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2. Avelumab first‐line maintenance in advanced urothelial carcinoma: Complete screening for prognostic and predictive factors using machine learning in the JAVELIN Bladder 100 phase 3 trial.

Author

Manitz, Juliane, Gerhold‐Ay, Aslihan, Kieslich, Pascal, Shah, Parantu, Mrowiec, Thomas, and Tyroller, Karin

Subjects
CLINICAL trials, PROGNOSIS, TRANSITIONAL cell carcinoma, MACHINE learning, MEDICAL screening
Abstract

Background: Avelumab first‐line (1 L) maintenance is a standard of care for advanced urothelial carcinoma (aUC) based on the JAVELIN Bladder 100 phase 3 trial, which showed that avelumab 1 L maintenance + best supportive care (BSC) significantly prolonged overall survival (OS) and progression‐free survival (PFS) vs BSC alone in patients who were progression free after receiving 1 L platinum‐containing chemotherapy. Here, we comprehensively screened JAVELIN Bladder 100 trial datasets to identify prognostic factors that define subpopulations of patients with longer or shorter OS irrespective of treatment, and predictive factors that select patients who could obtain a greater OS benefit from avelumab 1 L maintenance treatment. Methods: We performed machine learning analyses to screen a large set of baseline covariates, including patient demographics, disease characteristics, laboratory values, molecular biomarkers, and patient‐reported outcomes. Covariates were identified from previously reported analyses and established prognostic and predictive markers. Variables selected from random survival forest models were processed further in univariate Cox models with treatment interaction and visually inspected using correlation analysis and Kaplan–Meier curves. Results were summarized in a multivariable Cox model. Results: Prognostic baseline covariates associated with OS included in the final model were assignment to avelumab 1 L maintenance treatment, Eastern Cooperative Oncology Group performance status, site of metastasis, sum of longest target lesion diameters, levels of C‐reactive protein and alkaline phosphatase in blood, lymphocyte proportion in intratumoral stroma, tumor mutational burden, and tumor CD8+ T‐cell infiltration. Potential predictive factors included site of metastasis, tumor mutation burden, and tumor CD8+ T‐cell infiltration. An analysis in patients with PD‐L1+ tumors had similar findings to those in the overall population. Conclusions: Machine learning analyses of data from the JAVELIN Bladder 100 trial identified potential prognostic and predictive factors for avelumab 1 L maintenance treatment in patients with aUC, which warrant further evaluation in other clinical datasets. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Supplementary Methods, Figure Legends from The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies

Author

Vangamudi, Bhavatarini, primary, Paul, Thomas A., primary, Shah, Parantu K., primary, Kost-Alimova, Maria, primary, Nottebaum, Lisa, primary, Shi, Xi, primary, Zhan, Yanai, primary, Leo, Elisabetta, primary, Mahadeshwar, Harshad S., primary, Protopopov, Alexei, primary, Futreal, Andrew, primary, Tieu, Trang N., primary, Peoples, Mike, primary, Heffernan, Timothy P., primary, Marszalek, Joseph R., primary, Toniatti, Carlo, primary, Petrocchi, Alessia, primary, Verhelle, Dominique, primary, Owen, Dafydd R., primary, Draetta, Giulio, primary, Jones, Philip, primary, Palmer, Wylie S., primary, Sharma, Shikhar, primary, and Andersen, Jannik N., primary

Published
2023
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5. Data from Genetic Events That Limit the Efficacy of MEK and RTK Inhibitor Therapies in a Mouse Model of KRAS-Driven Pancreatic Cancer

Author

Pettazzoni, Piergiorgio, primary, Viale, Andrea, primary, Shah, Parantu, primary, Carugo, Alessandro, primary, Ying, Haoqiang, primary, Wang, Huamin, primary, Genovese, Giannicola, primary, Seth, Sahil, primary, Minelli, Rosalba, primary, Green, Tessa, primary, Huang-Hobbs, Emmet, primary, Corti, Denise, primary, Sanchez, Nora, primary, Nezi, Luigi, primary, Marchesini, Matteo, primary, Kapoor, Avnish, primary, Yao, Wantong, primary, Francesco, Maria E. Di, primary, Petrocchi, Alessia, primary, Deem, Angela K., primary, Scott, Kenneth, primary, Colla, Simona, primary, Mills, Gordon B., primary, Fleming, Jason B., primary, Heffernan, Timothy P., primary, Jones, Philip, primary, Toniatti, Carlo, primary, DePinho, Ronald A., primary, and Draetta, Giulio F., primary

