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221 results on '"Madan, Anup"'

1. Author Correction: TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes

Author

Miklas, Jason W, Clark, Elisa, Levy, Shiri, Detraux, Damien, Leonard, Andrea, Beussman, Kevin, Showalter, Megan R, Smith, Alec T, Hofsteen, Peter, Yang, Xiulan, Macadangdang, Jesse, Manninen, Tuula, Raftery, Daniel, Madan, Anup, Suomalainen, Anu, Kim, Deok-Ho, Murry, Charles E, Fiehn, Oliver, Sniadecki, Nathan J, Wang, Yuliang, and Ruohola-Baker, Hannele

Subjects
Engineering, Electrical Engineering
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

2. TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes.

Author

Miklas, Jason, Clark, Elisa, Levy, Shiri, Detraux, Damien, Leonard, Andrea, Beussman, Kevin, Showalter, Megan, Smith, Alec, Hofsteen, Peter, Yang, Xiulan, Macadangdang, Jesse, Manninen, Tuula, Raftery, Daniel, Madan, Anup, Suomalainen, Anu, Kim, Deok-Ho, Murry, Charles, Fiehn, Oliver, Sniadecki, Nathan, Wang, Yuliang, and Ruohola-Baker, Hannele

Subjects
Calcium, Cardiolipins, Cell Line, Electrophysiology, Fatty Acids, Homeodomain Proteins, Human Embryonic Stem Cells, Humans, MicroRNAs, Mitochondria, Mitochondrial Trifunctional Protein, Mitochondrial Trifunctional Protein, alpha Subunit, Myocytes, Cardiac, Oxidation-Reduction, Patch-Clamp Techniques, RNA-Seq, Tumor Suppressor Proteins
Abstract

Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX.  Here we report, matured HADHA mutant cardiomyocytes treated with an endogenous mixture of fatty acids manifest the disease phenotype: defective calcium dynamics and repolarization kinetics which results in a pro-arrhythmic state. Single cell RNA-seq reveals a cardiomyocyte developmental intermediate, based on metabolic gene expression. This intermediate gives rise to mature-like cardiomyocytes in control cells but, mutant cells transition to a pathological state with reduced fatty acid beta-oxidation, reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling. This study reveals that HADHA (tri-functional protein alpha), a monolysocardiolipin acyltransferase-like enzyme, is required for fatty acid beta-oxidation and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.

Published
2019

3. Amino acid primed mTOR activity is essential for heart regeneration

Author

Miklas, Jason W., Levy, Shiri, Hofsteen, Peter, Mex, Diego Ic, Clark, Elisa, Muster, Jeanot, Robitaille, Aaron M., Sivaram, Gargi, Abell, Lauren, Goodson, Jamie M., Pranoto, Inez, Madan, Anup, Chin, Michael T., Tian, Rong, Murry, Charles E., Moon, Randall T., Wang, Yuliang, and Ruohola-Baker, Hannele

Published
2022
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4. Publisher Correction: The DNA sequence and analysis of human chromosome 14

Author

Heilig, Roland, Eckenberg, Ralph, Petit, Jean-Louis, Fonknechten, Núria, Da Silva, Corinne, Cattolico, Laurence, Levy, Michaël, Barbe, Valérie, de Berardinis, Véronique, Ureta-Vidal, Abel, Pelletier, Eric, Vico, Virginie, Anthouard, Véronique, Rowen, Lee, Madan, Anup, Qin, Shizhen, Sun, Hui, Du, Hui, Pepin, Kymberlie, Artiguenave, François, Robert, Catherine, Cruaud, Corinne, Brüls, Thomas, Jaillon, Olivier, Friedlander, Lucie, Samson, Gaelle, Brottier, Philippe, Cure, Susan, Ségurens, Béatrice, Anière, Franck, Samain, Sylvie, Crespeau, Hervé, Abbasi, Nissa, Aiach, Nathalie, Boscus, Didier, Dickhoff, Rachel, Dors, Monica, Dubois, Ivan, Friedman, Cynthia, Gouyvenoux, Michel, James, Rose, Madan, Anuradha, Mairey–Estrada, Barbara, Mangenot, Sophie, Martins, Nathalie, Ménard, Manuela, Oztas, Sophie, Ratcliffe, Amber, Shaffer, Tristan, Trask, Barbara, Vacherie, Benoit, Bellemere, Chadia, Belser, Caroline, Besnard-Gonnet, Marielle, Bartol–Mavel, Delphine, Boutard, Magali, Briez-Silla, Stéphanie, Combette, Stephane, Dufossé-Laurent, Virginie, Ferron, Carolyne, Lechaplais, Christophe, Louesse, Claudine, Muselet, Delphine, Magdelenat, Ghislaine, Pateau, Emilie, Petit, Emmanuelle, Sirvain-Trukniewicz, Peggy, Trybou, Arnaud, Vega-Czarny, Nathalie, Bataille, Elodie, Bluet, Elodie, Bordelais, Isabelle, Dubois, Maria, Dumont, Corinne, Guérin, Thomas, Haffray, Sébastien, Hammadi, Rachid, Muanga, Jacqueline, Pellouin, Virginie, Robert, Dominique, Wunderle, Edith, Gauguet, Gilbert, Roy, Alice, Sainte-Marthe, Laurent, Verdier, Jean, Verdier-Discala, Claude, Hillier, LaDeana, Fulton, Lucinda, McPherson, John, Matsuda, Fumihiko, Wilson, Richard, Scarpelli, Claude, Gyapay, Gábor, Wincker, Patrick, Saurin, William, Quétier, Francis, Waterston, Robert, Hood, Leroy, and Weissenbach, Jean

