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1. Genetic risk factors for COVID-19 and influenza are largely distinct

Author

Kosmicki, Jack A., Marcketta, Anthony, Sharma, Deepika, Di Gioia, Silvio Alessandro, Batista, Samantha, Yang, Xiao-Man, Tzoneva, Gannie, Martinez, Hector, Sidore, Carlo, Kessler, Michael D., Horowitz, Julie E., Roberts, Genevieve H. L., Justice, Anne E., Banerjee, Nilanjana, Coignet, Marie V., Leader, Joseph B., Park, Danny S., Lanche, Rouel, Maxwell, Evan, Knight, Spencer C., Bai, Xiaodong, Guturu, Harendra, Baltzell, Asher, Girshick, Ahna R., McCurdy, Shannon R., Partha, Raghavendran, Mansfield, Adam J., Turissini, David A., Zhang, Miao, Mbatchou, Joelle, Watanabe, Kyoko, Verma, Anurag, Sirugo, Giorgio, Ritchie, Marylyn D., Salerno, William J., Shuldiner, Alan R., Rader, Daniel J., Mirshahi, Tooraj, Marchini, Jonathan, Overton, John D., Carey, David J., Habegger, Lukas, Reid, Jeffrey G., Economides, Aris, Kyratsous, Christos, Karalis, Katia, Baum, Alina, Cantor, Michael N., Rand, Kristin A., Hong, Eurie L., Ball, Catherine A., Siminovitch, Katherine, Baras, Aris, Abecasis, Goncalo R., and Ferreira, Manuel A. R.

Published
2024
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2. NOTCH3 p.Arg1231Cys is markedly enriched in South Asians and associated with stroke

Author

Rodriguez-Flores, Juan Lorenzo, Khalid, Shareef, Parikshak, Neelroop, Rasheed, Asif, Ye, Bin, Kapoor, Manav, Backman, Joshua, Sepehrband, Farshid, Gioia, Silvio Alessandro Di, Gelfman, Sahar, De, Tanima, Banerjee, Nilanjana, Sharma, Deepika, Martinez, Hector, Castaneda, Sofia, D’Ambrosio, David, Zhang, Xingmin A., Xun, Pengcheng, Tsai, Ellen, Tsai, I-Chun, Khan, Maleeha Zaman, Jahanzaib, Muhammad, Mian, Muhammad Rehan, Liaqat, Muhammad Bilal, Mahmood, Khalid, Salam, Tanvir Us, Hussain, Muhammad, Iqbal, Javed, Aslam, Faizan, Cantor, Michael N., Tzoneva, Gannie, Overton, John, Marchini, Jonathan, Reid, Jeffrey G., Baras, Aris, Verweij, Niek, Lotta, Luca A., Coppola, Giovanni, Karalis, Katia, Economides, Aris, Fazio, Sergio, Liedtke, Wolfgang, Danesh, John, Kamal, Ayeesha, Frossard, Philippe, Coleman, Thomas, Shuldiner, Alan R., and Saleheen, Danish

Published
2024
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3. Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis

Author

Zhou, Sirui, Sosina, Olukayode A., Bovijn, Jonas, Laurent, Laetitia, Sharma, Vasundhara, Akbari, Parsa, Forgetta, Vincenzo, Jiang, Lai, Kosmicki, Jack A., Banerjee, Nilanjana, Morris, John A., Oerton, Erin, Jones, Marcus, LeBlanc, Michelle G., Idone, Vincent, Overton, John D., Reid, Jeffrey G., Cantor, Michael, Abecasis, Goncalo R., Goltzman, David, Greenwood, Celia M. T., Langenberg, Claudia, Baras, Aris, Economides, Aris N., Ferreira, Manuel A. R., Hatsell, Sarah, Ohlsson, Claes, Richards, J. Brent, and Lotta, Luca A.

Published
2023
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8. Pharmacologic and Genetic Downregulation of Proprotein Convertase Subtilisin/Kexin Type 9 and Survival From Sepsis

Author

Lawler, Patrick R., Manvelian, Garen, Coppi, Alida, Damask, Amy, Cantor, Michael N., Ferreira, Manuel A. R., Paulding, Charles, Banerjee, Nilanjana, Li, Dadong, Jorgensen, Susan, Attre, Richa, Carey, David J., Krebs, Kristi, Milani, Lili, Hveem, Kristian, Damås, Jan K., Solligård, Erik, Stender, Stefan, Tybjærg-Hansen, Anne, Nordestgaard, Børge G., Hernandez-Beeftink, Tamara, Rogne, Tormod, Flores, Carlos, Villar, Jesús, Walley, Keith R., Liu, Vincent X., Fohner, Alison E., Lotta, Luca A., Kyratsous, Christos A., Sleeman, Mark W., Scemama, Michel, DelGizzi, Richard, Pordy, Robert, Horowitz, Julie E., Baras, Aris, Martin, Greg S., Steg, Philippe Gabriel, Schwartz, Gregory G., Szarek, Michael, and Goodman, Shaun G.

