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1. Unraveling Links between Chronic Inflammation and Long COVID: Workshop Report

Author

Tandon, Pushpa, primary, Abrams, Natalie D., additional, Avula, Leela Rani, additional, Carrick, Danielle M., additional, Chander, Preethi, additional, Divi, Rao L., additional, Dwyer, Johanna T., additional, Gannot, Gallya, additional, Gordiyenko, Nataliya, additional, Liu, Qian, additional, Moon, Kyung, additional, PrabhuDas, Mercy, additional, Singh, Anju, additional, Tilahun, Mulualem E., additional, Satyamitra, Merriline M., additional, Wang, Chiayeng, additional, Warren, Ronald, additional, and Liu, Christina H., additional

Published
2024
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5. Case Studies for Overcoming Challenges in Using Big Data in Cancer

Author

Sweeney, Shawn M., primary, Hamadeh, Hisham K., additional, Abrams, Natalie, additional, Adam, Stacey J., additional, Brenner, Sara, additional, Connors, Dana E., additional, Davis, Gerard J., additional, Fiore, Louis D., additional, Gawel, Susan H., additional, Grossman, Robert L., additional, Hanlon, Sean E., additional, Hsu, Karl, additional, Kelloff, Gary J., additional, Kirsch, Ilan R., additional, Louv, Bill, additional, McGraw, Deven, additional, Meng, Frank, additional, Milgram, Daniel, additional, Miller, Robert S., additional, Morgan, Emily, additional, Mukundan, Lata, additional, O'Brien, Thomas, additional, Robbins, Paul, additional, Rubin, Eric H., additional, Rubinstein, Wendy S., additional, Salmi, Liz, additional, Schaller, Teilo H., additional, Shi, George, additional, Sigman, Caroline C., additional, and Srivastava, Sudhir, additional

Published
2023
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6. Challenges to Using Big Data in Cancer

Author

Sweeney, Shawn M., primary, Hamadeh, Hisham K., additional, Abrams, Natalie, additional, Adam, Stacey J., additional, Brenner, Sara, additional, Connors, Dana E., additional, Davis, Gerard J., additional, Fiore, Louis, additional, Gawel, Susan H., additional, Grossman, Robert L., additional, Hanlon, Sean E., additional, Hsu, Karl, additional, Kelloff, Gary J., additional, Kirsch, Ilan R., additional, Louv, Bill, additional, McGraw, Deven, additional, Meng, Frank, additional, Milgram, Daniel, additional, Miller, Robert S., additional, Morgan, Emily, additional, Mukundan, Lata, additional, O'Brien, Thomas, additional, Robbins, Paul, additional, Rubin, Eric H., additional, Rubinstein, Wendy S., additional, Salmi, Liz, additional, Schaller, Teilo, additional, Shi, George, additional, Sigman, Caroline C., additional, and Srivastava, Sudhir, additional

Published
2023
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9. Metabolic Regulation of Inflammation and Its Resolution: Current Status, Clinical Needs, Challenges, and Opportunities

Author

Tandon, Pushpa, primary, Abrams, Natalie D., additional, Carrick, Danielle M., additional, Chander, Preethi, additional, Dwyer, Johanna, additional, Fuldner, Rebecca, additional, Gannot, Gallya, additional, Laughlin, Maren, additional, McKie, George, additional, PrabhuDas, Mercy, additional, Singh, Anju, additional, Tsai, Shang-Yi Anne, additional, Vedamony, Merriline M., additional, Wang, Chiayeng, additional, and Liu, Christina H., additional

Published
2021
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14. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability

Author

Joardar Vinita, Abrams Natalie F, Hostetler Jessica, Paukstelis Paul J, Pakala Suchitra, Pakala Suman B, Zafar Nikhat, Abolude Olukemi O, Payne Gary, Andrianopoulos Alex, Denning David W, and Nierman William C

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Results Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. Conclusions The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.

Published
2012
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15. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

Author

Moktali Venkatesh, Park Jongsun, Fedorova-Abrams Natalie D, Park Bongsoo, Choi Jaeyoung, Lee Yong-Hwan, and Kang Seogchan

