles of Advanced Discrete Simulation).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    Open Access
    10 Scopus citations
  • 2015

    Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

    Autism Sequencing Consortium, 23 Sep 2015, In: Neuron. 87, 6, p. 1215-1233 19 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    917 Scopus citations
  • 2014

    Most genetic risk for autism resides with common variation

    Gaugler, T., Klei, L., Sanders, S. J., Bodea, C. A., Goldberg, A. P., Lee, A. B., Mahajan, M., Manaa, D., Pawitan, Y., Reichert, J., Ripke, S., Sandin, S., Sklar, P., Svantesson, O., Reichenberg, A., Hultman, C. M., Devlin, B., Roeder, K. & Buxbaum, J. D., Aug 2014, In: Nature Genetics. 46, 8, p. 881-885 5 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    789 Scopus citations
  • Synaptic, transcriptional and chromatin genes disrupted in autism

    De Rubeis, S., He, X., Goldberg, A. P., Poultney, C. S., Samocha, K., Cicek, A. E., Kou, Y., Liu, L., Fromer, M., Walker, S., Singh, T., Klei, L., Kosmicki, J., Fu, S. C., Aleksic, B., Biscaldi, M., Bolton, P. F., Brownfeld, J. M., Cai, J., Campbell, N. G., & 71 othersCarracedo, A., Chahrour, M. H., Chiocchetti, A. G., Coon, H., Crawford, E. L., Crooks, L., Curran, S. R., Dawson, G., Duketis, E., Fernandez, B. A., Gallagher, L., Geller, E., Guter, S. J., Hill, R. S., Ionita-Laza, I., Gonzalez, P. J., Kilpinen, H., Klauck, S. M., Kolevzon, A., Lee, I., Lei, J., Lehtimäki, T., Lin, C. F., Ma'ayan, A., Marshall, C. R., McInnes, A. L., Neale, B., Owen, M. J., Ozaki, N., Parellada, M., Parr, J. R., Purcell, S., Puura, K., Rajagopalan, D., Rehnström, K., Reichenberg, A., Sabo, A., Sachse, M., Sanders, S. J., Schafer, C., Schulte-Rüther, M., Skuse, D., Stevens, C., Szatmari, P., Tammimies, K., Valladares, O., Voran, A., Wang, L. S., Weiss, L. A., Willsey, A. J., Yu, T. W., Yuen, R. K. C., Cook, E. H., Freitag, C. M., Gill, M., Hultman, C. M., Lehner, T., Palotie, A., Schellenberg, G. D., Sklar, P., State, M. W., Sutcliffe, J. S., Walsh, C. A., Scherer, S. W., Zwick, M. E., Barrett, J. C., Cutler, D. J., Roeder, K., Devlin, B., Daly, M. J. & Buxbaum, J. D., 13 Nov 2014, In: Nature. 515, 7526, p. 209-215 7 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1855 Scopus citations
  • 2013

    Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder

    Poultney, C. S., Goldberg, A. P., Drapeau, E., Kou, Y., Harony-Nicolas, H., Kajiwara, Y., De Rubeis, S., Durand, S., Stevens, C., Rehnström, K., Palotie, A., Daly, M. J., Ma'Ayan, A., Fromer, M. & Buxbaum, J. D., 3 Oct 2013, In: American Journal of Human Genetics. 93, 4, p. 607-619 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    126 Scopus citations
  • 2012