Published
2023
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9. Common and rare variant associations with clonal haematopoiesis phenotypes

Author

Kessler, Michael D., Damask, Amy, O’Keeffe, Sean, Banerjee, Nilanjana, Li, Dadong, Watanabe, Kyoko, Marketta, Anthony, Van Meter, Michael, Semrau, Stefan, Horowitz, Julie, Tang, Jing, Kosmicki, Jack A., Rajagopal, Veera M., Zou, Yuxin, Houvras, Yariv, Ghosh, Arkopravo, Gillies, Christopher, Mbatchou, Joelle, White, Ryan R., Verweij, Niek, Bovijn, Jonas, Parikshak, Neelroop N., LeBlanc, Michelle G., Jones, Marcus, Glass, David J., Lotta, Luca A., Cantor, Michael N., Atwal, Gurinder S., Locke, Adam E., Ferreira, Manuel A. R., Deering, Raquel, Paulding, Charles, Shuldiner, Alan R., Thurston, Gavin, Ferrando, Adolfo A., Salerno, Will, Reid, Jeffrey G., Overton, John D., Marchini, Jonathan, Kang, Hyun M., Baras, Aris, Abecasis, Gonçalo R., and Jorgenson, Eric

Published
2022
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10. An Association Study of Gamma-Aminobutyric Acid Type a Receptor Variants and Susceptibility to Autism Spectrum Disorders

Author

Adak, Pallabi, Sinha, Swagata, and Banerjee, Nilanjana

Abstract

In this pilot study, we aim to identify the role of few genetic variants of GABA-receptor type A subunits "GABRB[subscript 3]" (rs4906902, rs7171660), "GABRG[subscript 3]" (rs208129, rs140679), "GABRA[subscript 5]" (rs 140681) in the aetiology of autism spectrum disorders in a population of West Bengal. 192 ASD probands, their parents and 184 ethnically-matched healthy controls were recruited for the study. The rs4906902G and the rs140679T conferred significant risk towards ASD. rs7171660 and rs140679 had transmission bias in the family. Neither alleles of rs 208129 and rs 140681 showed significant over-representation in either groups. All these variants were associated with at least one deficit in ASD-associated phenotypes like 'relating to people', 'Imitation', 'emotional response', 'body use', 'taste, smell, touch response' and 'activity levels'.

Published
2021
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12. “PMS2CL interference leading to erroneous identification of a pathogenic PMS2 variant in Black Patients”