Published
2023
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6. Supplementary Figures 1 - 8 from The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies

Author

Vangamudi, Bhavatarini, primary, Paul, Thomas A., primary, Shah, Parantu K., primary, Kost-Alimova, Maria, primary, Nottebaum, Lisa, primary, Shi, Xi, primary, Zhan, Yanai, primary, Leo, Elisabetta, primary, Mahadeshwar, Harshad S., primary, Protopopov, Alexei, primary, Futreal, Andrew, primary, Tieu, Trang N., primary, Peoples, Mike, primary, Heffernan, Timothy P., primary, Marszalek, Joseph R., primary, Toniatti, Carlo, primary, Petrocchi, Alessia, primary, Verhelle, Dominique, primary, Owen, Dafydd R., primary, Draetta, Giulio, primary, Jones, Philip, primary, Palmer, Wylie S., primary, Sharma, Shikhar, primary, and Andersen, Jannik N., primary

Published
2023
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7. supplementary material and method from Genetic Events That Limit the Efficacy of MEK and RTK Inhibitor Therapies in a Mouse Model of KRAS-Driven Pancreatic Cancer

Author

Pettazzoni, Piergiorgio, primary, Viale, Andrea, primary, Shah, Parantu, primary, Carugo, Alessandro, primary, Ying, Haoqiang, primary, Wang, Huamin, primary, Genovese, Giannicola, primary, Seth, Sahil, primary, Minelli, Rosalba, primary, Green, Tessa, primary, Huang-Hobbs, Emmet, primary, Corti, Denise, primary, Sanchez, Nora, primary, Nezi, Luigi, primary, Marchesini, Matteo, primary, Kapoor, Avnish, primary, Yao, Wantong, primary, Francesco, Maria E. Di, primary, Petrocchi, Alessia, primary, Deem, Angela K., primary, Scott, Kenneth, primary, Colla, Simona, primary, Mills, Gordon B., primary, Fleming, Jason B., primary, Heffernan, Timothy P., primary, Jones, Philip, primary, Toniatti, Carlo, primary, DePinho, Ronald A., primary, and Draetta, Giulio F., primary

Published
2023
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8. Data from The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies

Author

Vangamudi, Bhavatarini, primary, Paul, Thomas A., primary, Shah, Parantu K., primary, Kost-Alimova, Maria, primary, Nottebaum, Lisa, primary, Shi, Xi, primary, Zhan, Yanai, primary, Leo, Elisabetta, primary, Mahadeshwar, Harshad S., primary, Protopopov, Alexei, primary, Futreal, Andrew, primary, Tieu, Trang N., primary, Peoples, Mike, primary, Heffernan, Timothy P., primary, Marszalek, Joseph R., primary, Toniatti, Carlo, primary, Petrocchi, Alessia, primary, Verhelle, Dominique, primary, Owen, Dafydd R., primary, Draetta, Giulio, primary, Jones, Philip, primary, Palmer, Wylie S., primary, Sharma, Shikhar, primary, and Andersen, Jannik N., primary

Published
2023
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9. supplementary Figures S1-S10 from Genetic Events That Limit the Efficacy of MEK and RTK Inhibitor Therapies in a Mouse Model of KRAS-Driven Pancreatic Cancer