Subjects
Cytochrome P450, Genome annotation, Clustering, Fungi, Evolution, Phylogenetics, Mycotoxin, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable “CYPomes” ranging from one to more than 300 CYPs. Despite the rapid growth of sequenced fungal and oomycete genomes and the resulting influx of predicted CYPs, the vast majority of CYPs remain functionally uncharacterized. To facilitate the curation and functional and evolutionary studies of CYPs, we previously developed Fungal Cytochrome P450 Database (FCPD), which included CYPs from 70 fungal and oomycete species. Here we present a new version of FCPD (1.2) with more data and an improved classification scheme. Results The new database contains 22,940 CYPs from 213 species divided into 2,579 clusters and 115 clans. By optimizing the clustering pipeline, we were able to uncover 36 novel clans and to assign 153 orphan CYP families to specific clans. To augment their functional annotation, CYP clusters were mapped to David Nelson’s P450 databases, which archive a total of 12,500 manually curated CYPs. Additionally, over 150 clusters were functionally classified based on sequence similarity to experimentally characterized CYPs. Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. The most dramatic expansions in fungi were observed in clans CYP58 and CYP68 (Pezizomycotina), clans CYP5150 and CYP63 (Agaricomycotina), and family CYP509 (Mucoromycotina). Although much of the extraordinary diversity of the pan-fungal CYPome can be attributed to gene duplication and adaptive divergence, our analysis also suggests a few potential horizontal gene transfer events. Updated families and clans can be accessed through the new version of the FCPD database. Conclusions FCPD version 1.2 provides a systematic and searchable catalogue of 9,550 fungal CYP sequences (292 families) encoded by 108 fungal species and 147 CYP sequences (9 families) encoded by five oomycete species. In comparison to the first version, it offers a more comprehensive clan classification, is fully compatible with Nelson’s P450 databases, and has expanded functional categorization. These features will facilitate functional annotation and classification of CYPs encoded by newly sequenced fungal and oomycete genomes. Additionally, the classification system will aid in studying the roles of CYPs in the evolution of fungal adaptation to specific ecological niches.

Published
2012
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16. Imaging inflammation and its resolution in health and disease: current status, clinical needs, challenges, and opportunities

Author

Liu, Christina H., primary, Abrams, Natalie D., additional, Carrick, Danielle M., additional, Chander, Preethi, additional, Dwyer, Johanna, additional, Hamlet, Michelle R. J., additional, Kindzelski, Andrei L., additional, PrabhuDas, Mercy, additional, Tsai, Shang‐Yi Anne, additional, Vedamony, Merriline M., additional, Wang, Chiayeng, additional, and Tandon, Pushpa, additional

Published
2019
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17. Abstract 2463: Prototype open-access biomarker knowledgebase for genetic tests for breast cancer

Author

Baker, Dara, primary, Abrams, Natalie Fedorova, additional, Bell, Amanda, additional, Colbert, Maureen, additional, Dingerdissen, Hayley, additional, Holmes, Evan, additional, Gupta, Samir, additional, Kahsay, Robel, additional, Kincaid, Heather, additional, Liu, David, additional, Mahmood, A. S. M. Ashique, additional, Bastian, Frédéric B., additional, Robinson-Rechavi, Marc, additional, Schwartz, Elena, additional, Vijay-Shanker, K., additional, Crichton, Daniel, additional, and Mazumder, Raja, additional

Published
2019
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21. The histone variant H2A.X is a regulator of the epithelial–mesenchymal transition

Author

Weyemi, Urbain, primary, Redon, Christophe E., additional, Choudhuri, Rohini, additional, Aziz, Towqir, additional, Maeda, Daisuke, additional, Boufraqech, Myriem, additional, Parekh, Palak R., additional, Sethi, Taresh K., additional, Kasoji, Manjula, additional, Abrams, Natalie, additional, Merchant, Anand, additional, Rajapakse, Vinodh N., additional, and Bonner, William M., additional

Published
2016
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27. Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP

Author

Cubeta, Marc A., primary, Thomas, Elizabeth, additional, Dean, Ralph A., additional, Jabaji, Suha, additional, Neate, Stephen M., additional, Tavantzis, Stellos, additional, Toda, Takeshi, additional, Vilgalys, Rytas, additional, Bharathan, Narayanaswamy, additional, Fedorova-Abrams, Natalie, additional, Pakala, Suman B., additional, Pakala, Suchitra M., additional, Zafar, Nikhat, additional, Joardar, Vinita, additional, Losada, Liliana, additional, and Nierman, William C., additional

Published
2014
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28. Cripto-1 as a novel therapeutic target for triple negative breast cancer

Author

Castro, Nadia P., primary, Fedorova-Abrams, Natalie D., additional, Merchant, Anand S., additional, Rangel, Maria Cristina, additional, Nagaoka, Tadahiro, additional, Karasawa, Hideaki, additional, Klauzinska, Malgorzata, additional, Hewitt, Stephen M., additional, Biswas, Kajal, additional, Sharan, Shyam K., additional, and Salomon, David S., additional

Published
2014
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29. Identification of the Genomic Insertion Site of Pmel-1 TCR α and β Transgenes by Next-Generation Sequencing

Author

Ji, Yun, primary, Abrams, Natalie, additional, Zhu, Wei, additional, Salinas, Eddie, additional, Yu, Zhiya, additional, Palmer, Douglas C., additional, Jailwala, Parthav, additional, Franco, Zulmarie, additional, Roychoudhuri, Rahul, additional, Stahlberg, Eric, additional, Gattinoni, Luca, additional, and Restifo, Nicholas P., additional

Published
2014
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30. Scoop.