Published
2023
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5. A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer.

Author

Blau, C Anthony, Ramirez, Arturo B, Blau, Sibel, Pritchard, Colin C, Dorschner, Michael O, Schmechel, Stephen C, Martins, Timothy J, Mahen, Elisabeth M, Burton, Kimberly A, Komashko, Vitalina M, Radenbaugh, Amie J, Dougherty, Katy, Thomas, Anju, Miller, Christopher P, Annis, James, Fromm, Jonathan R, Song, Chaozhong, Chang, Elizabeth, Howard, Kellie, Austin, Sharon, Schmidt, Rodney A, Linenberger, Michael L, Becker, Pamela S, Senecal, Francis M, Mecham, Brigham H, Lee, Su-In, Madan, Anup, Ronen, Roy, Dutkowski, Janusz, Heimfeld, Shelly, Wood, Brent L, Stilwell, Jackie L, Kaldjian, Eric P, Haussler, David, and Zhu, Jingchun

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Breast Cancer, Clinical Trials and Supportive Activities, Biotechnology, Women's Health, Clinical Research, Health Disparities, Minority Health, Cancer, Good Health and Well Being, Antineoplastic Combined Chemotherapy Protocols, Bone Neoplasms, Community Networks, Drug Resistance, Neoplasm, Drug Screening Assays, Antitumor, Expert Testimony, Female, Follow-Up Studies, Humans, Leukapheresis, Longitudinal Studies, Middle Aged, Neoplasm Metastasis, Neoplastic Cells, Circulating, Research Personnel, Triple Negative Breast Neoplasms, Oncology & Carcinogenesis, Oncology and carcinogenesis, Health services and systems
Abstract

Accelerating cancer research is expected to require new types of clinical trials. This report describes the Intensive Trial of OMics in Cancer (ITOMIC) and a participant with triple-negative breast cancer metastatic to bone, who had markedly elevated circulating tumor cells (CTCs) that were monitored 48 times over 9 months. A total of 32 researchers from 14 institutions were engaged in the patient's evaluation; 20 researchers had no prior involvement in patient care and 18 were recruited specifically for this patient. Whole-exome sequencing of 3 bone marrow samples demonstrated a novel ROS1 variant that was estimated to be present in most or all tumor cells. After an initial response to cisplatin, a hypothesis of crizotinib sensitivity was disproven. Leukapheresis followed by partial CTC enrichment allowed for the development of a differential high-throughput drug screen and demonstrated sensitivity to investigational BH3-mimetic inhibitors of BCL-2 that could not be tested in the patient because requests to the pharmaceutical sponsors were denied. The number and size of CTC clusters correlated with clinical status and eventually death. Focusing the expertise of a distributed network of investigators on an intensively monitored patient with cancer can generate high-resolution views of the natural history of cancer and suggest new opportunities for therapy. Optimization requires access to investigational drugs.

Published
2016

6. Genetic Evaluation of Suspected Cases of Transient HIV-1 Infection of Infants

Author

Frenkel, Lisa M., Mullins, James I., Learn, Gerald H., Manns-Arcuino, Laura, Herring, Belinda L., Kalish, Marcia L., Steketee, Richard W., Thea, Donald M., Nichols, Joan E., Liu, Shan-Lu, Harmache, Abdallah, He, Xi, Muthui, David, Madan, Anup, Hood, Leroy, Haase, Ashley T., Zupancic, Mary, Staskus, Katherine, Wolinsky, Steven, Krogstad, Paul, Zhao, JiaQi, Chen, Irvin, Koup, Richard, Ho, David, Korber, Bette, Apple, Raymond J., Coombs, Robert W., Pahwa, Savita, and Roberts,, Norbert J.

