Publications

93. Epigenetic Reprogramming of RAS-driven Rhabdomyosarcoma via MEK Inhibition
Yohe, M.E.; Gryder, B.E.; Shern, J.F.; Chou, H.C.; Song, Y.K.; Liao, H.; Sindiri, S.; Mendoza, A.; Zhang, X.; Guha, R.; Haines, D.C.; Mathews-Griner, L.A.; Li, S.Q.; Ferrer, M.; Thomas, C.J.; Khan, J.
2016, submitted
92. PAX3-FOXO1 establishes myogenic super enhancers and confers BET bromodomain vulnerability
Gryder, B.E.; Yohe, M.E.; Chou, H.C.; Zhang, X.; Song, Y.; Marques, J.; Schaefer, B.; Sen, N.; Patidar, R.; Wen, X.; Wei, J.; Guha, R.; Ferrer, M.; Lal-Nag, M.; Andresson, T.; Shern, J.F.; Zhao, K.; Thomas, C.J.; Khan, J.
2016, submitted
91. The prediction of synergistic antimalarial drugs based upon known compound structure
Mason, D.J.; Eastman, R.T.; Guha, R.; Lewis, R.P.I.; Stott, I.P.; Bender, A.
2016, submitted
90. Large Scale Pharmacological Profiling of 3D Tumor Models of Cancer Cells
Mathews-Griner, L.A.; Zhang, X.; Guha, R.; McKnight, C.; Goldlust, I.S.; Lal, M.; Wilson, K.; Michael, S.; Titus, S.; Shinn, P.; Thomas, C.; Ferrer, M.
Cell Death & Disease, 2016, in press
89. Pharos: Collating Protein Information to Shed Light on the Druggable Genome
Nguyen, D.-T.; Mathias, S.; Bologa, C.; Brunak, S.; Fernandez, N.; Gaulton, A.; Hersey, A.; Holmes, J.; Jensen, L.J.; Karlsson, A.; Lu, G.; Mayan, A.; Mandava, G.; Mani, S.; Mehta, S.; Overington, J.P.; Patel, J.; Rouillard, A.D.; Schurer, S.; Sheils, T.; Simeonov, A.; Sklar, L.; Southall, N.; Ursu, O.; Vidovic, D.; Waller, A.; J., Y.; Jadhav, A.; Oprea, T.I.; Guha, R.
Nucl. Acids Res., 2016, in press
88. A high throughput screening model of the tumor microenvironment for ovarian cancer cell growth
Lal-Nag, M.; McGee, L.; Guha, R.; Lengyel, E.; Kenny, H.A.; Ferrer, M.
SLAS Discovery, 2016, in press
87. Cancer network activity associated with therapeutic response and synergism
Serra-Musach, J.; Mateo, F.; Capdevila-Busquets, E.; Zhang, X.; Guha, R.; Thomas, C.; Gruseo, J.; Ruiz de Garibay, G.; Villaneuva, A.; Gustafsson, M.; Benson, M.; Jaeger, S.; Heyn, H.; Vizoso, M.; Perez, H.; Cordero, A.; Gonzalez-Suarez, E.; Esteller, M.; Moreno-Bueno, G.; Lazaro, C.; Serra, V.; Arribas, J.; Ferrer, M.; Aloy, P.; Pujana, M.A.
Genome Medicine, 2016, 8, 1-12
86. Large Scale Screening and Identification of Novel Ebolavirus and Marburgvirus Entry Inhibitors
Anantpadma, M.; Kouznetsova, J.; Wang, H.; Huang, R.; Guha, R.; Lindstrom, A.; Shtanko, O.; Simeonov, A.; Maloney, D.J.; Maury, W.; LaCount, D.; Jadhav, A.; Davey, R.
Antimicrobial Agents and Chemotherapy, 2016, 60, 4471-4481