Author

Pettazzoni, Piergiorgio, primary, Viale, Andrea, primary, Shah, Parantu, primary, Carugo, Alessandro, primary, Ying, Haoqiang, primary, Wang, Huamin, primary, Genovese, Giannicola, primary, Seth, Sahil, primary, Minelli, Rosalba, primary, Green, Tessa, primary, Huang-Hobbs, Emmet, primary, Corti, Denise, primary, Sanchez, Nora, primary, Nezi, Luigi, primary, Marchesini, Matteo, primary, Kapoor, Avnish, primary, Yao, Wantong, primary, Francesco, Maria E. Di, primary, Petrocchi, Alessia, primary, Deem, Angela K., primary, Scott, Kenneth, primary, Colla, Simona, primary, Mills, Gordon B., primary, Fleming, Jason B., primary, Heffernan, Timothy P., primary, Jones, Philip, primary, Toniatti, Carlo, primary, DePinho, Ronald A., primary, and Draetta, Giulio F., primary

Published
2023
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11. A Small Molecule Inhibitor of Ubiquitin-Specific Protease-7 Induces Apoptosis in Multiple Myeloma Cells and Overcomes Bortezomib Resistance

Author

Chauhan, Dharminder, Tian, Ze, Nicholson, Benjamin, Kumar, K.G. Suresh, Zhou, Bin, Carrasco, Ruben, McDermott, Jeffrey L., Leach, Craig A., Fulcinniti, Mariaterresa, Kodrasov, Matthew P., Weinstock, Joseph, Kingsbury, William D., Hideshima, Teru, Shah, Parantu K., Minvielle, Stephane, Altun, Mikael, Kessler, Benedikt M., Orlowski, Robert, Richardson, Paul, Munshi, Nikhil, and Anderson, Kenneth C.

Published
2012
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12. First-line avelumab in a cohort of 116 patients with metastatic Merkel cell carcinoma (JAVELIN Merkel 200): primary and biomarker analyses of a phase II study

Author

D'Angelo, Sandra P, primary, Lebbé, Celeste, additional, Mortier, Laurent, additional, Brohl, Andrew S, additional, Fazio, Nicola, additional, Grob, Jean-Jacques, additional, Prinzi, Natalie, additional, Hanna, Glenn J, additional, Hassel, Jessica C, additional, Kiecker, Felix, additional, Georges, Sara, additional, Ellers-Lenz, Barbara, additional, Shah, Parantu, additional, Güzel, Gülseren, additional, and Nghiem, Paul, additional

Published
2021
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13. HLA-A*03 is a Predictive Biomarker of Poor Response to Immune Checkpoint Blockade in Cancer

Author

Naranbhai, Vivek, primary, Viard, Mathias, additional, Dean, Michael, additional, Groha, Stefan, additional, Braun, David A., additional, Labaki, Chris, additional, Shukla, Sachet A., additional, Yuki, Yuko, additional, Shah, Parantu, additional, Chin, Kevin, additional, Wind-Rotolo, Megan, additional, Mu, Xinmeng Jasmine, additional, Robbins, Paul B., additional, Gusev, Alexander, additional, Choueiri, Toni K., additional, Gulley, James, additional, and Carrington, Mary, additional

Published
2021
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14. Abstract 964: Induction of immunogenic cell death and interferon signaling by carboplatin and the ATR inhibitor M6620 may contribute to anti-tumor activity of M6620-carboplatin-avelumab triplet combination in MC38 tumor model

Author

Alimzhanov, Marat, primary, George, Ashwin, additional, Shah, Parantu, additional, Zimmerman, Astrid, additional, Schroeder, Andreas, additional, Falk, Martin, additional, Amendt, Christiane, additional, Halle, Joern-Peter, additional, Blaukat, Andree, additional, Zenke, Frank, additional, and Soulard, Patricia, additional

Published
2020
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17. A cis-regulatory map of the Drosophila genome

Author

Nègre, Nicolas, Brown, Christopher D., Ma, Lijia, Bristow, Christopher Aaron, Miller, Steven W., Wagner, Ulrich, Kheradpour, Pouya, Eaton, Matthew L., Loriaux, Paul, Sealfon, Rachel, Li, Zirong, Ishii, Haruhiko, Spokony, Rebecca F., Chen, Jia, Hwang, Lindsay, Cheng, Chao, Auburn, Richard P., Davis, Melissa B., Domanus, Marc, Shah, Parantu K., Morrison, Carolyn A., Zieba, Jennifer, Suchy, Sarah, Senderowicz, Lionel, Victorsen, Alec, Bild, Nicholas A., Grundstad, Jason A., Hanley, David, MacAlpine, David M., Mannervik, Mattias, Venken, Koen, Bellen, Hugo, White, Robert, Gerstein, Mark, Russell, Steven, Grossman, Robert L., Ren, Bing, Posakony, James W., Kellis, Manolis, and White, Kevin P.