Author

Warner, Kara, Falcone, Dana Rose, Nahas, Aili, Mcniece, Mia, Spain, Jamie, Nelson, Jeff, Guglielmi, Jodi, Telling, Gillian, Leonard, Elizabeth, Marx, Linda, Russian, Ale, Cedenheim, Pernilla, and Abrams, Natalie

Subjects
CELEBRITIES, CELEBRITY weddings
Abstract

The article presents celebrity news briefs as of May 7, 2018. Actor Richard Gere married his girlfriend Alejandra Silva earlier in 2018. Actor Dwayne "The Rock" Johnson and his girlfriend Lauren Hashian announced the birth of their daughter, Jasmine Lia Johnson. Actress Rachel Weisz and husband actor Daniel Craig announced they are expecting their first child together.

Published
2018

31. The Most Scandal-ous Moments.

Author

Abrams, Natalie and Gomez, Patrick

Subjects
*TELEVISION actors & actresses, *POLITICS on television
Abstract

The article presents comments from the actors on the television show "Scandal" regarding their favorite episodes. It mentions the political content of the show, the work of the show's creator Shonda Rhimes, and what the actors are doing next.

Published
2018

32. What to Watch.

Author

Schwartz, Dana, Baldwin, Kristen, Snierson, Dan, Abrams, Natalie, Lawrence, Derek, and Franich, Darren

Subjects
TELEVISION programs
Published
2018

33. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability

Author

Joardar, Vinita, Joardar, Vinita, Abrams, Natalie F, Hostetler, Jessica, Paukstelis, Paul J, Pakala, Suchitra, Pakala, Suman B, Zafar, Nikhat, Abolude, Olukemi O, Payne, Gary, Andrianopoulos, Alex, Denning, David W, Nierman, William C, Joardar, Vinita, Joardar, Vinita, Abrams, Natalie F, Hostetler, Jessica, Paukstelis, Paul J, Pakala, Suchitra, Pakala, Suman B, Zafar, Nikhat, Abolude, Olukemi O, Payne, Gary, Andrianopoulos, Alex, Denning, David W, and Nierman, William C

Abstract

The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies

Published
2012

35. Will & Grace.

Author

Rice, Lynette, Abrams, Natalie, Heldman, Breanne L., Highfill, Samantha, Kinane, Ruth, Li, Shirley, and Rahman, Ray

Subjects
WILL & Grace (TV program), MCCORMACK, Eric, 1963-, MESSING, Debra, 1968-
Published
2017

36. Riverdale.

Author

Stack, Tim, Abrams, Natalie, Heldman, Breanne L., Holub, Christian, Lawrence, Derek, Li, Shirley, Rice, Lynette, Ross, Dalton, Rovenstine, Dalene, and Vain, Madison

Subjects
RIVERDALE (TV program : 2017-), SPROUSE, Cole, REINHART, Lili
Published
2017

37. This Is Us.

Author

Snierson, Dan, Abrams, Natalie, Bacle, Ariana, Coggan, Devan, Lawrence, Derek, Rahman, Ray, Rice, Lynette, and Stack, Tim

Subjects
THIS Is Us (TV program), HARTLEY, Justin, 1977-, METZ, Chrissy, 1980-
Published
2017

38. A Tale of Two Sheldons.

Author

Franich, Darren, Abrams, Natalie, Holub, Christian, Kinane, Ruth, Rice, Lynette, and Vain, Madison

Subjects
*GUITAR instruction & study
Abstract

The article presents a conversation between actors Iain Armitage and Jim Parsons. Topics include the casting of Armitage as the lead actor in the television (TV) series "Young Sheldon," their mutual interest in theater and musicals, and Armitage's ability to play the guitar after learning to do so for the TV series "Big Little Lies."