Published
1998

7. Supplementary Data from Genome-Wide Analysis of Epigenetic Silencing Identifies BEX1 and BEX2 as Candidate Tumor Suppressor Genes in Malignant Glioma

Author

Foltz, Greg, primary, Ryu, Gi-Yung, primary, Yoon, Jae-Geun, primary, Nelson, Timothy, primary, Fahey, Jessica, primary, Frakes, Amanda, primary, Lee, Hwahyung, primary, Field, Lorie, primary, Zander, Kaitlin, primary, Sibenaller, Zita, primary, Ryken, Timothy C., primary, Vibhakar, Rajeev, primary, Hood, Leroy, primary, and Madan, Anup, primary

Published
2023
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8. Data from Genome-Wide Analysis of Epigenetic Silencing Identifies BEX1 and BEX2 as Candidate Tumor Suppressor Genes in Malignant Glioma

Author

Foltz, Greg, primary, Ryu, Gi-Yung, primary, Yoon, Jae-Geun, primary, Nelson, Timothy, primary, Fahey, Jessica, primary, Frakes, Amanda, primary, Lee, Hwahyung, primary, Field, Lorie, primary, Zander, Kaitlin, primary, Sibenaller, Zita, primary, Ryken, Timothy C., primary, Vibhakar, Rajeev, primary, Hood, Leroy, primary, and Madan, Anup, primary

Published
2023
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11. Metabolism as an early predictor of DPSCs aging

Author

Macrin, Dannie, Alghadeer, Ammar, Zhao, Yan Ting, Miklas, Jason W., Hussein, Abdiasis M., Detraux, Damien, Robitaille, Aaron M., Madan, Anup, Moon, Randall T., Wang, Yuliang, Devi, Arikketh, Mathieu, Julie, and Ruohola-Baker, Hannele

Published
2019
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12. Whole exome sequencing in the rat

Author

Foley, Julie F., Phadke, Dhiral P., Hardy, Owen, Hardy, Sara, Miller, Victor, Madan, Anup, Howard, Kellie, Kruse, Kimberly, Lord, Cara, Ramaiahgari, Sreenivasa, Solomon, Gregory G., Shah, Ruchir R., Pandiri, Arun R., Herbert, Ronald A., Sills, Robert C., and Merrick, B. Alex

Published
2018
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14. Distinctive repertoire of contingency genes conferring mutation-based phase variation and combinatorial expression of surface lipoproteins in Mycoplasma capricolum subsp, capricolum of the Mycoplasma mycoides phylogenetic cluster

Author

Wise, Kim S., Foecking, Mark F., Roske, Kerstin, Lee, Young Jin, Lee, Young Moo, Madan, Anup, and Calcutt, Michael J.

Subjects
Mycoplasma -- Research, Mycoplasma -- Genetic aspects, Bacterial genetics -- Research, Mycoplasmatales -- Genetic aspects, Mycoplasmatales -- Research, Biological sciences
Abstract

The generation of surface variation among many divergent species of Mollicutes (mycoplasmas) occurs through stochastic expression patterns of diverse lipoprotein genes. The size and wide distribution of such variable gene sets in minimal (~0.6- to 1.4-Mb) mycoplasmal genomes suggest their key role in the adaptation and survival of these wall-less monoderms. Diversity through variable genes is less clearly established among phylogenetically similar mycoplasmas, such as the Mycoplasma mycoides cluster of ruminant pathogens, which vary widely in host range and pathobiology. Using (i) genome sequences from two members of this clade, Mycoplasma capricolum subsp, capricolum and M. mycoides subsp, mycoides small colony biotype (SC), (ii) antibodies to specific peptide determinants of predicted M. capricolum subsp, capricolum gene products, and (iii) analysis of the membrane-associated proteome of M. capricolum subsp, capricolum, a novel set of six genes (vmcA to vmcF) expressing distinct Vmc (variable M. capricolum subsp, capricolum) lipoproteins is demonstrated. These occur at two separate loci in the M. capricolum subsp, capricolum genome, which shares striking overall similarity and gene synteny with the M. mycoides subsp, mycoides SC genome. Collectively, Vmc expression is noncoordinate and combinatorial, subject to a single-unit insertion/deletion in a 5' flanking dinucleotide repeat that governs expression of each vmc gene. All vmc genes share modular regions affecting expression and membrane translocation. In contrast, vmcA to wncD genes at one locus express surface proteins with highly structured size-variable repeating domains, whereas vmcE to vmcF genes express products with short repeats devoid of predicted structure. These genes confer a distinctive, dynamic surface architecture that may represent adaptive differences within this important group of pathogens as well as exploitable diagnostic targets.