Author

Cappadocia, Jacqueline, primary, Aiello, Lisa B., additional, Kelley, Michael J., additional, Katona, Bryson W., additional, Maxwell, Kara N., additional, Verma, Anurag, additional, Verma, Shefali S., additional, Bradford, Yuki, additional, Brock, Ashlei, additional, DerOhannessian, Stephanie, additional, Dudek, Scott, additional, Dunn, Joseph, additional, Drivas, Theodore, additional, Haubein, Ned, additional, Hu-Sain, Khadijah, additional, Judy, Renae, additional, Kloter, Ashley, additional, Ko, Yi-An, additional, Livingstone, Meghan, additional, Morrel, Linda, additional, Morse, Colleen, additional, Poindexter, Afiya, additional, Risman, Marjorie, additional, Tran, Teo, additional, Vadivieso, Fred, additional, Weaver, JoEllen, additional, Rader, Daniel J., additional, Ritchie, Marylyn D., additional, Feldman, Michael D., additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Overton, John D., additional, Padilla, Maria Sotiropoulos, additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Schleicher, Thomas D., additional, Widom, Louis, additional, Wolf, Sarah E., additional, Ulloa, Ricardo H., additional, Averitt, Amelia, additional, Banerjee, Nilanjana, additional, Cantor, Michael, additional, Li, Dadong, additional, Malhotra, Sameer, additional, Sharma, Deepika, additional, Staples, Jeffrey, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Bao, Suying, additional, Boutkov, Boris, additional, Chen, Siying, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Mitra, George, additional, Nafde, Mona, additional, O’Keeffe, Sean, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Reid, Jeffrey G., additional, Salerno, William, additional, Staples, Jeffrey C., additional, Sun, Kathie, additional, Abecasis, Goncalo, additional, Backman, Joshua, additional, Damask, Amy, additional, Dobbyn, Lee, additional, Revez Ferreira, Manuel Allen, additional, Ghosh, Arkopravo, additional, Gillies, Christopher, additional, Gurski, Lauren, additional, Jorgenson, Eric, additional, Kang, Hyun Min, additional, Kessler, Michael, additional, Kosmicki, Jack, additional, Li, Alexander, additional, Lin, Nan, additional, Liu, Daren, additional, Locke, Adam, additional, Marchini, Jonathan, additional, Marcketta, Anthony, additional, Mbatchou, Joelle, additional, Moscati, Arden, additional, Paulding, Charles, additional, Sidore, Carlo, additional, Stahl, Eli, additional, Watanabe, Kyoko, additional, Ye, Bin, additional, Zhang, Blair, additional, Ziyatdinov, Andrey, additional, Ayer, Ariane, additional, Guvenek, Aysegul, additional, Hindy, George, additional, Coppola, Giovanni, additional, Freudenberg, Jan, additional, Bovijn, Jonas, additional, Siminovitch, Katherine, additional, Praveen, Kavita, additional, Lotta, Luca A., additional, Kapoor, Manav, additional, Haas, Mary, additional, Riaz, Moeen, additional, Verweij, Niek, additional, Sosina, Olukayode, additional, Akbari, Parsa, additional, Nakka, Priyanka, additional, Gelfman, Sahar, additional, Gokhale, Sujit, additional, De, Tanima, additional, Rajagopal, Veera, additional, Shuldiner, Alan, additional, Tzoneva, Gannie, additional, Rodriguez-Flores, Juan, additional, Chen, Esteban, additional, Jones, Marcus B., additional, LeBlanc, Michelle G., additional, Mighty, Jason, additional, Mitnaul, Lyndon J., additional, Nishtala, Nirupama, additional, Rana, Nadia, additional, Hernandez, Jaimee, additional, Baras, Aris, additional, Deubler, Andrew, additional, and Economides, Aris, additional

Published
2024
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15. Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease

Author

Horowitz, Julie E., Kosmicki, Jack A., Damask, Amy, Sharma, Deepika, Roberts, Genevieve H. L., Justice, Anne E., Banerjee, Nilanjana, Coignet, Marie V., Yadav, Ashish, Leader, Joseph B., Marcketta, Anthony, Park, Danny S., Lanche, Rouel, Maxwell, Evan, Knight, Spencer C., Bai, Xiaodong, Guturu, Harendra, Sun, Dylan, Baltzell, Asher, Kury, Fabricio S. P., Backman, Joshua D., Girshick, Ahna R., O’Dushlaine, Colm, McCurdy, Shannon R., Partha, Raghavendran, Mansfield, Adam J., Turissini, David A., Li, Alexander H., Zhang, Miao, Mbatchou, Joelle, Watanabe, Kyoko, Gurski, Lauren, McCarthy, Shane E., Kang, Hyun M., Dobbyn, Lee, Stahl, Eli, Verma, Anurag, Sirugo, Giorgio, Ritchie, Marylyn D., Jones, Marcus, Balasubramanian, Suganthi, Siminovitch, Katherine, Salerno, William J., Shuldiner, Alan R., Rader, Daniel J., Mirshahi, Tooraj, Locke, Adam E., Marchini, Jonathan, Overton, John D., Carey, David J., Habegger, Lukas, Cantor, Michael N., Rand, Kristin A., Hong, Eurie L., Reid, Jeffrey G., Ball, Catherine A., Baras, Aris, Abecasis, Gonçalo R., and Ferreira, Manuel A. R.

