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The Genetic Landscape of a Cell

Science, 22 January 2010
Vol. 327, Issue 5964, p. 425-431
DOI: 10.1126/science.1180823

The Genetic Landscape of a Cell

  1. Michael Costanzo1,2,*,
  2. Anastasia Baryshnikova1,2,*,
  3. Jeremy Bellay3,
  4. Yungil Kim3,
  5. Eric D. Spear4,
  6. Carolyn S. Sevier4,
  7. Huiming Ding1,2,
  8. Judice L.Y. Koh1,2,
  9. Kiana Toufighi1,2,
  10. Sara Mostafavi1,5,
  11. Jeany Prinz1,2,
  12. Robert P. St. Onge6,
  13. Benjamin VanderSluis3,
  14. Taras Makhnevych7,
  15. Franco J. Vizeacoumar1,2,
  16. Solmaz Alizadeh1,2,
  17. Sondra Bahr1,2,
  18. Renee L. Brost1,2,
  19. Yiqun Chen1,2,
  20. Murat Cokol8,
  21. Raamesh Deshpande3,
  22. Zhijian Li1,2,
  23. Zhen-Yuan Lin9,
  24. Wendy Liang1,2,
  25. Michaela Marback1,2,
  26. Jadine Paw1,2,
  27. Bryan-Joseph San Luis1,2,
  28. Ermira Shuteriqi1,2,
  29. Amy Hin Yan Tong1,2,
  30. Nydia van Dyk1,2,
  31. Iain M. Wallace1,2,10,
  32. Joseph A. Whitney1,5,
  33. Matthew T. Weirauch11,
  34. Guoqing Zhong1,2,
  35. Hongwei Zhu1,2,
  36. Walid A. Houry7,
  37. Michael Brudno1,5,
  38. Sasan Ragibizadeh12,
  39. Balázs Papp13,
  40. Csaba Pál13,
  41. Frederick P. Roth8,
  42. Guri Giaever2,10,
  43. Corey Nislow1,2,
  44. Olga G. Troyanskaya14,
  45. Howard Bussey15,
  46. Gary D. Bader1,2,
  47. Anne-Claude Gingras9,
  48. Quaid D. Morris1,2,5,
  49. Philip M. Kim1,2,
  50. Chris A. Kaiser4,
  51. Chad L. Myers3,,
  52. Brenda J. Andrews1,2,,
  53. Charles Boone1,2,
  1. 1Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
  2. 2Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
  3. 3Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
  4. 4Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
  5. 5Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada.
  6. 6Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
  7. 7Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
  8. 8Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
  9. 9Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.
  10. 10Department of Pharmacy, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
  11. 11Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
  12. 12S&P Robotics, Inc., 1181 Finch Avenue West, North York, Ontario M3J 2V8, Canada.
  13. 13Institute of Biochemistry, Biological Research Center, H-6701 Szeged, Hungary.
  14. 14Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA.
  15. 15Biology Department, McGill University, Montreal, Quebec H3A 1B1, Canada.
  1. To whom correspondence should be addressed. E-mail: cmyers{at}cs.umn.edu (C.L.M.); brenda.andrews{at}utoronto.ca (B.J.A.); charlie.boone{at}utoronto.ca (C.B.)

Abstract

A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles for ~75% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function. The global network identifies functional cross-connections between all bioprocesses, mapping a cellular wiring diagram of pleiotropy. Genetic interaction degree correlated with a number of different gene attributes, which may be informative about genetic network hubs in other organisms. We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification.

  • * These authors contributed equally to this work.

  • Received for publication 20 August 2009.
  • Accepted for publication 12 November 2009.