Published
2006

15. Analysis of the DNA sequence and duplication history of human chromosome 15

Author

Zody, Michael C., Garber, Manuel, Sharpe, Ted, Young, Sarah K., Rowen, Lee, O'Neill, Keith, Whittaker, Charles A., Kamal, Michael, Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Kodira, Chinnappa D., Madan, Anup, Qin, Shizhen, Yang, Xiaoping, Abbasi, Nissa, Abouelleil, Amr, Arachchi, Harindra M., Baradarani, Lida, Birditt, Brian, Bloom, Scott, Bloom, Toby, Borowsky, Mark L., Burke, Jeremy, Butler, Jonathan, Cook, April, DeArellano, Kurt, DeCaprio, David, Dorris, III, Lester, Dors, Monica, Eichler, Evan E., Engels, Reinhard, Fahey, Jessica, Fleetwood, Peter, Friedman, Cynthia, Gearin, Gary, Hall, Jennifer L., Hensley, Grace, Johnson, Ericka, Jones, Charlien, Kamat, Asha, Kaur, Amardeep, Locke, Devin P., Madan, Anuradha, Munson, Glen, Jaffe, David B., Lui, Annie, Macdonald, Pendexter, Mauceli, Evan, Naylor, Jerome W., Nesbitt, Ryan, Nicol, Robert, O'Leary, Sinead B., Ratcliffe, Amber, Rounsley, Steven, She, Xinwei, Sneddon, Katherine M. B., Stewart, Sandra, Sougnez, Carrie, Stone, Sabrina M., Topham, Kerri, Vincent, Dascena, Wang, Shunguang, Zimmer, Andrew R., Birren, Bruce W., Hood, Leroy, Lander, Eric S., and Nusbaum, Chad

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Michael C. Zody (corresponding author) [1]; Manuel Garber [1]; Ted Sharpe [1]; Sarah K. Young [1]; Lee Rowen [2]; Keith O'Neill [1]; Charles A. Whittaker [1, 6]; Michael Kamal [...]

Published
2006
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16. The DNA sequence and analysis of human chromosome 14

Author

Heilig, Roland, Eckenberg, Ralph, Petit, Jean-Louis, Fonknechten, Núria, Da Silva, Corinne, Cattolico, Laurence, Levy, Michaël, Barbe, Valérie, de Berardinis, Véronique, Ureta-Vidal, Abel, Pelletier, Eric, Vico, Virginie, Anthouard, Véronique, Rowen, Lee, Madan, Anup, Qin, Shizhen, Sun, Hui, Du, Hui, Pepin, Kymberlie, Artiguenave, François, Robert, Catherine, Cruaud, Corinne, Brüls, Thomas, Jaillon, Olivier, Friedlander, Lucie, Samson, Gaelle, Brottier, Philippe, Cure, Susan, Ségurens, Béatrice, Anière, Franck, Samain, Sylvie, Crespeau, Hervé, Abbasi, Nissa, Aiach, Nathalie, Boscus, Didier, Dickhoff, Rachel, Dors, Monica, Dubois, Ivan, Friedman, Cynthia, Gouyvenoux, Michel, James, Rose, Madan, Anuradha, Mairey–Estrada, Barbara, Mangenot, Sophie, Martins, Nathalie, Ménard, Manuela, Oztas, Sophie, Ratcliffe, Amber, Shaffer, Tristan, Trask, Barbara, Vacherie, Benoit, Bellemere, Chadia, Belser, Caroline, Besnard-Gonnet, Marielle, Bartol–Mavel, Delphine, Boutard, Magali, Briez-Silla, Stéphanie, Combette, Stephane, Dufossé-Laurent, Virginie, Ferron, Carolyne, Lechaplais, Christophe, Louesse, Claudine, Muselet, Delphine, Magdelenat, Ghislaine, Pateau, Emilie, Petit, Emmanuelle, Sirvain-Trukniewicz, Peggy, Trybou, Arnaud, Vega-Czarny, Nathalie, Bataille, Elodie, Bluet, Elodie, Bordelais, Isabelle, Dubois, Maria, Dumont, Corinne, Guérin, Thomas, Haffray, Sébastien, Hammadi, Rachid, Muanga, Jacqueline, Pellouin, Virginie, Robert, Dominique, Wunderle, Edith, Gauguet, Gilbert, Roy, Alice, Sainte-Marthe, Laurent, Verdier, Jean, Verdier-Discala, Claude, Hillier, LaDeana, Fulton, Lucinda, McPherson, John, Matsuda, Fumihiko, Wilson, Richard, Scarpelli, Claude, Gyapay, Gábor, Wincker, Patrick, Saurin, William, Quétier, Francis, Waterston, Robert, Hood, Leroy, and Weissenbach, Jean

Published
2003
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17. The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain [R.sub.low]

Author

Papazisi, Leka, Gorton, Timothy S., Kutish, Gerald, Markham, Philip F., Browning, Glenn F., Nguyen, Di Kim, Swartzell, Steven, Madan, Anup, Mahairas, Greg, and Geary, Steven J.