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85. mQC: A Heuristic Quality-Control Metric for High-Throughput Drug Combination Screening
Chen, L.; Wilson, K.; Goldlust, I.S.; Mott, B.T.; Eastman, R.T.; Davis, M.I.; Zhang, X.; McKnight, C.; Klumpp-Thomas, C.; Shinn, P.; Simmons, J.; Gormally, M.; Michael, S.; Thomas, C.J.; Ferrer, M.; Guha, R.
Sci. Rep., 2016, 6, 1
84. A druggable TCF4- and BRD4-dependent transcriptional network sustains malignancy in blastic plasmacytoid dendritic cell neoplasm
Ceribelli, M.; Kelly, P.N.; Ganapathi, K.; Evbuomwan, M.; Stefania, P.; Shaffer, A.L.; Wright, G.; Xiao, W.; Guha, R.; Zhang, X.; Ferrer, M.; Hou, E.Z.; Jaffe, E.S.; Reizis, B.; Thomas, C.; Staudt, L.M.
Cancer Cell, 2016, 30, 764-778
83. Ranking Differential Drug Activities from Dose Response Synthetic Lethality Screens
Guha, R.; Mathews-Griner, L.A.; Keller, J.; Fitzgerald, D.J.; Atignani, A.; Pastan, I.; Thomas, C.J.; Ferrer, M.
J. Biomol. Screen., 2016, 21, 942-955
82. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription
Baranello, L.; Wojtowicz, D.; Kouzine, F.; Cui, K.; Chan-Salis, K.Y.; Devaiah, B.; Wilson, K.; Guha, R.; Thomas, C.; Singer, D.; Pommier, Y.; Pugh, B.F.; Przytyka, T.M.; Lewis, B.A.; Zhao, K.; Levens, D.
Cell, 2016, 165, 357-371
81. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond
Van Voorhis, W.C. et al
PLoS Pathogens, 2016, 12, e1005763
80. Augmented efficacy of brentuximab vedotin combined with ruxolitinib and/or Navitoclax in a murine model of human Hodgkin’s Lymphoma
Jun, W.; Zhang, M.; Wilson, K.; Petrus, M.N.; Bamford, R.; Zhang, X.; Guha, R.; Ferrer, M.; Thomas, C.; Waldmann, T.A.
Proc. Nat. Acad. Sci., 2016, 113, 1624-1629

[ Link ]

79. Evaluation of the Activity of Lamivudine and Zidovudine against Ebola Virus In Vitro and In Vivo
Cong, Y.; Dyall, J.; Hart, B.J.; DeWald, L.E.; Johnson, J.C.; Postnikova, E.; Zhou, H.; Gross, R.; Rojas, O.; Alexander, I.; Josleyn, N.; Zhang, T.; Michelotti, J.; Janosko, K.; Honko, A.; Holbrook, M.; Bennett, R.S.; Olinger, G.O.; Glass, P.J.; Thomas, C.; Mierzwa, T.; Guha, R.; Shinn, P.; Michael, S.; Klumpp-Thomas, K.; McKnight, C.; Hensley, L.; Jahrling, P.B.
PLoS One, 2016, 11, e0166318
78. Chemical Screens Identify Drugs that Enhance or Mitigate Cellular Responses to Antibody-toxin fusion proteins
Antignani, A.; Mathews Griner, L.; Guha, R.; Simmon, N.; Pasetto, M.; Keller, J.; Huang, M.; Angelus, E.; Pastan, I.; Ferrer, M.; FitzGerald, D.; Thomas, C.
PLoS One, 2016, 11, e0161415
77. Actinoramide A stereoisomer identified as potent anti-malarial from titration-based screening of marine natural product extracts
Cheng, K.Chih-Chien.; Cao, S.; Raveh, A.; MacArthur, R.; Dranchak, P.; Chlipala, G.; Okoneski, M.T.; Guha, R.; Eastman, R.T.; Yuan, J.; Schultz, P.J.; Su, X.; Tamayo-Castillo, G.; Matainaho, T.; Clardy, J.; Sherman, D.H.; Inglese, J.
J. Nat. Prod., 2015, 78, 2411-2422
76. Synergy Maps: Exploring compound combinations using network-based visualization
Lewis, R.; Guha, R.; Korcsmaros, T.; Bender, A.
J. Cheminf., 2015, 7,

[ Link ]