Citation:

M. Costanzo, A. Baryshnikova, J. Bellay, Y. Kim, E. D. Spear, C. S. Sevier, H. Ding, J. L. Koh, K. Toufighi, S. Mostafavi, J. Prinz, R. P. St. Onge, B. VanderSluis, T. Makhnevych, F. J. Vizeacoumar, S. Alizadeh, S. Bahr, R. L. Brost, Y. Chen, M. Cokol, R. Deshpande, Z. Li, Z.-Y. Lin, W. Liang, M. Marback, J. Paw, B.-J. San Luis, E. Shuteriqi, A. H. Tong, N. van Dyk, I. M. Wallace, J. A. Whitney, M. T. Weirauch, G. Zhong, H. Zhu, W. A. Houry, M. Brudno, S. Ragibizadeh, B. Papp, C. Pál, F. P. Roth, G. Giaever, C. Nislow, O. G. Troyanskaya, H. Bussey, G. D. Bader, A.-C. Gingras, Q. D. Morris, P. M. Kim, C. A. Kaiser, C. L. Myers, B. J. Andrews, and C. Boone, The Genetic Landscape of a Cell. Science 327, 425-431 (2010).

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B. Schwer, and S. Shuman
RNA 21, 1173-1186 (1 June 2015)

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P. W. Gunning, U. Ghoshdastider, S. Whitaker, D. Popp, and R. C. Robinson
J. Cell Sci. 128, 2009-2019 (1 June 2015)

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A. H. Kachroo, J. M. Laurent, C. M. Yellman, A. G. Meyer, C. O. Wilke, and E. M. Marcotte
Science 348, 921-925 (22 May 2015)

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D. M. van Pel, P. C. Stirling, S. W. Minaker, P. Sipahimalani, and P. Hieter
G3 3, 273-282 (20 May 2015)

Differential genetic interactions of yeast stress response MAPK pathways
H. Martin, M. Shales, P. Fernandez-Pinar, P. Wei, M. Molina, D. Fiedler, K. M. Shokat, P. Beltrao, W. Lim, N. J. Krogan et al.
Mol Syst Biol 11, 800-800 (7 May 2015)

Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression
M. J. Li, B. Yan, P. C. Sham, and J. Wang
Brief Bioinform 16, 393-412 (1 May 2015)

Inferential modeling of 3D chromatin structure
S. Wang, J. Xu, and J. Zeng
Nucleic Acids Res 43, e54-e54 (30 April 2015)

Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness
C. R. Bauer, S. Li, and M. L. Siegal
Mol Syst Biol 11, 773-773 (27 April 2015)

Control of lipid organization and actin assembly during clathrin-mediated endocytosis by the cytoplasmic tail of the rhomboid protein Rbd2
C. L. Cortesio, E. B. Lewellyn, and D. G. Drubin
Mol. Biol. Cell 26, 1509-1522 (15 April 2015)

Role of the Unfolded Protein Response in Regulating the Mucin-Dependent Filamentous-Growth Mitogen-Activated Protein Kinase Pathway
H. Adhikari, N. Vadaie, J. Chow, L. M. Caccamise, C. A. Chavel, B. Li, A. Bowitch, C. J. Stefan, and P. J. Cullen
Mol. Cell. Biol. 35, 1414-1432 (15 April 2015)

Systematic identification of signal integration by protein kinase A
M. Filteau, G. Diss, F. Torres-Quiroz, A. K. Dube, A. Schraffl, V. A. Bachmann, I. Gagnon-Arsenault, A.-E. Chretien, A.-L. Steunou, U. Dionne et al.
Proc. Natl. Acad. Sci. USA 112, 4501-4506 (7 April 2015)

Replisome Function During Replicative Stress Is Modulated by Histone H3 Lysine 56 Acetylation Through Ctf4
P. Luciano, P.-M. Dehe, S. Audebert, V. Geli, and Y. Corda
Genetics 199, 1047-1063 (1 April 2015)

Cytosolic chaperones mediate quality control of higher-order septin assembly in budding yeast
C. R. Johnson, A. D. Weems, J. M. Brewer, J. Thorner, and M. A. McMurray
Mol. Biol. Cell 26, 1323-1344 (1 April 2015)

Cwc21p promotes the second step conformation of the spliceosome and modulates 3' splice site selection
A. Gautam, R. J. Grainger, J. Vilardell, J. D. Barrass, and J. D. Beggs
Nucleic Acids Res 43, 3309-3317 (31 March 2015)