Subjects
Gene expression -- Physiological aspects, Pathogenic microorganisms -- Genetic aspects, Pathogenic microorganisms -- Physiological aspects, Genomes -- Physiological aspects, Transfer RNA -- Genetic aspects, Bacterial proteins -- Genetic aspects, Bacterial proteins -- Physiological aspects, DNA -- Genetic aspects, Mycoplasma -- Physiological aspects, Mycoplasma -- Genetic aspects, Microbiology -- Research, Biological sciences
Abstract

The complete genome of Mycoplasma gallisepticum strain [R.sub.low] has been sequenced. The genome is composed of 996 422 bp with an overall G + C content of 31 mol%. It contains 742 putative coding DNA sequences (CDSs), representing a 91% coding density. Function has been assigned to 469 of the CDSs, while 150 encode conserved hypothetical proteins and 123 remain as unique hypothetical proteins. The genome contains two copies of the rRNA genes and 33 tRNA genes. The origin of replication has been localized based on sequence analysis in the region of the dnaA gene. The vlhA family (previously termed pMGA) contains 43 genes distributed among five loci containing 8, 2, 9, 12 and 12 genes. This family of genes constitutes 10.4% (103 kb) of the total genome. Two CDSs were identified immediately downstream of gapA and crmA encoding proteins that share homology to cytadhesins GapA and CrmA. Based on motif analysis it is predicted that 80 genes encode lipoproteins and 149 proteins contain multiple transmembrane domains. The authors have identified 75 proteins putatively involved in transport of biomolecules, 12 transposases, and a number of potential virulence factors. The completion of this sequence has spawned multiple projects directed at defining the biological basis of M. gallisepticum.

Published
2003

18. Initial sequencing and analysis of the human genome

Author

Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, McKernan, Kevin, Meldrim, James, Mesirov, Jill P., Miranda, Cher, Morris, William, Naylor, Jerome, Raymond, Christina, Rosetti, Mark, Santos, Ralph, Sheridan, Andrew, Sougnez, Carrie, Stange-Thomann, Nicole, Stojanovic, Nikola, Subramanian, Aravind, Wyman, Dudley, Rogers, Jane, Sulston, John, Ainscough, Rachael, Beck, Stephan, Bentley, David, Burton, John, Clee, Christopher, Carter, Nigel, Coulson, Alan, Deadman, Rebecca, Deloukas, Panos, Dunham, Andrew, Dunham, Ian, Durbin, Richard, French, Lisa, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Humphray, Sean, Hunt, Adrienne, Jones, Matthew, Lloyd, Christine, McMurray, Amanda, Matthews, Lucy, Mercer, Simon, Milne, Sarah, Mullikin, James C., Mungall, Andrew, Plumb, Robert, Ross, Mark, Shownkeen, Ratna, Sims, Sarah, Waterston, Robert H., Wilson, Richard K., Hillier, LaDeana W., McPherson, John D., Marra, Marco A., Mardis, Elaine R., Fulton, Lucinda A., Chinwalla, Asif T., Pepin, Kymberlie H., Gish, Warren R., Chissoe, Stephanie L., Wendl, Michael C., Delehaunty, Kim D., Miner, Tracie L., Delehaunty, Andrew, Kramer, Jason B., Cook, Lisa L., Fulton, Robert S., Johnson, Douglas L., Minx, Patrick J., Clifton, Sandra W., Hawkins, Trevor, Branscomb, Elbert, Predki, Paul, Richardson, Paul, Wenning, Sarah, Slezak, Tom, Doggett, Norman, Cheng, Jan-Fang, Olsen, Anne, Lucas, Susan, Elkin, Christopher, Uberbacher, Edward, Frazier, Marvin, Gibbs, Richard A., Muzny, Donna M., Scherer, Steven E., Bouck, John B., Sodergren, Erica J., Worley, Kim C., Rives, Catherine M., Gorrell, James H., Metzker, Michael L., Naylor, Susan L., Kucherlapati, Raju S., Nelson, David L., Weinstock, George M., Sakaki, Yoshiyuki, Fujiyama, Asao, Hattori, Masahira, Yada, Tetsushi, Toyoda, Atsushi, Itoh, Takehiko, Kawagoe, Chiharu, Watanabe, Hidemi, Totoki, Yasushi, Taylor, Todd, Weissenbach, Jean, Heilig, Roland, Saurin, William, Artiguenave, Francois, Brottier, Philippe, Bruls, Thomas, Pelletier, Eric, Robert, Catherine, Wincker, Patrick, Rosenthal, Andre, Platzer, Matthias, Nyakatura, Gerald, Taudien, Stefan, Rump, Andreas, Smith, Douglas R., Doucette-Stamm, Lynn, Rubenfield, Marc, Weinstock, Keith, Lee, Hong Mei, Dubois, JoAnn, Yang, Huanming, Yu, Jun, Wang, Jian, Huang, Guyang, Gu, Jun, Hood, Leroy, Rowen, Lee, Madan, Anup, Qin, Shizen, Davis, Ronald W., Federspiel, Nancy A., Abola, A. Pia, Proctor, Michael J., Roe, Bruce A., Chen, Feng, Pan, Huaqin, Ramser, Juliane, Lehrach, Hans, Reinhardt, Richard, McCombie, W. Richard, de la Bastide, Melissa, Dedhia, Neilay, Blocker, Helmut, Hornischer, Klaus, Nordsiek, Gabriele, Agarwala, Richa, Aravind, L., Bailey, Jeffrey A., Bateman, Alex, Batzoglou, Serafim, Birney, Ewan, Bork, Peer, Brown, Daniel G., Burge, Christopher B., Cerutti, Lorenzo, Chen, Hsiu-Chuan, Church, Deanna, Clamp, Michele, Copley, Richard R., Doerks, Tobias, Eddy, Sean R., Eichler, Evan E., Furey, Terrence S., Galagan, James, Gilbert, James G. R., Harmon, Cyrus, Hayashizaki, Yoshihide, Haussler, David, Hermjakob, Henning, Hokamp, Karsten, Jang, Wonhee, Johnson, L. Steven, Jones, Thomas A., Kasif, Simon, Kaspryzk, Arek, Kennedy, Scot, Kent, W. James, Kitts, Paul, Koonin, Eugene V., Korf, Ian, Kulp, David, Lancet, Doron, Lowe, Todd M., McLysaght, Aoife, Mikkelsen, Tarjei, Moran, John V., Mulder, Nicola, Pollara, Victor J., Ponting, Chris P., Schuler, Greg, Schultz, Jorg, Slater, Guy, Smit, Arian F. A., Stupka, Elia, Szustakowki, Joseph, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Wallis, John, Wheeler, Raymond, Williams, Alan, Wolf, Yuri I., Wolfe, Kenneth H., Yang, Shiaw-Pyng, Yeh, Ru-Fang, Collins, Francis, Guyer, Mark S., Peterson, Jane, Felsenfeld, Adam, Wetterstrand, Kris A., Myers, Richard M., Schmutz, Jeremy, Dickson, Mark, Grimwood, Jane, Cox, David R., Olson, Maynard V., Kaul, Rajinder, Raymond, Christopher, Shimizu, Nobuyoshi, Kawasaki, Kazuhiko, Minoshima, Shinsei, Evans, Glen A., Athanasiou, Maria, Schultz, Roger, Patrinos, Aristides, and Morgan, Michael J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Published
2001
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27. Solution structure of the conserved segment of the Myb cognate DNA sequence by 2D NMR, spectral simulation, restrained energy minimization, and distance geometry calculations