75. Aurora B Kinase is a Potent and Selective Target in MYCN-driven Neuroblastoma
Bogen, D.; Wei, J.S.; Azorsa, D.O.; Ormanoglu, P.; Buehler, E.; Guha, R.; Keller, J.M.; Mathews-Griner, L.A.; Ferrer, M.; Song, Y.K.; Liao, H.; Mendoza, A.; Gryder, B.E.; Sindri, S.; He, J.; Wen, X.; Zhang, S.; Shern, J.F.; Yohe, M.E.; Taschner-Mandl, S.; Shohet, J.M.; Thomas, C.J.; Martin, S.E.; Ambros, P.F.; Khan, J.
Oncotarget, 2015, 6, 35247-35262
74. High-throughput matrix screening identifies synergistic and antagonistic antimalarial drug combinations
Mott, B.T.; Eastman, R.T.; Guha, R.; Sherlach, K.S.; Siriwardana, A.; Shinn, P.; McKnight, C.; Michael, S.; Lacerda-Quieroz, N.; Patel, P.R.; Khine, P.; Sun, H.; Kasbeka, M.; Aghdam, N.; Fontaine, S.D.; Liu, D.; Mierzwa, T.; Mathews-Griner, L.A.; Ferrer, M.; Renslo, A.R.; Inglese, J.; Yuan, J.; Roepe, P.D.; Su, X.; Thomas, C.J.
Scientific Reports, 2015, 5,
73. MP68-17 Novel Intravesical Therapies Identified from High Throughput Screening
Lewi, K.; Nair, A.; Railkar, R.; Brancato, S.; Hsu, I.; Li, Q.; Zhang, X.; Guha, R.; Apolo, A.; Theodorescu, D.
J. Urology, 2015, 193, e864-e865
72. Selective targeting of JAK/STAT signaling is potentiated by Bcl-xL blockade in IL-2-dependent adult T-cell leukemia
Zhang, M.; Mathews-Griner, L.A.; Ju, W.; Duveau, D.; Guha, R.; Petrus, M.N.; Wen, B.; Maeda, M.; Shinn, P.; Ferrer, M.; Conlon, K.D.; Bamford, R.; Oshea, J.; Thomas, C.J.; Waldmann, T.A.
Proc. Nat. Acad. Sci., 2015, 112, 12480-12485
71. A whole genome RNAi screen highlights components of the ER/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity
Pasetto, M.; Antignani, A.; Ormanoglu, P.; Buehler, E.; Guha, R.; Pastan, I.; Fitzgerald, D.J.
Proc. Nat. Acad. Sci., 2015, 112, 1135-1142
70. Novel Phenotypic Outcomes Identified for a Public Collection of Approved Drugs from a Publicly Accessible Panel of Assays
Lee, J.A.; Shinn, P.; Jaken, S.; Oliver, S.; Willard, F.S.; Heidler, S.; Peery, R.B.; Oler, J.; Chu, S.; Southall, N.; Dexheimer, T.S.; Smallwood, J.; Huang, R.; Guha, R.; Jadhav, A.; Cox, K.; Austin, C.P.; Simeonov, A.; Sittampalam, G.Sitta.; Husain, S.; Franklin, N.; Wild, D.J.; Yang, J.J.; Sutherland, J.J.; Thomas, C.J.
PLoS ONE, 2015, 10, e0130796 EP –
69. Chemogenomic profiling of endogenous PARK2 expression using a genome-edited coincidence reporter
Hasson, S.; Fogel, A.I.; Wang, C.; MacArthur, R.; Guha, R.; Heman-Ackah, S.; Martin, S.E.; Youle, R.J.; Inglese, J.
ACS Chem. Biol., 2015, 10, 1188-1197
68. A high-throughput assay for small molecule destabilizers of the KRAS oncoprotein
Carver, J.; Dexheimer, T.S.; Hsu, D.; Weng, M.T.; Guha, R.; Jadhav, A.; Simeonov, A.; Luo, J.
PLoS One, 2014, 9, e103836
67. Genome editing-enabled HTS assays expand drug target pathways for Charcot-Marie-Tooth disease