Published
2022
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17. Exome sequencing and analysis of 454,787 UK Biobank participants

Author

Backman, Joshua D., Li, Alexander H., Marcketta, Anthony, Sun, Dylan, Mbatchou, Joelle, Kessler, Michael D., Benner, Christian, Liu, Daren, Locke, Adam E., Balasubramanian, Suganthi, Yadav, Ashish, Banerjee, Nilanjana, Gillies, Christopher E., Damask, Amy, Liu, Simon, Bai, Xiaodong, and Hawes, Alicia

Subjects
Exome sequencing -- Methods, Genetic variation -- Identification and classification, Gene banks -- Usage, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

A major goal in human genetics is to use natural variation to understand the phenotypic consequences of altering each protein-coding gene in the genome. Here we used exome sequencing.sup.1 to explore protein-altering variants and their consequences in 454,787 participants in the UK Biobank study.sup.2. We identified 12 million coding variants, including around 1 million loss-of-function and around 1.8 million deleterious missense variants. When these were tested for association with 3,994 health-related traits, we found 564 genes with trait associations at P [less than or equal to] 2.18 × 10.sup.-11. Rare variant associations were enriched in loci from genome-wide association studies (GWAS), but most (91%) were independent of common variant signals. We discovered several risk-increasing associations with traits related to liver disease, eye disease and cancer, among others, as well as risk-lowering associations for hypertension (SLC9A3R2), diabetes (MAP3K15, FAM234A) and asthma (SLC27A3). Six genes were associated with brain imaging phenotypes, including two involved in neural development (GBE1, PLD1). Of the signals available and powered for replication in an independent cohort, 81% were confirmed; furthermore, association signals were generally consistent across individuals of European, Asian and African ancestry. We illustrate the ability of exome sequencing to identify gene-trait associations, elucidate gene function and pinpoint effector genes that underlie GWAS signals at scale. Whole-exome sequencing analysis of 454,787 individuals in the UK Biobank is used to examine the association of protein-coding variants with nearly 4,000 health-related traits, identifying 564 distinct genes with significant trait associations., Author(s): Joshua D. Backman [sup.1] , Alexander H. Li [sup.1] , Anthony Marcketta [sup.1] , Dylan Sun [sup.1] , Joelle Mbatchou [sup.1] , Michael D. Kessler [sup.1] , Christian Benner [...]

Published
2021
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18. An Association Study of Gamma-Aminobutyric Acid Type A Receptor Variants and Susceptibility to Autism Spectrum Disorders

Author

Adak, Pallabi, Sinha, Swagata, and Banerjee, Nilanjana

Subjects
Pervasive developmental disorders -- Diagnosis -- Risk factors -- Genetic aspects, Genetic variation -- Health aspects, Genetic susceptibility -- Analysis, GABA -- Health aspects, Health
Abstract

In this pilot study, we aim to identify the role of few genetic variants of GABA-receptor type A subunits GABRB3 (rs4906902, rs7171660), GABRG3 (rs208129, rs140679), GABRA5 (rs 140681) in the aetiology of autism spectrum disorders in a population of West Bengal. 192 ASD probands, their parents and 184 ethnically-matched healthy controls were recruited for the study. The rs4906902G and the rs140679T conferred significant risk towards ASD. rs7171660 and rs140679 had transmission bias in the family. Neither alleles of rs 208129 and rs 140681 showed significant over-representation in either groups. All these variants were associated with at least one deficit in ASD-associated phenotypes like 'relating to people', 'Imitation', 'emotional response', 'body use', 'taste, smell, touch response' and 'activity levels'., Author(s): Pallabi Adak [sup.1] , Swagata Sinha [sup.2] , Nilanjana Banerjee [sup.1] Author Affiliations: (1) Manovikas Biomedical Research and Diagnostic Centre, , Manovikas Kendra, 482 Madudah, Plot I-24, Sector J, [...]

Published
2021
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24. Author Correction: Common and rare variant associations with clonal haematopoiesis phenotypes

Author

Kessler, Michael D., Damask, Amy, O’Keeffe, Sean, Banerjee, Nilanjana, Li, Dadong, Watanabe, Kyoko, Marketta, Anthony, Van Meter, Michael, Semrau, Stefan, Horowitz, Julie, Tang, Jing, Kosmicki, Jack A., Rajagopal, Veera M., Zou, Yuxin, Houvras, Yariv, Ghosh, Arkopravo, Gillies, Christopher, Mbatchou, Joelle, White, Ryan R., Verweij, Niek, Bovijn, Jonas, Parikshak, Neelroop N., LeBlanc, Michelle G., Jones, Marcus, Glass, David J., Lotta, Luca A., Cantor, Michael N., Atwal, Gurinder S., Locke, Adam E., Ferreira, Manuel A. R., Deering, Raquel, Paulding, Charles, Shuldiner, Alan R., Thurston, Gavin, Ferrando, Adolfo A., Salerno, Will, Reid, Jeffrey G., Overton, John D., Marchini, Jonathan, Kang, Hyun M., Baras, Aris, Abecasis, Gonçalo R., and Jorgenson, Eric

Published
2023
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27. Liquefied Natural Gas Value Chain: A Comprehensive Review and Analysis.