Author

Radha, P.K., Madan, Anup, Nibedita R., and Hosur, R. V.

Subjects
Nuclear magnetic resonance spectroscopy -- Methods, DNA -- Research, Biological sciences, Chemistry
Abstract

Determination of the solution structure of a DNA duplex d-ACCGTTAACGGT containing the conserved segment TAACGG of Myb protein by 2D NMR, spectral simulation, restrained energy minimization, and distance geometry calculations indicates that the NOE data defines a unique structure for the DNA segment. Calculations with the TANDY-2S algorithm confirm the unique structure of the DNA segment. The DNA helix displays a nonregular path and H-bonds were seen at AA, AC and CC steps in the major groove of the helix.

Published
1995

28. Sequence-specific DNA displaces 6-p-toluidino-2-naphthalenesulfonate bound to a hydrophobic site on the DNA-binding domain of Drosophila c-myb

Author

Madan, Anup, Hosur, R.V., and Padhy, L.C.

Subjects
DNA-ligand interactions -- Research, Binding sites (Biochemistry) -- Research, Biological sciences, Chemistry
Abstract

An oligomeric DNA duplex having a cognate myb-binding region displaces 6-p-toluidino-2-naphthalenesulfonate (TNS) which is bound to a hydrophobic domain on the DNA-binding site of Drosophila c-myb protein (R123). Nonspecific DNA duplex oligomers have no influence and this suggests that displacement of TNS is sequence-specific. A portion of the DNA-binding domain of the protein comprises the bound TNS.