Published
2011
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18. Digital pathology to evaluate PD-L1 IHC scoring as a predictor of outcome with second-line avelumab treatment in patients with non-small cell lung cancer (NSCLC).

Author

Mrowiec, Thomas, primary, Svenson, Elena, additional, Gerhold-Ay, Aslihan, additional, Wolf, Corinna M, additional, Grote, Hans Juergen, additional, Otte, Marcus, additional, Rolfe, P. Alexander, additional, Shah, Parantu K., additional, von Heydebreck, Anja, additional, Scheuenpflug, Juergen, additional, Ruisi, Mary M., additional, Labarta-Beceiro, Violeta, additional, Beeman, Glenn, additional, and Cai, Ti, additional

Published
2020
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19. Avelumab in patients with previously treated metastatic Merkel cell carcinoma: long-term data and biomarker analyses from the single-arm phase 2 JAVELIN Merkel 200 trial

Author

D'Angelo, Sandra P, primary, Bhatia, Shailender, additional, Brohl, Andrew S, additional, Hamid, Omid, additional, Mehnert, Janice M, additional, Terheyden, Patrick, additional, Shih, Kent C, additional, Brownell, Isaac, additional, Lebbé, Celeste, additional, Lewis, Karl D, additional, Linette, Gerald P, additional, Milella, Michele, additional, Georges, Sara, additional, Shah, Parantu, additional, Ellers-Lenz, Barbara, additional, Bajars, Marcis, additional, Güzel, Gülseren, additional, and Nghiem, Paul T, additional

Published
2020
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28. Determinants of antigenicity and specificity in immune response for protein sequences

Author

Li Cheng, White Kevin P, Negre Nicolas N, Wu Wenjun, Wang Yulong, and Shah Parantu K

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Target specific antibodies are pivotal for the design of vaccines, immunodiagnostic tests, studies on proteomics for cancer biomarker discovery, identification of protein-DNA and other interactions, and small and large biochemical assays. Therefore, it is important to understand the properties of protein sequences that are important for antigenicity and to identify small peptide epitopes and large regions in the linear sequence of the proteins whose utilization result in specific antibodies. Results Our analysis using protein properties suggested that sequence composition combined with evolutionary information and predicted secondary structure, as well as solvent accessibility is sufficient to predict successful peptide epitopes. The antigenicity and the specificity in immune response were also found to depend on the epitope length. We trained the B-Cell Epitope Oracle (BEOracle), a support vector machine (SVM) classifier, for the identification of continuous B-Cell epitopes with these protein properties as learning features. The BEOracle achieved an F1-measure of 81.37% on a large validation set. The BEOracle classifier outperformed the classical methods based on propensity and sophisticated methods like BCPred and Bepipred for B-Cell epitope prediction. The BEOracle classifier also identified peptides for the ChIP-grade antibodies from the modENCODE/ENCODE projects with 96.88% accuracy. High BEOracle score for peptides showed some correlation with the antibody intensity on Immunofluorescence studies done on fly embryos. Finally, a second SVM classifier, the B-Cell Region Oracle (BROracle) was trained with the BEOracle scores as features to predict the performance of antibodies generated with large protein regions with high accuracy. The BROracle classifier achieved accuracies of 75.26-63.88% on a validation set with immunofluorescence, immunohistochemistry, protein arrays and western blot results from Protein Atlas database. Conclusions Together our results suggest that antigenicity is a local property of the protein sequences and that protein sequence properties of composition, secondary structure, solvent accessibility and evolutionary conservation are the determinants of antigenicity and specificity in immune response. Moreover, specificity in immune response could also be accurately predicted for large protein regions without the knowledge of the protein tertiary structure or the presence of discontinuous epitopes. The dataset prepared in this work and the classifier models are available for download at https://sites.google.com/site/oracleclassifiers/.