Inglese, J.; Dranchak, P.; Moran, P.; Jang, S.-W.; Cost, G.J.; Srinivasan, R.; Guha, R.; Martinez, N.; MacArthur, R.; Urnov, F.D.; Svaren, J.
ACS Chem. Biol., 2014, 9, 2594-2602
66. ATR inhibitors VE-821 and VX-970 sensitize cancer cells to topoisomerase I inhibitors by disabling DNA replication initiation and fork elongation responses
Josse, R.; S.E., M.; Guha, R.; Ormanoglu, P.; Pfister, T.; Morris, J.; Doroshow, J.; Pommier, Y.
Cancer. Res., 2014, 74, 6968-6979
65. On the Validity versus Utility of Activity Landscapes: Are All Activity Cliffs Statistically Significant?
Guha, R.; Medina-Franco, J.L.
J. Cheminf., 2014, 6,
64. BioAssay Research Database (BARD): Chemical biology and probe-development enabled by structured metadata and result types
Howe, E.; de Souza, A.; Lahr, D.; Chatwin, S.; Montgomery, P.; Alexander, B.; Nguyen, D.-T.; Cruz, Y.; Stonish, D.; Walzer, G.; Jason, R.; Picard, S.; Liu, Z.; Rose, J.; Xiang, X.; Asiedu, J.; Durkin, D.; Levine, J.; Yang, J.; Sch\”urer, S.; Braisted, J.; Southall, N.; Southern, M.; Chung, T.D.Y.; Brudz, S.; Tanega, C.; Schreiber, S.L.; Bittker, J.; Guha, R.; Clemons, P.
Nucl. Acids Res., 2014, 43, D1163-D1170
63. An overview of the challenges in designing, integrating, and delivering BARD: A public chemical-biology resource and query portal for multiple organizations, locations, and disciplines
de Souza, A.; Bittker, J.; Lahr, D.; Brudz, S.; Chatwin, S.; Oprea, T.I.; Waller, A.; Yang, A.; Southall, N.; Guha, R.; Schurer, S.; Vempati, U.; Southern, M.R.; Dawson, E.S.; Clemons, P.A.; Chung, T.D.Y.
J. Biomol. Screen., 2014, 19, 614-627
62. Blockade of oncogenic I$\kappa$B kinase activity in ABC DLBCL by small molecule BET protein inhibitors
Ceribelli, M.; Priscilla, K.; Shaffer, A.L.; Wright, G.; Yang, Y.; Mathews-Griner, L.A.; Guha, R.; Shinn, P.; Keller, J.M.; Liu, D.; Patel, P.R.; Ferrer, M.; Joshi, S.; Nerle, S.; Sandy, P.; Normant, E.; Thomas, C.J.; Staudt, L.M.
Proc. Natl. Acad. Sci., 2014, 111, 11365-11370
61. High-throughput combinatorial screening identifies drugs that cooperate with Ibrutinib to kill ABC Diffuse Large B Cell Lymphoma cells
Mathews, L.; Guha, R.; Shinn, P.; Young, R.A.; Keller, J.; Liu, D.; Goldlust, I.S.; Yasgar, A.; McKnight, C.; Boxer, M.B.; Duveau, D.; Jiang, J.K.; Michael, S.; Mierzwa, T.; Huang, W.; Walsh, M.J.; Mott, B.T.; Patel, P.R.; Leister, W.; Maloney, D.J.; LeClair, C.A.; Rai, G.; Jadhav, A.; Peyser, B.D.; Austin, C.P.; Martin, S.; Simeonov, A.; Ferrer, M.; Staudt, L.M.; Thomas, C.J.
Proc. Nat. Acad. Sci., 2014, 111, 2349-2354
60. Inhibition of Ceramide Metabolism Sensitizes Human Leukemia Cells to Inhibition of BCL2-like Proteins
Casson, L.; Howell, L.; Mathews, L.A.; Ferrer, M.; Southall, N.; Guha, R.; Keller, J.M.; Thomas, C.; Varmus, H.; Siskind, L.J.; Beverly, L.J.
PLoS One, 2013, 8, e54525