Published
1994

29. Abstracts of posters presented at the symposium

Author

Maiya, Bhaskar G., Chauhan, S. M. S., Bhyrappa, P., Krishnan, V., Bhardwaj, P. K., Sarkar, Sabyasachi, Pandeya, Krishna B., Mathur, Pavan, Chakravarty, Akhil R., Das, Birinchi K., Behere, Digambar V., Modi, Sandeep, Mitra, Samaresh, Modi, Sandeep, Behere, Digambar V., Mitra, Samaresh, Saxena, Anil, Modi, Sandeep, Behere, Digambar V., Mitra, S., Mazumdar, Shyamalava, Medhi, Okhil K., Mitra, Samaresh, Mazumdar, Shyamalava, Mitra, Samaresh, Madan, Anup, Modi, Sandeep, Saxena, Anil, Behere, Digamber V., Mitra, S., Pandiyan, T., Palaniandavar, M., Narayanan, K. L., Manohar, H., Ramaraj, R., Thomas, C. C., Rajagopal, S., Rajendra, T., Srinivasan, C., Ramamurthy, P., Roy, R., Saha, M. C., Panchanan, S., Roy, P. S., Balagopalakrishna, C., Rajasekharan, M. V., Agarwala, B. V., Hingorani, S., Gowda, G. A. Nagena, Ramaswamy, Y. S., Halesha, R., Gowda, N. M. N., Reddy, G. K. N., Saxena, G. C., Gupta, K. L., Srivastava, P., Gupta, V. D., Ray, M., Mukherjee, R. N., Mohanty, R. N., Dash, K. C., Kapoor, Ramesh, Yadav, S., Sood, V., Kapoor, P., Anand, B. N., Bains, R., Usha, Aggarwal, K., Garge, P., Chikate, R., Padhye, S., Savariault, J. M., De Loth, P., Tuchgues, J. P., Jain, V. K., Vaidya, M. A., Jain, S. C., Kumar, S. Kalyan, Singh, Harkesh B., Mangaonkar, K. M., Patkar, D. N., Jha, N. K., Sharma, Pankaj, Date, S. K., Deshpande, C. E., Sathaye, S. D., Deshpande, S. B., Potdar, H. S., Darshane, V. S., Dash, A. C., Nanda, R. K., Das, N. N., Gangopadhyay, S., Banerjee, P., Kulshreshtha, S. K., Zacharias, P. S., Arulsamy, N., Ramasami, T., Subramanian, V., Nair, B. U., Kanthimathi, M., Sundararajan, G., Shivasubramanian, V., Bhattacharya, R. G., Biswas, S., Armstrong, J., Holt, E. M., and Koley, A. P.

Published
1990
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30. Discovery of high affinity, pan-allelic, and pan-mammalian reactive antibodies against the myeloid checkpoint receptor SIRPα

Author

Sim, Janet, primary, Sockolosky, Jonathan T., additional, Sangalang, Emma, additional, Izquierdo, Shelley, additional, Pedersen, Darlene, additional, Harriman, William, additional, Wibowo, Ardian S., additional, Carter, Josh, additional, Madan, Anup, additional, Doyle, Laura, additional, Harrabi, Ons, additional, Kauder, Steven E., additional, Chen, Amy, additional, Kuo, Tracy C., additional, Wan, Hong, additional, and Pons, Jaume, additional

Published
2019
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32. TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes.

Author

Miklas, Jason W, Miklas, Jason W, Clark, Elisa, Levy, Shiri, Detraux, Damien, Leonard, Andrea, Beussman, Kevin, Showalter, Megan R, Smith, Alec T, Hofsteen, Peter, Yang, Xiulan, Macadangdang, Jesse, Manninen, Tuula, Raftery, Daniel, Madan, Anup, Suomalainen, Anu, Kim, Deok-Ho, Murry, Charles E, Fiehn, Oliver, Sniadecki, Nathan J, Wang, Yuliang, Ruohola-Baker, Hannele, Miklas, Jason W, Miklas, Jason W, Clark, Elisa, Levy, Shiri, Detraux, Damien, Leonard, Andrea, Beussman, Kevin, Showalter, Megan R, Smith, Alec T, Hofsteen, Peter, Yang, Xiulan, Macadangdang, Jesse, Manninen, Tuula, Raftery, Daniel, Madan, Anup, Suomalainen, Anu, Kim, Deok-Ho, Murry, Charles E, Fiehn, Oliver, Sniadecki, Nathan J, Wang, Yuliang, and Ruohola-Baker, Hannele

Abstract

Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via an engineered microRNA maturation cocktail that upregulated the epigenetic regulator, HOPX.  Here we report, matured HADHA mutant cardiomyocytes treated with an endogenous mixture of fatty acids manifest the disease phenotype: defective calcium dynamics and repolarization kinetics which results in a pro-arrhythmic state. Single cell RNA-seq reveals a cardiomyocyte developmental intermediate, based on metabolic gene expression. This intermediate gives rise to mature-like cardiomyocytes in control cells but, mutant cells transition to a pathological state with reduced fatty acid beta-oxidation, reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling. This study reveals that HADHA (tri-functional protein alpha), a monolysocardiolipin acyltransferase-like enzyme, is required for fatty acid beta-oxidation and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.