Published
2017

39. What to Watch.

Author

Rahman, Ray, Greenblatt, Leah, Franich, Darren, Serrao, Nivea, Holub, Christian, Heching, Dan, Maslow, Nick, Jensen, Jeff, Li, Shirley, Bacle, Ariana, and Abrams, Natalie

Subjects
TELEVISION programs
Published
2017

40. A KNIGHT'S Tale.

Author

Abrams, Natalie

Subjects
KNIGHT, T. R., 1973-, CATCH, The (TV program), RHIMES, Shonda, 1970-, GREY'S Anatomy (TV program), YOST, Elvy
Abstract

The article presents an interview with actor T.R. Knight. Topics include his role on the television (TV) program "The Catch," his relationship with director, screenwriter, and producer Shonda Rhimes after having been cut from his role on the TV program "Grey's Anatomy," and his friendship with actress Elvy Yost who also stars on "The Catch."

Published
2017

42. ALL IN THE FAMILY.

Author

Jensen, Jeff and Abrams, Natalie

Subjects
*SUPERHERO television programs, *INTERPERSONAL relations on television
Abstract

The article discusses a crossover episode of the television (TV) program "Supergirl," in which several actors from the superhero TV programs "Arrow," "The Flash," and "Legends of Tomorrow" are featured. Topics include the shows' references to the Silver Age of comics, producer Greg Berlanti's focus on genuine relationship drama and team dynamics in all of the TV shows, and Berlanti's expression of his personal views on diversity, equal rights, and justice through all of the shows. A brief overview of the shows before and after the crossover episode are given.

Published
2016

43. WESTWORLD.

Author

Hibberd, James, Abrams, Natalie, Agard, Chancellor, Collis, Clark, and Rovenstine, Dalene

Subjects
WESTWORLD (TV program), HOPKINS, Anthony, 1937-, HARRIS, Ed, 1950-
Published
2016

44. CRAZY EX-GIRLFRIEND.

Author

Snetiker, Marc, Abrams, Natalie, Agard, Chancellor, Biedenharn, Isabella, Collis, Clark, and Smith, C. Molly

Subjects
CRAZY Ex-Girlfriend (TV program), BLOOM, Rachel, 1987-, RODRIGUEZ, Vincent
Published
2016

45. BLACK-ISH.

Author

Sperling, Nicole, Abrams, Natalie, Agard, Chancellor, Franich, Darren, Highfill, Samantha, Ross, Dalton, Snetiker, Marc, and Snierson, Dan

Subjects
BLACK-ish (TV program), ANDERSON, Anthony, 1970-, ROSS, Tracee Ellis, 1972-
Published
2016

46. TV GOES BACK TO WORK.

Author

Rice, Lynette, Terrero, Nina, Abrams, Natalie, and Stack, Tim

Subjects
HOW to Get Away With Murder (TV program), SUPERSTORE (TV program), CHICAGO P.D. (TV program), SOUZA, Karla, 1986-, FERRERA, America, 1984-, BUSH, Sophia, 1982-
Published
2016

47. Stars Shine at Comic-Con!

Author

Abrams, Natalie, Franich, Darren, Breznican, Anthony, Highfill, Samantha, Li, Shirley, McIntyre, Gina, Rice, Lynette, Snetiker, Marc, Sperling, Nicole, Stack, Tim, and Vilkomerson, Sara

Subjects
*COMIC book conventions, SAN Diego Comic-Con
Abstract

The article presents information on the 2016 comic book and film convention held in San Diego, California, known as Comic-Con. Topics include the film "Black Panther," starring Ryan Coogler, actress Brie Larson's roles in the films "Captain Marvel" and "Kong: Skull Island," and the space opera "Valérian and the City of a Thousand Planets," directed by Luc Benson.

Published
2016

48. Prison Break.

Author

Abrams, Natalie

Subjects
PRISON Break (TV program), MILLER, Wentworth, 1972-, PURCELL, Dominic
Published
2016

49. YOUR REALLY EARLY FALL TV PREVIEW.

Author

Rice, Lynette, Snetiker, Marc, Hibberd, James, and Abrams, Natalie

Subjects
TELEVISION programs, TELEVISION adaptations
Abstract

The article provides information on television shows set to air during fall 2016. Several television shows are being released that are based on films, including "Lethal Weapon," "The Exorcist," and "Training Day." The American Broadcasting Company (ABC) announced the cancellation of the show "Nashville." An interview is presented with actress Ellen Pompeo in which she discusses her show "Grey's Anatomy."

Published
2016

50. What to Watch.

Author

Rahman, Ray, Rovenstine, Dalene, Abrams, Natalie, Maerz, Melissa, Highfill, Samantha, and Ross, Dalton

Subjects
100, The (TV program), MIKE & Molly (TV program), CASTLE (TV program), AGENTS of S.H.I.E.L.D. (TV program), CHICAGO Fire (TV program), FRESH off the Boat (TV program), BLACK-ish (TV program), GREY'S Anatomy (TV program)
Published
2016

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