Author

Shingan, Bhalchandra, Banerjee, Nilanjana, Kumawat, Monika, Mitra, Purnayan, Parthasarthy, Vijay, and Singh, Varunpratap

Subjects
*LIQUEFIED natural gas, *VALUE chains, *GREENHOUSE gas mitigation, *NATURAL gas reserves, *NATURAL gas consumption, *NATURAL gas extraction
Abstract

Over the past few decades, the liquefied natural gas (LNG) business has experienced astounding expansion and gained global relevance. LNG has emerged as a key element in meeting the world's rising energy demand while working to cut carbon emissions, since it is a cleaner and more adaptable energy source. The entire process from natural gas extraction to consumption is covered in the presented analysis of the LNG value chain, starting out by looking at the discovery and production of natural gas reserves, highlighting important innovations and methods used during the extraction stage. The procedures used to treat and purify natural gas in order to meet the strict standards for liquefaction are detailed. Analysis of the liquefaction process reveals numerous liquefaction technologies, e.g. the well‐known conventional liquefaction and the cutting‐edge floating LNG and small‐scale LNG facilities. LNG storage and transportation, as critical components in the value chain, are examined in great detail. When the LNG reaches its destination, regasification plays a crucial role in repurposing it as a gas for distribution and consumption. Regasification technologies, such as conventional onshore terminals, floating storage and regasification units, and land‐based regasification facilities, are covered. Concerns regarding methane emissions and the carbon footprint, the potential for reducing greenhouse gas emissions through new technology, the environmental impact of LNG, and the economics of LNG are also considered across its value chain. [ABSTRACT FROM AUTHOR]

Published
2024
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29. NOTCH3p.Arg1231Cys is Markedly Enriched in South Asians and Associated with Stroke

Author

Rodriguez-Flores, Juan L., primary, Khalid, Shareef, additional, Parikshak, Neelroop, additional, Rasheed, Asif, additional, Ye, Bin, additional, Kapoor, Manav, additional, Backman, Joshua, additional, Sepehrband, Farshid, additional, DiGioia, Silvio Alessandro, additional, Gelfman, Sahar, additional, De, Tanima, additional, Banerjee, Nilanjana, additional, Sharma, Deepika, additional, Martinez, Hector, additional, Castaneda, Sofia, additional, D’Ambrosio, David, additional, Zhang, Xingmin A., additional, Xun, Pengcheng, additional, Tsai, Ellen, additional, Tsai, I-Chun, additional, Center, Regeneron Genetics, additional, Jahanzaib, Muhammad, additional, Khan, Maleeha Zaman, additional, Mian, Muhammad Rehan, additional, Liaqat, Muhammad Bilal, additional, Mahmood, Khalid, additional, Salam, Tanvir Us, additional, Hussain, Muhammad, additional, Iqbal, Javed, additional, Aslam, Faizan, additional, Cantor, Michael N., additional, Tzoneva, Gannie, additional, Overton, John, additional, Marchini, Jonathan, additional, Reid, Jeff, additional, Baras, Aris, additional, Verweij, Niek, additional, Lotta, Luca A., additional, Coppola, Giovanni, additional, Karalis, Katia, additional, Economides, Aris, additional, Fazio, Sergio, additional, Liedtke, Wolfgang, additional, Danesh, John, additional, Kamal, Ayeesha, additional, Frossard, Philippe, additional, Coleman, Thomas, additional, Shuldiner, Alan R., additional, and Saleheen, Danish, additional

Published
2023
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32. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes

Author

Wang, Kai, Nemenman, Ilya, Banerjee, Nilanjana, Margolin, Adam, and Califano, Andrea

Subjects
Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription factor activation by phosphorylation and acetylation, formation of active complexes with one or more co-factors, and mRNA/protein degradation and stabilization processes. This paper presents a first step towards the systematic, genome-wide computational inference of genes that modulate the interactions of specific transcription factors at the post-transcriptional level. The method uses a statistical test based on changes in the mutual information between a transcription factor and each of its candidate targets, conditional on the expression of a third gene. The approach was first validated on a synthetic network model, and then tested in the context of a mammalian cellular system. By analyzing 254 microarray expression profiles of normal and tumor related human B lymphocytes, we investigated the post transcriptional modulators of the MYC proto-oncogene, an important transcription factor involved in tumorigenesis. Our method discovered a set of 100 putative modulator genes, responsible for modulating 205 regulatory relationships between MYC and its targets. The set is significantly enriched in molecules with function consistent with their activities as modulators of cellular interactions, recapitulates established MYC regulation pathways, and provides a notable repertoire of novel regulators of MYC function. The approach has broad applicability and can be used to discover modulators of any other transcription factor, provided that adequate expression profile data are available., Comment: 15 pages, 3 figures, 2 tables; minor changes following referees' comments; accepted to RECOMB06