Published
2011
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29. The dChip survival analysis module for microarray data

Author

Minvielle Stéphane, Adamia Sophia, Yan Aimin, Shah Parantu K, Amin Samir B, Avet-Loiseau Hervé, Munshi Nikhil C, and Li Cheng

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Genome-wide expression signatures are emerging as potential marker for overall survival and disease recurrence risk as evidenced by recent commercialization of gene expression based biomarkers in breast cancer. Similar predictions have recently been carried out using genome-wide copy number alterations and microRNAs. Existing software packages for microarray data analysis provide functions to define expression-based survival gene signatures. However, there is no software that can perform survival analysis using SNP array data or draw survival curves interactively for expression-based sample clusters. Results We have developed the survival analysis module in the dChip software that performs survival analysis across the genome for gene expression and copy number microarray data. Built on the current dChip software's microarray analysis functions such as chromosome display and clustering, the new survival functions include interactive exploring of Kaplan-Meier (K-M) plots using expression or copy number data, computing survival p-values from the log-rank test and Cox models, and using permutation to identify significant chromosome regions associated with survival. Conclusions The dChip survival module provides user-friendly way to perform survival analysis and visualize the results in the context of genes and cytobands. It requires no coding expertise and only minimal learning curve for thousands of existing dChip users. The implementation in Visual C++ also enables fast computation. The software and demonstration data are freely available at http://dchip-surv.chenglilab.org.

Published
2011
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30. PASBio: predicate-argument structures for event extraction in molecular biology

Author

Shah Parantu K, Wattarujeekrit Tuangthong, and Collier Nigel

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction. Results We introduce PASBio by extending a model based on PropBank to the MB domain. The hypothesis we explore is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions. We chose predicates describing gene expression, molecular interactions and signal transduction events with the aim of covering a number of research areas in MB. Analysis was performed on sentences containing a set of verbal predicates from MEDLINE and full text journals. Results confirm the necessity to analyze PAS specifically for MB domain. Conclusions At present PASBio contains the analyzed PAS of over 30 verbs, publicly available on the Internet for use in advanced applications. In the future we aim to expand the knowledge base to cover more verbs and the nominal form of each predicate.

Published
2004
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31. Information extraction from full text scientific articles: Where are the keywords?

Author

Perez-Iratxeta Carolina, Shah Parantu K, Bork Peer, and Andrade Miguel A

Subjects
Information extraction, full text article, gene name, data mining, text mining, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, which offer larger sources of data, are currently available. Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant. Results In this work we addressed those questions showing that the keyword content of the different sections of a standard scientific article (abstract, introduction, methods, results, and discussion) is very heterogeneous. Conclusions Although the abstract contains the best ratio of keywords per total of words, other sections of the article may be a better source of biologically relevant data.

Published
2003
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33. TRIM28 and Interacting KRAB-ZNFs Control Self-Renewal of Human Pluripotent Stem Cells through Epigenetic Repression of Pro-differentiation Genes

Author

Oleksiewicz, Urszula, primary, Gładych, Marta, additional, Raman, Ayush T., additional, Heyn, Holger, additional, Mereu, Elisabetta, additional, Chlebanowska, Paula, additional, Andrzejewska, Anastazja, additional, Sozańska, Barbara, additional, Samant, Neha, additional, Fąk, Katarzyna, additional, Auguścik, Paulina, additional, Kosiński, Marcin, additional, Wróblewska, Joanna P., additional, Tomczak, Katarzyna, additional, Kulcenty, Katarzyna, additional, Płoski, Rafał, additional, Biecek, Przemysław, additional, Esteller, Manel, additional, Shah, Parantu K., additional, Rai, Kunal, additional, and Wiznerowicz, Maciej, additional

Published
2017
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34. Identification of functional elements and regulatory circuits by Drosophila modENCODE