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59. Profile of the GSK published protein kinase inhibitor set across ATP-dependent and-independent luciferases: Implications for reporter-gene assays
Dranchak, P.; MacArthur, R.; Guha, R.; Zuercher, W.J.; Drewry, D.H.; Auld, D.S.; Inglese, J.
PLoS One, 2013, 8,
58. Genome-wide high-content RNAi screens identify regulators of Parkin upstream of mitophagy
Hasson, S.; Kane, L.; Sliter, D.; Hessa, T.; Wang, C.; Buehler, E.; Guha, R.; Martin, S.; Yamano, K.; Huang, C.H.; Heman-Ackah, S.; Youle, R.
Nature, 2013, 504, 291-295
57. What are we “tweeting” About Obesity? Mapping Tweets with Topic Modeling and Geographic Information System
Ghosh, D.; Guha, R.
Cartography and GIS, 2013, 4, 90-102
56. RNAi Screen Reveals Candidate miRNAs Associated with the NF-kappaB Pathway
Redan, B.W.; Motobar, O.; Tuzmen, P.; Guha, R.; Caplen, N.J.; S.E., M.
FASEB J., 2013, 27, 780-781
55. Targeting IRAK1 as a Novel Therapeutic Approach for Myelodysplastic Syndrome
Rhyasen, G.W.; Bolanos, L.; Fang, J.; Rasch, C.; Jerez, A.; Varney, M.; Wunderlicj, M.; Rigolino, C.; Mathews, L.; Ferrer, M.; Southall, N.; Guha, R.; Keller, J.; Thomas, C.; Beverly, L.J.; Agostino, C.; Oliva, E.N.; Cuzzola, M.; Maciejewski, J.P.; Mulloy, J.C.; Starczynowski, D.T.
Cancer Cell, 2013, 24, 90-104
54. Large-Scale Screening Identifies a Novel microRNA, miR-15a-3p, which Induces Apoptosis in Human Cancer Cell Lines
Druz, A.; Chen, Y.C.; Guha, R.; Betenbaugh, M.; Martin, S.; Shiloaoch, J.
RNAi Biology, 2013, 10, 1-14
53. Cisplatin Sensitivity Mediated by WEE1 and CHK1 is Mediated by miR-155 and the miR-15 Family
Pouliot, L.M.; Chen, Y.-C.; Bai, J.; Guha, R.; Martin, S.E.; Gottesman, M.M.; Hall, M.D.
Cancer Cell, 2012, 72, 5945-5955
52. Identification of Mammalian Protein Quality Control Factors by High-throughput Cellular Imaging
Pegoraro, G.; Voss, T.C.; Martin, S.E.; Tuzmen, P.; Guha, R.; Mistelli, T.
PLoS One, 2012, 7, e31684
51. High-Throughput Screening For Genes That Prevent Excess DNA Replication In Human Cells And For Molecules That Inhibit Them
Lee, C.; Johnson, R.L.; Wichterman-Kouznetsova, J.; Guha, R.; Ferrer, M.; Tuzmen, P.; Martin, S.; Zhu, W.; Depamphilis, M.L.
Methods, 2012, 57, 234-248
50. Cheminformatics, the Computer Science of Chemical Discovery Turning Open Source
Sterling, A.; Wegner, J.K.; Guha, R.; Bender, A.; Faulon, J.; Hastings, J.; O’Boyle, N.; Overington, J.P.; Vlijmen, H.V.; Willighagen, E.
Comm. ACM, 2012, 55, 65-75
49. Exploring Uncharted Territories — Predicting Activty Cliffs in Structure-Activity Landscapes
Guha, R.
J. Chem. Inf. Model., 2012, 52, 2181-2191
48. Dealing with the Data Deluge: Handling the Multitude of Chemical Biology Data Sources
Guha, R.; Nguyen, D.-T.; Southall, N.; Jadhav, A.
Curr. Protocols Chem. Biol., 2012, 4, 193-209
47. A Furoxan-Amodiaquine Hybrid as a Potential Therapeutic for Three Parasitic Diseases
Mott, B.T.; Cheng, C.C.; Guha, R.; Kommer, V.P.; Williams, D.L.; Vermeire, J.J.; Cappello, M.; Maloney, D.J.; Rai, G.; Jadhav, A.; Simeonov, A.; Inglese, J.; Posner, G.H; Thomas, C.J.
Med. Chem. Comm., 2012, 3, 1505-1511
46. Diversity-Oriented Synthesis Yields a Novel Lead for the Treatment of Malaria
Heidebrecht, R.W.; Mulrooney, C.; Austin, C.P.; Barker, R.H.; Beaudoin, J.A.; Cheng, K.Chih-Chien.; Comer, E.; Dandapani, S.; Dick, J.; Duvall, J.R.; Ekland, E.H.; Fidock, D.A.; Fitzgerald, M.E.; Foley, M.; Guha, R.; Hinkson, P.; Kramer, M.; Lukens, A.K.; Masi, D.; Marcaurelle, L.A.; Su, X.; Thomas, C.J.; Wewer, M.; Wiegand, R.C.; Wirth, D.; Xia, M.; Yuan, J.; Zhao, J.; Palmer, M.; Munoz, B.; Schreiber, S.
ACS Med. Chem. Lett., 2012, 3, 112-117