Published
2005
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33. Conditional Network Analysis Identifies Candidate Regulator Genes in Human B Cells

Author

Wang, Kai, Banerjee, Nilanjana, Margolin, Adam, Nemenman, Ilya, Basso, Katia, Favera, Riccardo, and Califano, Andrea

Subjects
Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic phenotypes. Existing methods for such "reverse engineering" of genetic networks from microarray expression data have been successful only in prokaryotes (E. coli) and lower eukaryotes (S. cerevisiae) with relatively simple genomes. Additionally, they have mostly attempted to reconstruct average properties about the network connectivity without capturing the highly conditional nature of the interactions. In this paper we extend the ARACNE algorithm, which we recently introduced and successfully applied to the reconstruction of whole-genome transcriptional networks from mammalian cells, precisely to link the existence of specific network structures to the expression or lack thereof of specific regulator genes. This is accomplished by analyzing thousands of alternative network topologies generated by constraining the data set on the presence or absence of putative regulator genes. By considering interactions that are consistently supported across several such constraints, we identify many transcriptional interactions that would not have been detectable by the original method. By selecting genes that produce statistically significant changes in network topology, we identify novel candidate regulator genes. Further analysis shows that transcription factors, kinases, phosphatases, and other gene families known to effect biochemical interactions, are significantly overrepresented among the set of candidate regulator genes identified in silico, indirectly supporting the validity of the approach., Comment: Submitted to RECOMB 2005 (11 pages, 4 figures, 2 tables)

Published
2004

37. PMS2CL interference leading to erroneous identification of a pathogenic PMS2 variant in Black patients

Author

Verma, Anurag, Verma, Shefali S., Bradford, Yuki, Brock, Ashlei, DerOhannessian, Stephanie, Dudek, Scott, Dunn, Joseph, Drivas, Theodore, Haubein, Ned, Hu-Sain, Khadijah, Judy, Renae, Kloter, Ashley, Ko, Yi-An, Livingstone, Meghan, Morrel, Linda, Morse, Colleen, Poindexter, Afiya, Risman, Marjorie, Tran, Teo, Vadivieso, Fred, Weaver, JoEllen, Rader, Daniel J., Ritchie, Marylyn D., Feldman, Michael D., Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Overton, John D., Padilla, Maria Sotiropoulos, Pradhan, Manasi, Manoochehri, Kia, Schleicher, Thomas D., Widom, Louis, Wolf, Sarah E., Ulloa, Ricardo H., Averitt, Amelia, Banerjee, Nilanjana, Cantor, Michael, Li, Dadong, Malhotra, Sameer, Sharma, Deepika, Staples, Jeffrey, Bai, Xiaodong, Balasubramanian, Suganthi, Bao, Suying, Boutkov, Boris, Chen, Siying, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Mansfield, Adam J., Maxwell, Evan K., Mitra, George, Nafde, Mona, O’Keeffe, Sean, Orelus, Max, Panea, Razvan, Polanco, Tommy, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Staples, Jeffrey C., Sun, Kathie, Abecasis, Goncalo, Backman, Joshua, Damask, Amy, Dobbyn, Lee, Ferreira, Manuel Allen Revez, Ghosh, Arkopravo, Gillies, Christopher, Gurski, Lauren, Jorgenson, Eric, Kang, Hyun Min, Kessler, Michael, Kosmicki, Jack, Li, Alexander, Lin, Nan, Liu, Daren, Locke, Adam, Marchini, Jonathan, Marcketta, Anthony, Mbatchou, Joelle, Moscati, Arden, Paulding, Charles, Sidore, Carlo, Stahl, Eli, Watanabe, Kyoko, Ye, Bin, Zhang, Blair, Ziyatdinov, Andrey, Ayer, Ariane, Guvenek, Aysegul, Hindy, George, Coppola, Giovanni, Freudenberg, Jan, Bovijn, Jonas, Siminovitch, Katherine, Praveen, Kavita, Lotta, Luca A., Kapoor, Manav, Haas, Mary, Riaz, Moeen, Verweij, Niek, Sosina, Olukayode, Akbari, Parsa, Nakka, Priyanka, Gelfman, Sahar, Gokhale, Sujit, De, Tanima, Rajagopal, Veera, Shuldiner, Alan, Tzoneva, Gannie, Rodriguez-Flores, Juan, Chen, Esteban, Jones, Marcus B., LeBlanc, Michelle G., Mighty, Jason, Mitnaul, Lyndon J., Nishtala, Nirupama, Rana, Nadia, Hernandez, Jaimee, Baras, Aris, Deubler, Andrew, Economides, Aris, Cappadocia, Jacqueline, Aiello, Lisa B., Kelley, Michael J., Katona, Bryson W., and Maxwell, Kara N.

