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23 results on '"Kumar, Swathi A."'

3. National Technology Validation and Implementation Collaborative (NTVIC): Guidelines for Establishing Forensic Investigative Genetic Genealogy (FIGG) programs

Author

Wickenheiser, Ray A., primary, Naugle, Jennifer, additional, Hoey, Brian, additional, Nowlin, Rylene, additional, Kumar, Swathi A., additional, Kubinski, Mark A., additional, Glynn, Claire, additional, Valerio, Raymond, additional, Allen, Lance, additional, Stoiloff, Stephanie, additional, Kochanski, Jennifer, additional, Guerrini, Christi, additional, and Schubert, Anne Marie, additional

Published
2023
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7. Developmental Validation of the Forenseq® Kintelligence Kit, MiSeq Fgx®Sequencing System and ForenSeq Universal Analysis Software

Author

Antunes, Joana, primary, Walichiewicz, Paulina, additional, Forouzmand, Elmira, additional, Barta, Richelle, additional, Didier, Meghan, additional, Han, Yonmee, additional, Perez, Juan Carlos, additional, Snedecor, June, additional, Zlatkov, Clare, additional, Radecke, Sarah, additional, Holt, Cydne L., additional, Kumar, Swathi, additional, Padmabandu, Gothami, additional, Stephens, Kathryn M., additional, and Budowle, Bruce, additional

Published
2023
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10. Post COVID-19 sequelae: A prospective observational study from Northern India

Author

Naik, Shivdas, primary, Soneja, Manish, additional, Haldar, Soumendra, additional, Mundadan, Netto George, additional, Garg, Prerna, additional, Mittal, Ankit, additional, Desai, Devashish, additional, Trilangi, Praveen Kumar, additional, Chakraborty, Sayan, additional, Begam, Nazneen Nahar, additional, Bhattacharya, Bisakh, additional, Maher, Ganesh, additional, Kumar, Swathi S, additional, Kirthana, J, additional, Arunan, Bharathi, additional, Gupta, Ankesh, additional, Mahishi, Niranjan, additional, Rajanna, Chaitra, additional, Parsoon, Prateek, additional, Kumar, Nikhil A, additional, Maharatna, Sayan, additional, Bhattacharya, Akashneel, additional, Keri, Vishakh C, additional, Samed, Sameer A, additional, Adarsh, AK, additional, Shareef, Imtiyaz, additional, Ravela, Neeren, additional, Swain, Satish, additional, Sarda, Radhika, additional, Kadnur, Harshith B, additional, Dudhwal, Ashok, additional, Agarwal, Ayush, additional, Vedula, Kartik, additional, Gupta, Ashish, additional, Agarwal, Shubham, additional, Anand, R, additional, Lalikar, Pratima, additional, Jagtap, Pallavi, additional, Premjeet, B, additional, Kodan, Parul, additional, Sethi, Prayas, additional, Ray, Animesh, additional, Jorwal, Pankaj, additional, Kumar, Arvind, additional, Nischal, Neeraj, additional, Sinha, Sanjeev, additional, Biswas, Ashutosh, additional, and Wig, Naveet, additional

Published
2021
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13. An encyclopedia of mouse DNA elements (Mouse ENCODE)

Author

Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa, Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, and Adams, Leslie B

Published
2012
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16. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Author

Yong Cheng, Weisheng Wu, Kumar, Swathi Ashok, Duonan Yu, Deng, Wulan, Tripic, Tamara, King, David C., Kuan-Bei Chen, Ying Zhang, Drautz, Daniela, Giardine, Belinda, Schuster, Stephan C., Miller,Webb, Chiaromonte, Francesca, Yu Zhang, Blobel, Gerd A., Weiss, Mitchell J., and Hardison, Ross C.

Subjects
Histones -- Structure, Gene expression -- Analysis, Genetic transcription -- Research, Binding proteins -- Research, Health
Published
2009

17. Transciptional enhancement by GATA1-occupaied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Author

Yong Cheng, King, David C., Dore, Louis C., Xinmin Zhang, Yuepin Zhou, Ying Zhang, Dorman, Christine, Abebe, Demesew, Kumar, Swathi A., Chiaromonte, Francesca, Miller, Webb, Green, Ronald D., Weiss, Mitchell J., and Hardison, Ross C.

Subjects
Genetic transcription -- Research, Chromatin -- Usage, Chromatin -- Genetic aspects, DNA replication -- Research, Health
Published
2008

18. Label‐free Voltammetric Detection of Products of Terminal Deoxynucleotidyl Transferase Tailing Reaction.

Author

Hermanová, Monika, Havranová‐Vidláková, Pavlína, Ondráčková, Anna, Kumar, Swathi Senthil, Bowater, Richard, and Fojta, Miroslav

Subjects
VOLTAMMETRY, NUCLEOTIDYLTRANSFERASES, ELECTROCHEMICAL analysis, BASE pairs, OLIGONUCLEOTIDES
Abstract