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45. Exploiting Synthetic Lethality for the Therapy of ABC Diffuse Large B Cell Lymphoma
Yang, Y.; Shaffer, A.; Emre, N. C. ?Tolga; Ceribelli, M.; Zhang, M.; Wright, G.; Xiao, W.; Powell, J.; Platig, J.; Kohlhammer, H.; Young, R.; Zhao, H.; Yang, Y.; Xu, W.; Buggy, J.; Balasubramanian, S.; Mathews, L.; Shinn, P.; Guha, R.; Ferrer, M.; Thomas, C.; Waldmann, T.; Staudt, L.
Cancer Cell, 2012, 21, 723-737

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44. Exploring Structure-Activity Data Using the Landscape Paradigm
Guha, R.
WIREs Comput. Mol. Sci., 2012, 2, 829-841
43. A 1536-well Quantitative High Throughput Screen to Identify Compounds Targeting Cancer Stem Cells
Mathews, L.A.; Keller, J.M.; Goodwin, B.; Guha, R.; Shinn, P.; Mull, R.; Thomas, C.; de Kluyver, R.; Sayers, T.; Ferrer, M.
J. Biomol. Screen., 2012, 17, 1231-1242
42. A Survey of Quantitative Descriptions of Molecular Structure
Guha, R.; Willighagen, E.L.
Curr. Topics Med. Chem., 2012, 12, 1946-1956
41. Genome-Wide RNAi Screen For Lysosomal Storage Disorders
Velayati, A.; Tuzmen, P.; Guha, R.; Martin, S.; Goldin, E.; Sidransky, E.
Molecular Genetics and Metabolism, 2012, 105, S63
40. Chemical Genomic Profiling for Antimalarial Therapies, Response Signatures, and Molecular Targets
Yuan, J.; Cheng, K.Chih-Chien.; Johnson, R.L.; Huang, R.; Pattaradilokrat, S.; Liu, A.; Guha, R.; Fidock, D.A.; Inglese, J.; Wellems, T.E.; Austin, C.P.; Su, X.
Science, 2011, 333, 724-729
39. KNIME workflow to assess PAINS filters in SMARTS format. Comparison of RDKit and Indigo cheminformatics libraries
Saubern, S.; Guha, R.; Baell, J.B.
Mol. Inf., 2011, 30, 847-850
38. Open Data, Open Source and Open Standards in Chemistry: The Blue Obelisk Five Years On
O’Boyle, N.; Guha, R.; Willighagen, E.; Adams, S.E.; Alvarsson, J.; Bradley, J.C.; Filippov, I.; Hanson, R.M.; Hanwell, M.D.; Hutchison, G.R.; James, C.A.; Jeliazkova, N.; Lang, A.; Langner, K.M.; Lonie, D.C.; Lowe, D.M.; Pansanel, J.; Pavlov, D.; Spjuth, O.; Steinbeck, C.; Tenderholt, A.; Theisen, K.; Murray-Rust, P.
J. Cheminf., 2011, 3,
37. Exploratory analysis of kinetic solubility measurements of a small molecule library
Guha, R.; Dexheimer, T.S.; Kestranek, A.N.; Jadhav, A.; Chervenak, A.M.; Ford, M.G.; Simeonov, A.; Roth, G.P.; Thomas, C.J.
Bioorg. Med. Chem., 2011, 19, 4127-4134
36. RNAi Screening Identifies TAK1 as a Potential Target for the Enhanced Efficacy of Topoisomerase Inhibitors
Martin, S.E.; Wu, Z.H.; Gehlhaus, K.Jones.; Zhang, Y.W.; Guha, R.; Miyamoto, S.; Pommier, Y.; Caplen, N.J.
Curr. Cancer Drug Targets, 2011, 11, 976-986
35. Improving Usability and Accessibility of Cheminformatics Tools for Chemists Through Cyberinfrastructure and Education
Guha, R.; Wiggins, G.D.; Wild, D.J.; Baik, M.H.; Pierce, M.E.; Fox, G.C.
In Silico Biol., 2011, 11, 41-60
34. Discovery of New Antimalarial Chemotypes Through Chemical Methodology and Library Development
Brown, L.E.; Chih-Chien Cheng, K.; Wei, W.; Yuan, P.; Dai, P.; Trilles, R.; Ni, F.; Yuan, J.; MacArthur, R.; Guha, R.; Johnson, R.L.; Su, X.; Dominguez, M.M.; Snyder, J.K.; Beeler, A.B.; Schaus, S.E.; Inglese, J.; Porco, J.
Proc. Nat. Acad. Sci., 2011, 108, 6775-6780
33. Advances in Cheminformatics Methodologies and Infrastructure to Support the Data Mining of Large, Heterogeneous Chemical Datasets
Guha, R.; Gilbert, K.; Fox, G.C.; Pierce, M.; Wild, D.; Yuan, H.
Curr. Comp. Aid. Drug Des., 2010, 6, 50-67
32. Use of Genetic Algorithm and Neural Network Approaches for Risk Factor Selection: A Case Study of West Nile Virus Dynamics in an Urban Environment
Ghosh, D.; Guha, R.
Computers, Environment and Urban Systems, 2010, 34, 189-203
31. Towards interoperable and reproducible QSAR analyses: Exchange of datasets.
Spjuth, O.; Willighagen, E.L.; Guha, R.; Eklund, M.; Wikberg, J.
Journal of Cheminformatics, 2010, 2,
30. PubChem as a Source of Polypharmacology
Chen, B.; Wild, D.; Guha, R.
J. Chem. Inf. Model., 2009, 49, 2044-2055
29. Chemoinformatic Analysis of Drugs, Natural Products, Molecular Libraries Small Molecule Repository and Combinatorial Libraries
Singh, N.; Guha, R.; Guilianotti, M.; Houghten, R.; Medina-Franco, J.L.
J. Chem. Inf. Model., 2009, 49, 1010-1024
28. Navigating Structure Activity Landscapes
Bajorath, J.; Peltason, L.; Wawer, M.; Guha, R.; Lajiness, M.S.; van Drie, J.H.
Drug Discov. Today, 2009, 14, 698-705
27. Pharmacophore Representation and Searching
Guha, R.; Van Drie, J.H.
CDK News, 2008, ASAP