Published
2024
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38. Physicochemical and antistaphylococcal evaluation of two herbal ointments from Mikania micrantha Kunth and Tridax procumbens Linn.

Author

Bera, Arnab and Banerjee, Nilanjana

Subjects
*OINTMENTS, *STAPHYLOCOCCUS aureus, *PARAFFIN wax
Abstract

Objectves: This present work was carried out to formulate and evaluate herbal ointments using Mikania micrantha and Tridax procumbens. Materials and Methods: The extracts were prepared using maceration technique. A simple ointment base was prepared using white soft paraffin and liquid paraffin. The extracts were incorporated into the ointment base following levigation method. The amount of extract to be incorporated into the ointment base was determined according to their minimum inhibitory concentration (MIC) against Staphylococcus aureus MTCC 87. The formulated ointments were evaluated for several physicochemical characteristics like colour, odour, homogeneity, washability, spredability, irritation potential etc. Antistaphylococcal assay was conducted using well diffusion method. Ointment base containing white soft paraffin and liquid paraffin was used as negative control and Supragent containing Gentamicin sulphate was used as a positive control. Results: The formulated ointments showed satisfactory results for tested physicochemical parameters. Both ointments showed moderate antistaphylococcal activity with reference to the activity showed by Supragent. Conclusion: The results of this study indicate that the formulated ointments can be incorporated into India's medicine system for treating Staphylococcus aureus induced skin ailments in future. [ABSTRACT FROM AUTHOR]

Published
2023
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39. Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female‐Specific Health Conditions

Author

Xiao, Brenda, primary, Velez Edwards, Digna R., additional, Lucas, Anastasia, additional, Drivas, Theodore, additional, Gray, Kathryn, additional, Keating, Brendan, additional, Weng, Chunhua, additional, Jarvik, Gail P., additional, Hakonarson, Hakon, additional, Kottyan, Leah, additional, Elhadad, Noemie, additional, Wei, Wei‐Qi, additional, Luo, Yuan, additional, Kim, Dokyoon, additional, Ritchie, Marylyn, additional, Verma, Shefali Setia, additional, Abecasis, Goncalo, additional, Baras, Aris, additional, Cantor, Michael, additional, Coppola, Giovanni, additional, Deubler, Andrew, additional, Economides, Aris, additional, Karalis, Katia, additional, Lotta, Luca A., additional, Overton, John D., additional, Reid, Jeffrey G., additional, Siminovitch, Katherine, additional, Shuldiner, Alan, additional, Beechert, Christina, additional, Forsythe, Caitlin, additional, Fuller, Erin D., additional, Gu, Zhenhua, additional, Lattari, Michael, additional, Lopez, Alexander, additional, Padilla, Maria Sotiropoulos, additional, Pradhan, Manasi, additional, Manoochehri, Kia, additional, Schleicher, Thomas D., additional, Widom, Louis, additional, Wolf, Sarah E., additional, Ulloa, Ricardo H., additional, Averitt, Amelia, additional, Banerjee, Nilanjana, additional, Li, Dadong, additional, Malhotra, Sameer, additional, Sharma, Deepika, additional, Staples, Jeffrey, additional, Bai, Xiaodong, additional, Balasubramanian, Suganthi, additional, Bao, Suying, additional, Boutkov, Boris, additional, Chen, Siying, additional, Eom, Gisu, additional, Habegger, Lukas, additional, Hawes, Alicia, additional, Khalid, Shareef, additional, Krasheninina, Olga, additional, Lanche, Rouel, additional, Mansfield, Adam J., additional, Maxwell, Evan K., additional, Mitra, George, additional, Nafde, Mona, additional, O’Keeffe, Sean, additional, Orelus, Max, additional, Panea, Razvan, additional, Polanco, Tommy, additional, Rasool, Ayesha, additional, Salerno, William, additional, Staples, Jeffrey C., additional, Sun, Kathie, additional, Backman, Joshua, additional, Damask, Amy, additional, Dobbyn, Lee, additional, Ferreira, Manuel Allen Revez, additional, Ghosh, Arkopravo, additional, Gillies, Christopher, additional, Gurski, Lauren, additional, Jorgenson, Eric, additional, Kang, Hyun Min, additional, Kessler, Michael, additional, Kosmicki, Jack, additional, Li, Alexander, additional, Lin, Nan, additional, Liu, Daren, additional, Locke, Adam, additional, Marchini, Jonathan, additional, Marcketta, Anthony, additional, Mbatchou, Joelle, additional, Moscati, Arden, additional, Paulding, Charles, additional, Sidore, Carlo, additional, Stahl, Eli, additional, Watanabe, Kyoko, additional, Ye, Bin, additional, Zhang, Blair, additional, Ziyatdinov, Andrey, additional, Ayer, Ariane, additional, Guvenek, Aysegul, additional, Hindy, George, additional, Freudenberg, Jan, additional, Bovijn, Jonas, additional, Praveen, Kavita, additional, Kapoor, Manav, additional, Haas, Mary, additional, Riaz, Moeen, additional, Verweij, Niek, additional, Sosina, Olukayode, additional, Akbari, Parsa, additional, Nakka, Priyanka, additional, Gelfman, Sahar, additional, Gokhale, Sujit, additional, De, Tanima, additional, Rajagopal, Veera, additional, Tzoneva, Gannie, additional, Rodriguez‐Flores, Juan, additional, Chim, Shek Man, additional, Donato, Valerio, additional, Fernandez, Daniel, additional, Gatta, Giusy Della, additional, Di Gioia, Alessandro, additional, Howell, Kristen, additional, Khrimian, Lori, additional, Kim, Minhee, additional, Martinez, Hector, additional, Miloscio, Lawrence, additional, Nunez, Sheilyn, additional, Pavlopoulos, Elias, additional, Persaud, Trikaldarshi, additional, Chen, Esteban, additional, Jones, Marcus B., additional, LeBlanc, Michelle G., additional, Mighty, Jason, additional, Mitnaul, Lyndon J., additional, Nishtala, Nirupama, additional, and Rana, Nadia, additional