    Comprehensive molecular characterization of human colon and rectal cancer

    Muzny, D. M., Bainbridge, M. N., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Reid, J. G., Santibanez, J., Shinbrot, E., Trevino, L. R., Wu, Y. Q., Wang, M., Gunaratne, P., Donehower, L. A., Creighton, C. J., Wheeler, D. A., & 293 othersGibbs, R. A., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Ding, L., Fulton, R. S., Koboldt, D. C., Wylie, T., Walker, J., Dooling, D. J., Fulton, L., Delehaunty, K. D., Fronick, C. C., Demeter, R., Mardis, E. R., Wilson, R. K., Chu, A., Chun, H. J. E., Mungall, A. J., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Bass, A. J., Ramos, A. H., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Pho, N. H., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Meyerson, M., Protopopov, A., Hadjipanayis, A., Lee, E., Xi, R., Yang, L., Ren, X., Sathiamoorthy, N., Chen, P. C., Haseley, P., Xiao, Y., Lee, S., Seidman, J., Chin, L., Park, P. J., Kucherlapati, R., Todd Auman, J., Hoadley, K. A., Du, Y., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Prins, J. F., Chiang, D. Y., Neil Hayes, D., Perou, C. M., Hinoue, T., Weisenberger, D. J., Maglinte, D. T., Pan, F., Berman, B. P., Van Den Berg, D. J., Shen, H., Triche, T., Baylin, S. B., Laird, P. W., Getz, G., Noble, M., Voat, D., Gehlenborg, N., Dicara, D., Zhang, J., Zhang, H., Wu, C. J., Liu, S. Y., Shukla, S., Zhou, L., Lin, P., Park, R. W., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Thorsson, V., Reynolds, S. M., Bernard, B., Kreisberg, R., Lin, J., Iype, L., Bressler, R., Erkkilä, T., Gundapuneni, M., Liu, Y., Norberg, A., Robinson, T., Yang, D., Zhang, W., Shmulevich, I., De Ronde, J. J., Schultz, N., Cerami, E., Ciriello, G., Goldberg, A. P., Gross, B., Jacobsen, A., Gao, J., Kaczkowski, B., Sinha, R., Arman Aksoy, B., Antipin, Y., Reva, B., Shen, R., Taylor, B. S., Ladanyi, M., Sander, C., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Hamilton, S. R., Craig Cason, R., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Zachary Sanborn, J., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Ellrott, K., Collisson, E., Cozen, A. E., Zerbino, D., Wilks, C., Craft, B., Spellman, P., Penny, R., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Gastier-Foster, J. M., Bowen, J., Ramirez, N. C., Black, A., Pyatt, R., Wise, L., White, P., Bertagnolli, M., Brown, J., Chan, T. A., Chu, G. C., Czerwinski, C., Denstman, F., Dhir, R., Dörner, A., Fuchs, C. S., Guillem, J. G., Iacocca, M., Juhl, H., Kaufman, A., Iii, B. K., Van Le, X., Mariano, M. C., Medina, E. N., Meyers, M., Nash, G. M., Paty, P. B., Petrelli, N., Rabeno, B., Richards, W. G., Solit, D., Swanson, P., Temple, L., Tepper, J. E., Thorp, R., Vakiani, E., Weiser, M. R., Willis, J. E., Witkin, G., Zeng, Z., Zinner, M. J., Zornig, C., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Ayala, B., Backus, M., Walton, J., Whitmore, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Shaw, K. R. M., Dillon, L. A. L., Buetow, K., Davidsen, T., Demchok, J. A., Eley, G., Ferguson, M., Fielding, P., Schaefer, C., Sheth, M., Yang, L., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J. & Thomson., E., 19 Jul 2012, In: Nature. 487, 7407, p. 330-337 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    6420 Scopus citations
  • The Autism Sequencing Consortium: Large-Scale, High-Throughput Sequencing in Autism Spectrum Disorders

    The Autism Sequencing Consortium, 20 Dec 2012, In: Neuron. 76, 6, p. 1052-1056 5 p.

    Research output: Contribution to journalShort surveypeer-review

    Open Access
    134 Scopus citations
  • The cBio Cancer Genomics Portal: An open platform for exploring multidimensional cancer genomics data

    Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., Antipin, Y., Reva, B., Goldberg, A. P., Sander, C. & Schultz, N., May 2012, In: Cancer Discovery. 2, 5, p. 401-404 4 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    11250 Scopus citations
  • 2010

    VirtualPlant: A software platform to support systems biology research

    Katari, M. S., Nowicki, S. D., Aceituno, F. F., Nero, D., Kelfer, J., Thompson, L. P., Cabello, J. M., Davidson, R. S., Goldberg, A. P., Shasha, D. E., Coruzzi, G. M. & Gutiérrez, R. A., Feb 2010, In: Plant Physiology. 152, 2, p. 500-515 16 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    215 Scopus citations