Published
2019

35. Abstract 3418: Cross-comparison of targeted gene expression technologies for patient stratification

Author

Venkatramanan, Raghavee, primary, Saloranta, Tuuli, additional, Golez, Inah, additional, Swanson, Elliot, additional, Kruse, Kimberly, additional, Satele, Vickie, additional, Tahir, Saman, additional, Dow, Sally, additional, Anderson, Evan, additional, Hudson, Briana, additional, Chee, Spencer, additional, Deutsch, Kerry, additional, Anderson, Steve, additional, Lo, Fang Yin, additional, and Madan, Anup, additional

Published
2018
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42. Abstract 3983: A cross comparison of technologies for the detection of immune system related gene expression signatures in clinical FFPE samples of metastatic prostate cancer patients

Author

Kruse, Kimberly, primary, Lo, Fang Yin, additional, Fleming, Ryan, additional, Chung, Douglas, additional, Satele, Vickie, additional, Maassel, Lindsey, additional, Saloranta, Tuuli, additional, Golez, Inah, additional, Tahir, Saman, additional, Dow, Sally, additional, Anderson, Evan, additional, Chee, Spencer, additional, Venkatramanan, Raghavee, additional, Anderson, Steve, additional, Nelson, Peter S., additional, Morrissey, Colm, additional, Madan, Anup, additional, Austin, Sharon, additional, and Howard, Kellie, additional

Published
2017
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44. Abstract 2757: Using liquid biopsies and NGS as tools to analyze mutation burden and copy number variation in the blood of a patient with triple negative breast cancer to better inform therapeutic targets

Author

Howard, Kellie, primary, Kruse, Kimberly, additional, Greenwood, Brianna, additional, Swanson, Elliott, additional, Ehrich, Mathias, additional, Ellison, Christopher K., additional, Jensen, Taylor, additional, Austin, Sharon, additional, Ramirez, Arturo, additional, Boles, Debbie, additional, Pruitt, John, additional, Mahen, Elisabeth, additional, Stilwell, Jackie L., additional, Kaldjian, Eric P., additional, Dorschner, Michael, additional, Blau, Sibel, additional, Eisenberg, Marcia, additional, Anderson, Steve, additional, and Madan, Anup, additional

Published
2017
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45. Systems biology and cancer stem cells

Author

Price, Nathan D, Foltz, Greg, Madan, Anup, Hood, Leroy, and Tian, Qiang

Subjects
transcriptomics, proteomics, networks, Neoplasms, Systems Biology, Neoplastic Stem Cells, Reviews, Animals, Humans, molecular signature
Abstract

The identification, purification, and characterization of cancer stem cells holds tremendous promise for improving the treatment of cancer. Mounting evidence is demonstrating that only certain tumor cells (i.e. the cancer stem cells) can give rise to tumors when injected and that these purified cell populations generate heterogeneous tumors. While the cell of origin is still not determined definitively, specific molecular markers for populations containing these cancer stem cells have been found for leukemia, brain cancer, and breast cancer, among others. Systems approaches, particularly molecular profiling, have proven to be of great utility for cancer diagnosis and characterization. These approaches also hold significant promise for identifying distinctive properties of the cancer stem cells, and progress is already being made.

Published
2007

47. Abstract 104: Investigation of genetic architecture of multiple myeloma by next generation sequencing

Author

Deutsch, Kerry, primary, Lo, Fang Yin, additional, Olson, Claire, additional, Austin, Sharon, additional, Howard, Kellie, additional, Leonti, Amanda, additional, Maassel, Lindsey, additional, Subia, Christopher, additional, Saloranta, Tuuli, additional, Christopherson, Nicole, additional, Shiji, Kathryn, additional, Patil, Shradha, additional, Schwartz, Stuart, additional, Papenhausen, Peter, additional, Anderson, Steven, additional, and Madan, Anup, additional

Published
2016
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48. Abstract 498: Meta-analysis of genomic aberrations identified in CTCs andctDNA in triple negative breast cancer

Author

Howard, Kellie, primary, Austin, Sharon, additional, Lo, Fang Yin, additional, Ramirez, Arturo, additional, Boles, Debbie, additional, Pruitt, John, additional, Mahen, Elisabeth, additional, Collins, Heather, additional, Leonti, Amanda, additional, Maassel, Lindsey, additional, Subia, Christopher, additional, Saloranta, Tuuli, additional, Christopherson, Nicole, additional, Deutsch, Kerry, additional, Stilwell, Jackie, additional, Kaldjian, Eric, additional, Dorschner, Michael, additional, Blau, Sibel, additional, Blau, Anthony, additional, Eisenberg, Marcia, additional, Anderson, Steven, additional, and Madan, Anup, additional

Published
2016
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50. Abstract 3946: Stratification of metastatic colorectal cancer patients using DNA and RNA sequencing and in-silico prediction of tumor antigens for consideration in immunotherapy

Author

Lo, FangYin, primary, Austin, Sharon, additional, Howard, Kellie, additional, McWhorter, Mollie, additional, Collins, Heather, additional, Leonti, Amanda, additional, Maassel, Lindsey, additional, Subia, Christopher, additional, Saloranta, Tuuli, additional, Christopherson, Nicole, additional, Shiji, Kathryn, additional, Patil, Shradha, additional, Tahir, Saman, additional, Dow, Sally, additional, Anderson, Evan, additional, Oblad, Jon, additional, Deutsch, Kerry, additional, Yeatman, Timothy, additional, Anderson, Steven, additional, and Madan, Anup, additional

Published
2016
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