A label‐free approach that takes advantage of intrinsic electrochemical activity of nucleobases has been applied to study the products of terminal deoxynucleotidyl transferase (TdT) tailing reaction. DNA homooligonucleotides A30, C30 and T30 were used as primers for the tailing reaction to which a dNTP – or a mixture of dNTPs – and TdT were added to form the tails. Electrochemical detection enabled study of the tailing reaction products created by various combinations of primers and dNTPs, with pyrolytic graphite electrode (PGE) being suitable for remarkably precise analysis of the length of tailing reaction products. Furthermore, the hanging mercury drop electrode (HMDE) was able to reveal formation of various DNA structures, such as DNA hairpins and G‐quadruplexes, which influence the behavior of DNA molecules at the negatively charged surface of HMDE. Thus, the described approach proves to be an excellent tool for studying the TdT tailing reactions and for exploring how various DNA structures affect both the tailing reactions and electrochemical behavior of DNA oligonucleotides at electrode surfaces. [ABSTRACT FROM AUTHOR]

Published
2019
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19. Dynamics of the Epigenetic Landscape During Erythroid Differentiation after Gata1 Restoration

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Kellis, Manolis, Ernst, Jason, Wu, Weisheng, Cheng, Yong, Keller, Cheryl A., Kumar, Swathi Ashok, Mishra, Tejaswini, Morrissey, Christapher, Dorman, Christine M., Chen, Kuan-Bei, Drautz, Daniela, Giardine, Belinda, Shibata, Yoichiro, Song, Lingyun, Pimkin, Max, Crawford, Gregory E., Furey, Terrence S., Miller, Webb, Taylor, James, Schuster, Stephan C., Zhang, Yu, Chiaromonte, Francesca, Blobel, Gerd A., Weiss, Mitchell J., Hardison, Ross C., Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Kellis, Manolis, Ernst, Jason, Wu, Weisheng, Cheng, Yong, Keller, Cheryl A., Kumar, Swathi Ashok, Mishra, Tejaswini, Morrissey, Christapher, Dorman, Christine M., Chen, Kuan-Bei, Drautz, Daniela, Giardine, Belinda, Shibata, Yoichiro, Song, Lingyun, Pimkin, Max, Crawford, Gregory E., Furey, Terrence S., Miller, Webb, Taylor, James, Schuster, Stephan C., Zhang, Yu, Chiaromonte, Francesca, Blobel, Gerd A., Weiss, Mitchell J., and Hardison, Ross C.

Abstract

Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors, National Institutes of Health (U.S.) (Grant number RC1HG005334), National Science Foundation (U.S.). (Award 0905968)

Published
2012

20. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Author

Wu, Weisheng, primary, Cheng, Yong, additional, Keller, Cheryl A., additional, Ernst, Jason, additional, Kumar, Swathi Ashok, additional, Mishra, Tejaswini, additional, Morrissey, Christapher, additional, Dorman, Christine M., additional, Chen, Kuan-Bei, additional, Drautz, Daniela, additional, Giardine, Belinda, additional, Shibata, Yoichiro, additional, Song, Lingyun, additional, Pimkin, Max, additional, Crawford, Gregory E., additional, Furey, Terrence S., additional, Kellis, Manolis, additional, Miller, Webb, additional, Taylor, James, additional, Schuster, Stephan C., additional, Zhang, Yu, additional, Chiaromonte, Francesca, additional, Blobel, Gerd A., additional, Weiss, Mitchell J., additional, and Hardison, Ross C., additional

Published
2011
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21. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Author

Cheng, Yong, primary, Wu, Weisheng, additional, Ashok Kumar, Swathi, additional, Yu, Duonan, additional, Deng, Wulan, additional, Tripic, Tamara, additional, King, David C., additional, Chen, Kuan-Bei, additional, Zhang, Ying, additional, Drautz, Daniela, additional, Giardine, Belinda, additional, Schuster, Stephan C., additional, Miller, Webb, additional, Chiaromonte, Francesca, additional, Zhang, Yu, additional, Blobel, Gerd A., additional, Weiss, Mitchell J., additional, and Hardison, Ross C., additional

Published
2009
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22. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Author

Cheng, Yong, primary, King, David C., additional, Dore, Louis C., additional, Zhang, Xinmin, additional, Zhou, Yuepin, additional, Zhang, Ying, additional, Dorman, Christine, additional, Abebe, Demesew, additional, Kumar, Swathi A., additional, Chiaromonte, Francesca, additional, Miller, Webb, additional, Green, Roland D., additional, Weiss, Mitchell J., additional, and Hardison, Ross C., additional

Published
2008
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23. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Author

Weisheng Wu, Yong Cheng, Keller, Cheryl A., Ernst, Jason, Kumar, Swathi Ashok, Mishra, Tejaswini, Morrissey, Christapher, Dorman, Christine M., Kuan-Bei Chen, Drautz, Daniela, Giardine, Belinda, Shibata, Yoichiro, Lingyun Song, Pimkin, Max, Crawford, Gregory E., Furey, Terrence S., Kellis, Manolis, Miller, Webb, Taylor, James, and Schuster, Stephan C.

Subjects
*CHROMATIN, *NUCLEAR proteins, *PROTEINS, *TRANSCRIPTION factors, *GENETIC regulation
Abstract

Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors. [ABSTRACT FROM AUTHOR]

Published
2011
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