Published
2023
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42. Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps

Author

Banerjee, Nilanjana, Califano, Andrea, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Bourque, Guillaume, editor, and El-Mabrouk, Nadia, editor

Published
2006
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43. Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes

Author

Wang, Kai, Nemenman, Ilya, Banerjee, Nilanjana, Margolin, Adam A., Califano, Andrea, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Apostolico, Alberto, editor, Guerra, Concettina, editor, and Pevzner, Pavel A., editor

Published
2006
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46. Phytochemical Investigation and Antimutagenic Potential of Ethanolic Extracts of Emblica officinalis, Terminalia chebula and Terminalia bellirica

Author

Singamaneni Venugopal, Banerjee Nilanjana, Kumar Ashish, Chakrabarti Tulika, and Kumar Dokuparthi Sudheer

Subjects
Emblica officinalis, Traditional medicine, biology, 010405 organic chemistry, Chemistry, Terminalia, biology.organism_classification, 01 natural sciences, 0104 chemical sciences, Terminalia chebula, 010404 medicinal & biomolecular chemistry, Complementary and alternative medicine, Phytochemical, Drug Discovery
Abstract

Background: Emblica officinalis Gaertn. which belongs to the family Euphorbiaceae, Terminalia chebula Retz. and Terminalia bellerica Roxb. belong to the family Combretaceae. These are well known medicinal plants with phytochemical reservoir of great medicinal values and possess a vast ethnomedical history. Objective: The aim of the present study is to isolation of major compounds and to evaluate antimutagenic potential of the ethanol extracts of these plants. Methods: The dried fruits of E. officinalis, T. bellirica and T. chebula were powdered and extracted with 95% ethanol. The ethyl acetate portions were chromatographed over silica gel to isolate major compounds. Antimutagenic activity was determined by Ames test using TA98 and TA100 strains of Salmonella typhimurium. Results: Two major known compounds, gallic acid and ellagic acid were isolated from the dried fruits of Emblica officinalis, Terminalia chebula and T. bellirica. All the three extracts counteracted the mutagenicity induced by different genotoxic compounds in a dose dependent manner. Conclusion: This study showed that ethyl acetate portion of three extracts contain two major compounds, gallic acid and ellagic acid which might be responsible for potent antimutagenic activity of these extracts.

Published
2020

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