Plant-derived antifungal agent poacic acid targets {beta}-1,3-glucan
J. S. Piotrowski, H. Okada, F. Lu, S. C. Li, L. Hinchman, A. Ranjan, D. L. Smith, A. J. Higbee, A. Ulbrich, J. J. Coon et al.
Proc. Natl. Acad. Sci. USA 112, E1490-E1497 (24 March 2015)

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C. M. Allan, A. M. Awad, J. S. Johnson, D. I. Shirasaki, C. Wang, C. E. Blaby-Haas, S. S. Merchant, J. A. Loo, and C. F. Clarke
J Biol Chem 290, 7517-7534 (20 March 2015)

Differential Phosphorylation of a Regulatory Subunit of Protein Kinase CK2 by Target of Rapamycin Complex 1 Signaling and the Cdc-like Kinase Kns1
M. E. Sanchez-Casalongue, J. Lee, A. Diamond, S. Shuldiner, R. D. Moir, and I. M. Willis
J Biol Chem 290, 7221-7233 (13 March 2015)

Morphogenesis checkpoint kinase Swe1 is the executor of lipolysis-dependent cell-cycle progression
N. Chauhan, M. Visram, A. Cristobal-Sarramian, F. Sarkleti, and S. D. Kohlwein
Proc. Natl. Acad. Sci. USA 112, E1077-E1085 (10 March 2015)

Functional Profiling of Human Fungal Pathogen Genomes
A. I. Goranov, and H. D. Madhani
Cold Spring Harb Perspect Med 5, a019596-a019596 (1 March 2015)

Cohen Syndrome-associated Protein COH1 Physically and Functionally Interacts with the Small GTPase RAB6 at the Golgi Complex and Directs Neurite Outgrowth
W. Seifert, J. Kuhnisch, T. Maritzen, S. Lommatzsch, H. C. Hennies, S. Bachmann, D. Horn, and V. Haucke
J Biol Chem 290, 3349-3358 (6 February 2015)

Barriers to the free diffusion of proteins and lipids in the plasma membrane
W. S. Trimble, and S. Grinstein
JCB 208, 259-271 (2 February 2015)

Actin and Endocytosis in Budding Yeast
B. L. Goode, J. A. Eskin, and B. Wendland
Genetics 199, 315-358 (1 February 2015)

Linking Tumor Mutations to Drug Responses via a Quantitative Chemical-Genetic Interaction Map
M. M. Martins, A. Y. Zhou, A. Corella, D. Horiuchi, C. Yau, T. Rakshandehroo, J. D. Gordan, R. S. Levin, J. Johnson, J. Jascur et al.
Cancer Discovery 5, 154-167 (1 February 2015)

Functional importance of {Psi}38 and {Psi}39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast
L. Han, Y. Kon, and E. M. Phizicky
RNA 21, 188-201 (1 February 2015)

The BioGRID interaction database: 2015 update
A. Chatr-aryamontri, B.-J. Breitkreutz, R. Oughtred, L. Boucher, S. Heinicke, D. Chen, C. Stark, A. Breitkreutz, N. Kolas, L. O'Donnell et al.
Nucleic Acids Res 43, D470-D478 (28 January 2015)

A map of directional genetic interactions in a metazoan cell
B.-J. Breitkreutz, R. Oughtred, L. Boucher, S. Heinicke, D. Chen, C. Stark, A. Breitkreutz, N. Kolas, L. O'Donnell, T. Reguly et al.
elife 4, e05464-e05464 (1 January 2015)

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L. M. Lombardi, M. D. Davis, and J. Rine
Genetics 199, 105-116 (1 January 2015)

The Impact of Macroscopic Epistasis on Long-Term Evolutionary Dynamics
B. H. Good, and M. M. Desai
Genetics 199, 177-190 (1 January 2015)

Minimal metabolic pathway structure is consistent with associated biomolecular interactions
A. Bordbar, H. Nagarajan, N. E. Lewis, H. Latif, A. Ebrahim, S. Federowicz, J. Schellenberger, and B. O. Palsson
Mol Syst Biol 10, 737-737 (10 December 2014)