Author

Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia A., Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C.R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., Kellis, Manolis, Booth, Benjamin, Comstock, Charles L.G., Dobin, Alex, Drenkow, Jorg, Dudoit, Sandrine, Dumais, Jacqueline, Fagegaltier, Delphine, Ghosh, Srinka, Hansen, Kasper D., Jha, Sonali, Langton, Laura, Lin, Wei, Miller, David, Tenney, Aaron E., Wang, Huaien, Willingham, Aarron T., Zaleski, Chris, Zhang, Dayu, Acevedo, David, Bishop, Eric P., Gadel, Sarah E., Jung, Youngsook L., Kennedy, Cameron D., Lee, Ok Kyung, Linder-Basso, Daniela, Marchetti, Sarah E., Shanower, Gregory, Nègre, Nicolas, Grossman, Robert L., Auburn, Richard, Bellen, Hugo J., Chen, Jia, Domanus, Marc H., Hanley, David, Heinz, Elizabeth, Li, Zirong, Meyer, Folker, Miller, Steven W., Morrison, Carolyn A., Scheftner, Douglas A., Senderowicz, Lionel, Shah, Parantu K., Suchy, Sarah, Tian, Feng, Venken, Koen J.T., White, Robert, Wilkening, Jared, Zieba, Jennifer, Nordman, Jared T., Orr-Weaver, Terry L., DeNapoli, Leyna C., Ding, Queying, Eng, Thomas, Kashevsky, Helena, Li, Sharon, Prinz, Joseph A., Hannon, Gregory J., Hirst, Martin, Marra, Marco, Rooks, Michelle, Zhao, Yongjun, Bryson, Terri D., Perry, Marc D., Kent, William J., Lewis, Suzanna E., Barber, Galt, Chateigner, Aurelien, Clawson, Hiram, Contrino, Sergio, Guillier, Francois, Hinrichs, Angie S., Kephart, Ellen T., Lloyd, Paul, Lyne, Rachel, McKay, Sheldon, Moore, Richard A., Mungall, Chris, Rutherford, Kim M., Ruzanov, Peter, Smith, Richard, Stinson, E. O., Zha, Zheng, Artieri, Carlo G., Malone, John H., Jiang, Lichun, Mattiuzzo, Nicolas, Feingold, Elise A., Good, Peter J., Guyer, Mark S., Lowdon, Rebecca F., Stem Cell Aging Leukemia and Lymphoma (SALL), and Restoring Organ Function by Means of Regenerative Medicine (REGENERATE)

Subjects
Transcription, Genetic, Genome, Insect, Gene regulatory network, Genomics, Genes, Insect, Computational biology, Biology, Genome, Article, Epigenesis, Genetic, Histones, Nucleosome, Animals, Drosophila Proteins, Gene Regulatory Networks, Promoter Regions, Genetic, Gene, Genetics, Multidisciplinary, Binding Sites, REDfly, Computational Biology, Molecular Sequence Annotation, Chromatin, Nucleosomes, Drosophila melanogaster, Gene Expression Regulation, RNA, Small Untranslated, Drosophila Protein, Transcription Factors
Abstract

From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.

Published
2010

35. TRIM28 multi-domain protein regulates cancer stem cell population in breast tumor development

Author

Czerwińska, Patrycja, primary, Shah, Parantu K., additional, Tomczak, Katarzyna, additional, Klimczak, Marta, additional, Mazurek, Sylwia, additional, Sozańska, Barbara, additional, Biecek, Przemysław, additional, Korski, Konstanty, additional, Filas, Violetta, additional, Mackiewicz, Andrzej, additional, Andersen, Jannik N., additional, and Wiznerowicz, Maciej, additional

Published
2016
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36. In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer

