Search Results - "Abdill, Richard J"

Tracking the popularity and outcomes of all bioRxiv preprints by Abdill, Richard J, Blekhman, Ran

“…The growth of preprints in the life sciences has been reported widely and is driving policy changes for journals and funders, but little quantitative…”
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Public human microbiome data are dominated by highly developed countries by Abdill, Richard J, Adamowicz, Elizabeth M, Blekhman, Ran

“…The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack…”
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Rxivist.org: Sorting biology preprints using social media and readership metrics by Abdill, Richard J, Blekhman, Ran

“…Preprints have arrived. In increasing numbers, researchers across the life sciences are embracing the once-niche practice, shaking off decades of reluctance…”
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Challenges and recommendations to improve the installability and archival stability of omics computational tools by Mangul, Serghei, Mosqueiro, Thiago, Abdill, Richard J, Duong, Dat, Mitchell, Keith, Sarwal, Varuni, Hill, Brian, Brito, Jaqueline, Littman, Russell Jared, Statz, Benjamin, Lam, Angela Ka-Mei, Dayama, Gargi, Grieneisen, Laura, Martin, Lana S, Flint, Jonathan, Eskin, Eleazar, Blekhman, Ran

“…Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction…”
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Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression by Luppino, Jennifer M, Field, Andrew, Nguyen, Son C, Park, Daniel S, Shah, Parisha P, Abdill, Richard J, Lan, Yemin, Yunker, Rebecca, Jain, Rajan, Adelman, Karen, Joyce, Eric F

“…The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin…”
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An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype by Shah, Parisha P, Keough, Kathleen C, Gjoni, Ketrin, Santini, Garrett T, Abdill, Richard J, Wickramasinghe, Nadeera M, Dundes, Carolyn E, Karnay, Ashley, Chen, Angela, Salomon, Rachel E A, Walsh, Patrick J, Nguyen, Son C, Whalen, Sean, Joyce, Eric F, Loh, Kyle M, Dubois, Nicole, Pollard, Katherine S, Jain, Rajan

“…Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and…”
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International authorship and collaboration across bioRxiv preprints by Abdill, Richard J, Adamowicz, Elizabeth M, Blekhman, Ran

“…Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and…”
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BiomeHorizon : Visualizing Microbiome Time Series Data in R by Fink, Isaac, Abdill, Richard J, Blekhman, Ran, Grieneisen, Laura

“…Despite playing a key role in the health of their hosts, host-associated microbial communities demonstrate considerable variation over time. These communities…”
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Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature by Carneiro, Clarissa F D, Queiroz, Victor G S, Moulin, Thiago C, Carvalho, Carlos A M, Haas, Clarissa B, Rayêe, Danielle, Henshall, David E, De-Souza, Evandro A, Amorim, Felippe E, Boos, Flávia Z, Guercio, Gerson D, Costa, Igor R, Hajdu, Karina L, van Egmond, Lieve, Modrák, Martin, Tan, Pedro B, Abdill, Richard J, Burgess, Steven J, Guerra, Sylvia F S, Bortoluzzi, Vanessa T, Amaral, Olavo B

“…Preprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An…”
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A how-to guide for code sharing in biology by Abdill, Richard J, Talarico, Emma, Grieneisen, Laura

“…In 2024, all biology is computational biology. Computer-aided analysis continues to spread into new fields, becoming more accessible to researchers trained in…”
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Packaging and containerization of computational methods by Alser, Mohammed, Lawlor, Brendan, Abdill, Richard J., Waymost, Sharon, Ayyala, Ram, Rajkumar, Neha, LaPierre, Nathan, Brito, Jaqueline, Ribeiro-dos-Santos, André M., Almadhoun, Nour, Sarwal, Varuni, Firtina, Can, Osinski, Tomasz, Eskin, Eleazar, Hu, Qiyang, Strong, Derek, Kim, Byoung-Do (B.D), Abedalthagafi, Malak S., Mutlu, Onur, Mangul, Serghei

“…Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools…”
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High-throughput Oligopaint screen identifies druggable 3D genome regulators by Park, Daniel S., Nguyen, Son C., Isenhart, Randi, Shah, Parisha P., Kim, Wonho, Barnett, R. Jordan, Chandra, Aditi, Luppino, Jennifer M., Harke, Jailynn, Wai, May, Walsh, Patrick J., Abdill, Richard J., Yang, Rachel, Lan, Yemin, Yoon, Sora, Yunker, Rebecca, Kanemaki, Masato T., Vahedi, Golnaz, Phillips-Cremins, Jennifer E., Jain, Rajan, Joyce, Eric F.

“…The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions 1 – 3 . Although the molecular…”
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Public human microbiome data are dominated by highly developed countries by Richard J Abdill, Elizabeth M Adamowicz, Ran Blekhman

“…The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack…”
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High-throughput Oligopaints identifies druggable 3D genome regulators by Park, Daniel S., Nguyen, Son C., Isenhart, Randi, Shah, Parisha P., Kim, Wonho, Jordan Barnett, R., Chandra, Aditi, Luppino, Jennifer M., Harke, Jailynn, Wai, May, Walsh, Patrick J., Abdill, Richard J., Yang, Rachel, Lan, Yemin, Yoon, Sora, Yunker, Rebecca, Kanemaki, Masato T., Vahedi, Golnaz, Phillips-Cremins, Jennifer E., Jain, Rajan, Joyce, Eric F.

“…The human genome functions as a three-dimensional (3D) chromatin polymer, driven by a complex collection of chromosome interactions 1 – 3 . Although the…”
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A how-to guide for code-sharing in biology by Abdill, Richard J, Talarico, Emma, Grieneisen, Laura

“…Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of…”
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Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities by Alser, Mohammed, Waymost, Sharon, Ayyala, Ram, Lawlor, Brendan, Abdill, Richard J, Rajkumar, Neha, LaPierre, Nathan, Brito, Jaqueline, Ribeiro-dos-Santos, Andre M, Firtina, Can, Almadhoun, Nour, Sarwal, Varuni, Eskin, Eleazar, Hu, Qiyang, Strong, Derek, Byoung-Do, Kim, Abedalthagafi, Malak S, Mutlu, Onur, Mangul, Serghei

“…Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of…”
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