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T. Vogwill, M. Kojadinovic, V. Furio, and R. C. MacLean
Mol Biol Evol 31, 3314-3323 (1 December 2014)

Rewiring of Genetic Networks in Response to Modification of Genetic Background
D. Bajić, C. Moreno-Fenoll, and J. F. Poyatos
Genome Biol Evol 6, 3267-3280 (1 December 2014)

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I. Tur, A. Roverato, and R. Castelo
Genetics 198, 1377-1393 (1 December 2014)

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S. Deivasigamani, H. K. Verma, R. Ueda, A. Ratnaparkhi, and G. S. Ratnaparkhi
Biology Open 3, 1127-1138 (15 November 2014)

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C. C. Williams, C. H. Jan, and J. S. Weissman
Science 346, 748-751 (7 November 2014)

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J. V. Rogers, C. McMahon, A. Baryshnikova, F. M. Hughson, and M. D. Rose
Mol. Biol. Cell 25, 3401-3412 (1 November 2014)

Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
O. M. Keane, C. Toft, L. Carretero-Paulet, G. W. Jones, and M. A. Fares
Genome Res 24, 1830-1841 (1 November 2014)

Global Regulation of a Differentiation MAPK Pathway in Yeast
C. A. Chavel, L. M. Caccamise, B. Li, and P. J. Cullen
Genetics 198, 1309-1328 (1 November 2014)

Regulation of Mitotic Spindle Disassembly by an Environmental Stress-Sensing Pathway in Budding Yeast
A. Pigula, D. G. Drubin, and G. Barnes
Genetics 198, 1043-1057 (1 November 2014)

Identification of Candidate Substrates for the Golgi Tul1 E3 Ligase Using Quantitative diGly Proteomics in Yeast
Z. Tong, M.-S. Kim, A. Pandey, and P. J. Espenshade
MCP 13, 2871-2882 (1 November 2014)

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T. Qin, N. Matmati, L. C. Tsoi, B. K. Mohanty, N. Gao, J. Tang, A. B. Lawson, Y. A. Hannun, and W. J. Zheng
Nucleic Acids Res 42, e138-e138 (13 October 2014)

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C. Boone, N. Matmati, L. C. Tsoi, B. K. Mohanty, N. Gao, J. Tang, A. B. Lawson, Y. A. Hannun, and W. J. Zheng
Genetics 198, 435-437 (1 October 2014)

The role of the interactome in the maintenance of deleterious variability in human populations
L. Garcia-Alonso, J. Jimenez-Almazan, J. Carbonell-Caballero, A. Vela-Boza, J. Santoyo-Lopez, G. Antinolo, and J. Dopazo
Mol Syst Biol 10, 752-752 (26 September 2014)

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F. D. Mast, A. V. Ratushny, and J. D. Aitchison
JCB 206, 695-706 (15 September 2014)

Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network
S. Kaboli, T. Yamakawa, K. Sunada, T. Takagaki, Y. Sasano, M. Sugiyama, Y. Kaneko, and S. Harashima
Nucleic Acids Res 42, 9838-9853 (2 September 2014)

The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription
M. C. Miron-Garcia, A. I. Garrido-Godino, V. Martinez-Fernandez, A. Fernandez-Pevida, A. Cuevas-Bermudez, M. Martin-Exposito, S. Chavez, J. de la Cruz, and F. Navarro
Nucleic Acids Res 42, 9666-9676 (2 September 2014)

Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains
J. A. Lewis, A. T. Broman, J. Will, and A. P. Gasch
Genetics 198, 369-382 (1 September 2014)

Integration of molecular network data reconstructs Gene Ontology
V. Gligorijević, V. Janjić, and N. Pržulj
Bioinformatics 30, i594-i600 (1 September 2014)

Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks
X. Ma, T. Chen, and F. Sun
Brief Bioinform 15, 685-698 (1 September 2014)