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26. Assessing how well a modeling protocol captures a structure-activity landscape
Guha, R.; Van Drie, J.H.
J. Chem. Inf. Model., 2008, 48, 1716-1728
25. The Structure-Activity Landscape Index: Identifying and Quantifying Activity-Cliffs
Guha, R.; Van Drie, J.H.
J. Chem. Inf. Model., 2008, 48, 646-658
24. A Flexible Web Service Infrastructure for the Development and Deployment of Predictive Models
Guha, R.
J. Chem. Inf. Model., 2008, 48, 456-464
23. On the Interpretation and Interpretability of QSAR Models
Guha, R.
J. Comp. Aid. Molec. Des., 2008, 22, 857-871
22. Utilizing high throughput screening data for predictive toxicology models: Protocols and application to MLSCN assays
Guha, R.; Sch\”urer, S.C.
J. Comp. Aid. Molec. Des., 2008, 22, 367-384
21. Userscripts for the Life Sciences
Willighagen, E.L.; O’Boyle, N.; Gopalakrishnan, H.; Jiao, D.; Guha, R.; Steinbeck, C.; Wild, D.J.
BMC Bioinformatics, 2007, 8, 487
20. Chemical Data Mining of the NCI Human Tumor Cell Line Database
Wang, H.; Klinginsmith, J.; Dong, X.; Lee, A.; Guha, R.; Wu, Y.; Crippen, G.; Wild, D.J.
J. Chem. Inf. Model., 2007, 47, 2063-2076
19. Counting Clusters Using R-NN Curves
Guha, R.; Dutta, D.; Chen, T.; Wild, D.J.
J. Chem. Inf. Model., 2007, 47, 1308-1318
18. A Web Service Infrastructure for Chemoinformatics
Dong, X.; Gilbert, K.; Guha, R.; Heiland, R.; Kim, J.; Pierce, M.; Fox, G.; Wild, D.J.
J. Chem. Inf. Model., 2007, 47, 1303-1307
17. Ensemble Feature Selection: Consistent Descriptor Subsets for Multiple QSAR Models
Dutta, D.; Guha, R.; Chen, T.; Wild, D.J.
J. Chem. Inf. Model., 2007, 47, 989-997
16. Chemical Informatics Functionality in R
Guha, R.
J. Stat. Soft., 2007, 18,