Author

Carugo, Alessandro, primary, Genovese, Giannicola, additional, Seth, Sahil, additional, Nezi, Luigi, additional, Rose, Johnathon Lynn, additional, Bossi, Daniela, additional, Cicalese, Angelo, additional, Shah, Parantu Krushnakant, additional, Viale, Andrea, additional, Pettazzoni, Piergiorgio Francesco, additional, Akdemir, Kadir Caner, additional, Bristow, Christopher Aaron, additional, Robinson, Frederick Scott, additional, Tepper, James, additional, Sanchez, Nora, additional, Gupta, Sonal, additional, Estecio, Marcos Roberto, additional, Giuliani, Virginia, additional, Dellino, Gaetano Ivan, additional, Riva, Laura, additional, Yao, Wantong, additional, Di Francesco, Maria Emilia, additional, Green, Tessa, additional, D’Alesio, Carolina, additional, Corti, Denise, additional, Kang, Ya’an, additional, Jones, Philip, additional, Wang, Huamin, additional, Fleming, Jason Bates, additional, Maitra, Anirban, additional, Pelicci, Pier Giuseppe, additional, Chin, Lynda, additional, DePinho, Ronald Anthony, additional, Lanfrancone, Luisa, additional, Heffernan, Timothy Paul, additional, and Draetta, Giulio Francesco, additional

Published
2016
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39. The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies

Author

Vangamudi, Bhavatarini, primary, Paul, Thomas A., additional, Shah, Parantu K., additional, Kost-Alimova, Maria, additional, Nottebaum, Lisa, additional, Shi, Xi, additional, Zhan, Yanai, additional, Leo, Elisabetta, additional, Mahadeshwar, Harshad S., additional, Protopopov, Alexei, additional, Futreal, Andrew, additional, Tieu, Trang N., additional, Peoples, Mike, additional, Heffernan, Timothy P., additional, Marszalek, Joseph R., additional, Toniatti, Carlo, additional, Petrocchi, Alessia, additional, Verhelle, Dominique, additional, Owen, Dafydd R., additional, Draetta, Giulio, additional, Jones, Philip, additional, Palmer, Wylie S., additional, Sharma, Shikhar, additional, and Andersen, Jannik N., additional

Published
2015
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40. Abstract 3528: The SMARCA2/4 catalytic activity, but not the bromodomain, is a drug target in SWI/SNF mutant cancers

Author

Vangamudi, Bhavatarini, primary, Paul, Thomas, additional, Shah, Parantu K., additional, Alimova, Maria K., additional, Nottebaum, Lisa, additional, Shi, Xi, additional, Zhan, Yanai, additional, Leo, Elisabetta, additional, Mahadeshwar, Harshad S., additional, Protopopov, Alexei, additional, Futreal, Andrew, additional, Tieu, Trang N., additional, Peoples, Mike, additional, Petrocchi, Alessia, additional, Marszalek, Joseph R., additional, Toniatti, Carlo, additional, Heffernan, Timothy P., additional, Verhelle, Dominique, additional, Draetta, Giulio, additional, Owen, Dafydd, additional, Jones, Philip, additional, Palmer, Wylie, additional, Sharma, Shikhar, additional, and Andersen, Jannik N., additional

Published
2015
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41. Genetic Events That Limit the Efficacy of MEK and RTK Inhibitor Therapies in a Mouse Model of KRAS-Driven Pancreatic Cancer

Author

Pettazzoni, Piergiorgio, primary, Viale, Andrea, additional, Shah, Parantu, additional, Carugo, Alessandro, additional, Ying, Haoqiang, additional, Wang, Huamin, additional, Genovese, Giannicola, additional, Seth, Sahil, additional, Minelli, Rosalba, additional, Green, Tessa, additional, Huang-Hobbs, Emmet, additional, Corti, Denise, additional, Sanchez, Nora, additional, Nezi, Luigi, additional, Marchesini, Matteo, additional, Kapoor, Avnish, additional, Yao, Wantong, additional, Francesco, Maria E. Di, additional, Petrocchi, Alessia, additional, Deem, Angela K., additional, Scott, Kenneth, additional, Colla, Simona, additional, Mills, Gordon B., additional, Fleming, Jason B., additional, Heffernan, Timothy P., additional, Jones, Philip, additional, Toniatti, Carlo, additional, DePinho, Ronald A., additional, and Draetta, Giulio F., additional