Linking Genetics to Structural Biology: Complex Heterozygosity Screening with Actin Alanine Scan Alleles Identifies Functionally Related Surfaces on Yeast Actin
S. DiPrima, B. Haarer, S. Viggiano, C. Pons, C. L. Myers, and D. C. Amberg
G3 4, 1491-1501 (11 August 2014)

Genomic evidence for adaptation by gene duplication
W. Qian, and J. Zhang
Genome Res 24, 1356-1362 (1 August 2014)

Heritability and genetic basis of protein level variation in an outbred population
L. Parts, Y.-C. Liu, M. M. Tekkedil, L. M. Steinmetz, A. A. Caudy, A. G. Fraser, C. Boone, B. J. Andrews, and A. P. Rosebrock
Genome Res 24, 1363-1370 (1 August 2014)

Automated identification of pathways from quantitative genetic interaction data
A. Battle, M. C. Jonikas, P. Walter, J. S. Weissman, and D. Koller
Mol Syst Biol 6, 379-379 (28 July 2014)

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae
O. Gallego, M. J. Betts, J. Gvozdenovic-Jeremic, K. Maeda, C. Matetzki, C. Aguilar-Gurrieri, P. Beltran-Alvarez, S. Bonn, C. Fernandez-Tornero, L. J. Jensen et al.
Mol Syst Biol 6, 430-430 (28 July 2014)

A global protein-lipid interactome map
M. Brehme, and M. Vidal
Mol Syst Biol 6, 443-443 (28 July 2014)

Genetic interactions reveal the evolutionary trajectories of duplicate genes
B. VanderSluis, J. Bellay, G. Musso, M. Costanzo, B. Papp, F. J. Vizeacoumar, A. Baryshnikova, B. Andrews, C. Boone, C. L. Myers et al.
Mol Syst Biol 6, 429-429 (28 July 2014)

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S.-M. Fendt, A. P. Oliveira, S. Christen, P. Picotti, R. C. Dechant, and U. Sauer
Mol Syst Biol 6, 432-432 (28 July 2014)

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
T. Yamada, A. S. Waller, J. Raes, A. Zelezniak, N. Perchat, A. Perret, M. Salanoubat, K. R. Patil, J. Weissenbach, P. Bork et al.
Mol Syst Biol 8, 581-581 (23 July 2014)

Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
M. Spitzer, E. Griffiths, K. M. Blakely, J. Wildenhain, L. Ejim, L. Rossi, G. De Pascale, J. Curak, E. Brown, M. Tyers et al.
Mol Syst Biol 7, 499-499 (23 July 2014)

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes
K. K. Lee, M. E. Sardiu, S. K. Swanson, J. M. Gilmore, M. Torok, P. A. Grant, L. Florens, J. L. Workman, and M. P. Washburn
Mol Syst Biol 7, 503-503 (23 July 2014)

Predicting selective drug targets in cancer through metabolic networks
O. Folger, L. Jerby, C. Frezza, E. Gottlieb, E. Ruppin, and T. Shlomi
Mol Syst Biol 7, 501-501 (23 July 2014)

Systematic exploration of synergistic drug pairs
M. Cokol, H. N. Chua, M. Tasan, B. Mutlu, Z. B. Weinstein, Y. Suzuki, M. E. Nergiz, M. Costanzo, A. Baryshnikova, G. Giaever et al.
Mol Syst Biol 7, 544-544 (23 July 2014)

Differential network biology
T. Ideker, and N. J. Krogan
Mol Syst Biol 8, 565-565 (23 July 2014)

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities
F. J. Vizeacoumar, R. Arnold, F. S. Vizeacoumar, M. Chandrashekhar, A. Buzina, J. T. F. Young, J. H. M. Kwan, A. Sayad, P. Mero, S. Lawo et al.
Mol Syst Biol 9, 696-696 (21 July 2014)

Epigenetic epistatic interactions constrain the evolution of gene expression
S. Park, and B. Lehner
Mol Syst Biol 9, 645-645 (21 July 2014)