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15. Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions.
Guha, R.; Dutta, D.; Jurs, P.C.; Chen, T.
J. Chem. Inf. Model., 2006, 46, 1836-1847
14. R-NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method
Guha, R.; Dutta, D.; Jurs, P.C; Chen, T.
J. Chem. Inf. Model., 2006, 46, 1713-1722
13. The Blue Obelisk–Interoperability in Chemical Informatics.
Guha, R.; Howard, M.T.; Hutchison, G.R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E.L.
J. Chem. Inf. Model., 2006, 46, 991-998
12. Scalable Partitioning and Exploration of Chemical Spaces using Geometric Hashing
Dutta, D.; Guha, R.; Jurs, P.C.; Chen, T.
J. Chem. Inf. Model., 2006, 46, 321-333
11. Generating, Using and Visualizing Molecular Information in R
Guha, R.
R News, 2006, 3, 28-33

[ Link ]

10. Validation of the CDK Surface Area Routine
Guha, R.
CDK News, 2006, 3, 5-9
9. Recent Developments of the Chemistry Development Kit (CDK) – An Open-Source Java Library for Chemo- and Bioinformatics
Steinbeck, C.; Hoppe, C.; Kuhn, S.; Floris, M.; Guha, R.; Willighagen, E.L.
Curr. Pharm. Des., 2006, 12, 2110-2120
8. Interpreting Computational Neural Network QSAR Models: A Detailed Interpretation of the Weights and Biases
Guha, R.; Stanton, D.T.; Jurs, P.C.
J. Chem. Inf. Model., 2005, 45, 1109-1121
7. Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance
Guha, R.; Jurs, P.C.
J. Chem. Inf. Model., 2005, 45, 800-806
6. Determining the Validity of a QSAR Model–A Classification Approach
Guha, R.; Jurs, P.C.
J. Chem. Inf. Model., 2005, 45, 65-73
5. Using R to Provide Statistical Functionality for QSAR Modeling in CDK to Provide Statistical Functionality for QSAR Modeling in CDK
Guha, R.
CDK News, 2005, 2, 7-13

[ Link ]

4. Using the CDK as a Backend to R
Guha, R.
CDK News, 2005, 2, 2-6

[ Link ]

3. Development of Linear, Ensemble, and Nonlinear Models for the Prediction and Interpretation of the Biological Activity of a Set of PDGFR Inhibitors.
Guha, R.; Jurs, P.C.
J. Chem. Inf. Comput. Sci., 2004, 44, 2179-2189
2. The Development of QSAR Models To Predict and Interpret the Biological Activity of Artemisinin Analogues
Guha, R.; Jurs, P.C.
J. Chem. Inf. Comput. Sci., 2004, 44, 1440-1449
1. Generation of QSAR Sets with a Self-Organizing Map.
Guha, R.; Serra, J.R.; Jurs, P.C.
J. Mol. Graph. Model., 2004, 23, 1-14

One thought on “Publications

  1. […] but it’s also useful to use this data to keep my CV updated or generate a publications page. Since BibDesk can export to Endnote XML format, I put together a simple Python script to process […]

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