Published
2015
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43. Editorial

Author

Wiznerowicz, Maciej, primary, Shah, Parantu K, additional, and Andersen, Jannik N., additional

Published
2015
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44. Bone Marrow Microenvironment Regulates Alternative Splicing Events in Myeloma Cells through Downregulation of RNA Binding Protein Fox2

Author

Song, Weihua, primary, Zhang, Chaolin, additional, Hu, Yiguo, additional, Gkotzamanidou, Maria, additional, Shah, Parantu, additional, Shan, Weisong, additional, Yang, Guang, additional, Li, Yi, additional, Sperling, Adam, additional, Rashid, Naim, additional, Samur, Mehmet Kemal, additional, Amin, Samir B., additional, Tai, Yu-Tzu, additional, Hideshima, Teru, additional, Parmigiani, Giovanni, additional, Magrangeas, Florence, additional, Minvielle, Stephane, additional, Avet-Loiseau, Hervé, additional, Anderson, Kenneth C., additional, Li, Cheng, additional, and Munshi, Nikhil C., additional

Published
2014
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45. Abstract 4272: Applying TCGA data for breast cancer diagnostics and pathway analysis

Author

Andersen, Jannik, primary, Shah, Parantu, additional, Korski, Konstanty, additional, Ibbs, Matthew, additional, Filas, Violetta, additional, Kosiedowski, Michal, additional, Pukacki, Juliusz, additional, Mazurek, Cezary, additional, Wu, Yuanqing, additional, Chang, Edward, additional, Toniatti, Carlo, additional, Draetta, Giulio, additional, and Wiznerowicz, Maciej, additional

Published
2014
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46. Targeting Poly(ADP-Ribose) Polymerase and the c-Myb–Regulated DNA Damage Response Pathway in Castration-Resistant Prostate Cancer

Author

Li, Likun, primary, Chang, Wenjun, additional, Yang, Guang, additional, Ren, Chengzhen, additional, Park, Sanghee, additional, Karantanos, Theodoros, additional, Karanika, Styliani, additional, Wang, Jianxiang, additional, Yin, Jianhua, additional, Shah, Parantu K., additional, Takahiro, Hirayama, additional, Dobashi, Masato, additional, Zhang, Wenling, additional, Efstathiou, Eleni, additional, Maity, Sankar N., additional, Aparicio, Ana M., additional, Li Ning Tapia, Elsa M., additional, Troncoso, Patricia, additional, Broom, Bradley, additional, Xiao, Lianchun, additional, Lee, Hyun-Sung, additional, Lee, Ju-Seog, additional, Corn, Paul G., additional, Navone, Nora, additional, and Thompson, Timothy C., additional

Published
2014
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47. Bone Marrow Microenvironment Affects The Pathogenesis Of Multiple Myeloma Through Downregulation Of Alternative Splicing Factor Fox2 In Myeloma Cells

Author

Song, Weihua, primary, Zhang, Chaolin, additional, Hu, Yiguo, additional, Gkotzamanidou, Maria, additional, Shah, Parantu, additional, Shan, Weisong, additional, Yang, Guang, additional, Amin, Samir B., additional, Tai, Yu-Tzu, additional, Li, Yi, additional, Sperling, Adam, additional, Rashid, Naim, additional, Magrangeas, Florence, additional, Minvielle, Stephane, additional, Avet-Loiseau, Hervé, additional, Anderson, Kenneth C., additional, Li, Cheng, additional, and Munshi, Nikhil C., additional

Published
2013
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48. Functional and Molecular Impact Of Dp1-Dependent Alternate Splicing In Multiple Myeloma

Author

Fulciniti, Mariateresa, primary, Bashin, Manoj, additional, Samur, Mehmet Kemal, additional, Bandi, Rajya, additional, Shah, Parantu K, additional, Cagnetta, Antonia, additional, Li, Cheng, additional, Magrangeas, Florence, additional, Minvielle, Stephane, additional, Avet-Loiseau, Herve, additional, Anderson, Kenneth C., additional, and Munshi, Nikhil C., additional

Published
2013
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