Msp1/ATAD1 maintains mitochondrial function by facilitating the degradation of mislocalized tail-anchored proteins
Y.-C. Chen, G. K. E. Umanah, N. Dephoure, S. A. Andrabi, S. P. Gygi, T. M. Dawson, V. L. Dawson, and J. Rutter
EMBO J. 33, 1548-1564 (17 July 2014)

The Insertion Green Monster (iGM) Method for Expression of Multiple Exogenous Genes in Yeast
V. M. Labunskyy, Y. Suzuki, T. J. Hanly, A. Murao, F. P. Roth, and V. N. Gladyshev
G3 4, 1183-1191 (10 July 2014)

Topological properties of robust biological and computational networks
S. Navlakha, X. He, C. Faloutsos, and Z. Bar-Joseph
J R Soc Interface 11, 20140283-20140283 (6 July 2014)

Arabidopsis and Maize RidA Proteins Preempt Reactive Enamine/Imine Damage to Branched-Chain Amino Acid Biosynthesis in Plastids
T. D. Niehaus, T. N. D. Nguyen, S. K. Gidda, M. ElBadawi-Sidhu, J. A. Lambrecht, D. R. McCarty, D. M. Downs, A. J. L. Cooper, O. Fiehn, R. T. Mullen et al.
Plant Cell 26, 3010-3022 (1 July 2014)

Nuclear functions of prefoldin
G. Millan-Zambrano, and S. Chavez
Open Biol 4, 140085-140085 (1 July 2014)

Predicting microbial growth
J. Monk, and B. O. Palsson
Science 344, 1448-1449 (27 June 2014)

Gene network inference by probabilistic scoring of relationships from a factorized model of interactions
M. Žitnik, and B. Zupan
Bioinformatics 30, i246-i254 (15 June 2014)

Scale-space measures for graph topology link protein network architecture to function
M. Hulsman, C. Dimitrakopoulos, and J. de Ridder
Bioinformatics 30, i237-i245 (15 June 2014)

Inferring gene ontologies from pairwise similarity data
M. Kramer, J. Dutkowski, M. Yu, V. Bafna, and T. Ideker
Bioinformatics 30, i34-i42 (15 June 2014)

The conserved AAA-ATPase Msp1 confers organelle specificity to tail-anchored proteins
V. Okreglak, and P. Walter
Proc. Natl. Acad. Sci. USA 111, 8019-8024 (3 June 2014)

Epistasis analysis for quantitative traits by functional regression model
F. Zhang, E. Boerwinkle, and M. Xiong
Genome Res 24, 989-998 (1 June 2014)

Synthetic Cytotoxicity: Digenic Interactions with TEL1/ATM Mutations Reveal Sensitivity to Low Doses of Camptothecin
X. Li, N. J. O'Neil, N. Moshgabadi, and P. Hieter
Genetics 197, 611-623 (1 June 2014)

Controllability in protein interaction networks
S. Wuchty, N. J. O'Neil, N. Moshgabadi, and P. Hieter
Proc. Natl. Acad. Sci. USA 111, 7156-7160 (13 May 2014)

Stress-triggered Activation of the Metalloprotease Oma1 Involves Its C-terminal Region and Is Important for Mitochondrial Stress Protection in Yeast
I. Bohovych, G. Donaldson, S. Christianson, N. Zahayko, and O. Khalimonchuk
J Biol Chem 289, 13259-13272 (9 May 2014)

Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression
B. D. Landry, C. E. Mapa, H. E. Arsenault, K. E. Poti, and J. A. Benanti
EMBO J. 33, 1044-1060 (2 May 2014)

Antifungal Drug Development: Challenges, Unmet Clinical Needs, and New Approaches
T. Roemer, and D. J. Krysan
Cold Spring Harb Perspect Med 4, a019703-a019703 (1 May 2014)

A Saccharomyces cerevisiae RNase H2 Interaction Network Functions To Suppress Genome Instability
S. Allen-Soltero, S. L. Martinez, C. D. Putnam, and R. D. Kolodner
Mol. Cell. Biol. 34, 1521-1534 (15 April 2014)

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