Search Results - "Fuxman Bass, Juan I."

Compendium of human transcription factor effector domains by Soto, Luis F., Li, Zhaorong, Santoso, Clarissa S., Berenson, Anna, Ho, Isabella, Shen, Vivian X., Yuan, Samson, Fuxman Bass, Juan I.

“…Transcription factors (TFs) regulate gene expression by binding to DNA sequences and modulating transcriptional activity through their effector domains…”
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Using networks to measure similarity between genes: association index selection by Bass, Juan I Fuxman, Diallo, Alos, Nelson, Justin, Soto, Juan M, Myers, Chad L, Walhout, Albertha J M

“…This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses…”
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Human gene-centered transcription factor networks for enhancers and disease variants by Fuxman Bass, Juan I, Sahni, Nidhi, Shrestha, Shaleen, Garcia-Gonzalez, Aurian, Mori, Akihiro, Bhat, Numana, Yi, Song, Hill, David E, Vidal, Marc, Walhout, Albertha J M

“…Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous…”
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Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences by Eslami Rasekh, Marzieh, Hernández, Yözen, Drinan, Samantha D, Fuxman Bass, Juan I, Benson, Gary

“…Abstract Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we…”
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A functional screen identifies transcriptional networks that regulate HIV-1 and HIV-2 by Pedro, Kyle D., Agosto, Luis M., Sewell, Jared A., Eberenz, Kimberly A., He, Xianbao, Bass, Juan I. Fuxman, Henderson, Andrew J.

“…The molecular networks involved in the regulation of HIV replication, transcription, and latency remain incompletely defined. To expand our understanding of…”
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Intragenic proviral elements support transcription of defective HIV-1 proviruses by Kuniholm, Jeffrey, Armstrong, Elise, Bernabe, Brandy, Coote, Carolyn, Berenson, Anna, Patalano, Samantha D, Olson, Alex, He, Xianbao, Lin, Nina H, Fuxman Bass, Juan I, Henderson, Andrew J

“…HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this…”
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Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4+ T cell identity and function by Basu, Jayati, Reis, Bernardo S., Peri, Suraj, Zha, Jikun, Hua, Xiang, Ge, Lu, Ferchen, Kyle, Nicolas, Emmanuelle, Czyzewicz, Philip, Cai, Kathy Q., Tan, Yinfei, Fuxman Bass, Juan I., Walhout, Albertha J. M., Grimes, H. Leighton, Grivennikov, Sergei I., Mucida, Daniel, Kappes, Dietmar J.

“…The transcription factor ThPOK (encoded by the Zbtb7b gene) controls homeostasis and differentiation of mature helper T cells, while opposing their…”
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Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities by Narasimhan, Kamesh, Lambert, Samuel A, Yang, Ally W H, Riddell, Jeremy, Mnaimneh, Sanie, Zheng, Hong, Albu, Mihai, Najafabadi, Hamed S, Reece-Hoyes, John S, Fuxman Bass, Juan I, Walhout, Albertha J M, Weirauch, Matthew T, Hughes, Timothy R

“…Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of…”
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Identification of Single Nucleotide Non-coding Driver Mutations in Cancer by Gan, Kok A, Carrasco Pro, Sebastian, Sewell, Jared A, Bass, Juan I Fuxman

“…Recent whole-genome sequencing studies have identified millions of somatic variants present in tumor samples. Most of these variants reside in non-coding…”
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Human Virus Transcriptional Regulators by Liu, Xing, Hong, Ted, Parameswaran, Sreeja, Ernst, Kevin, Marazzi, Ivan, Weirauch, Matthew T., Fuxman Bass, Juan I.

“…Viral genomes encode transcriptional regulators that alter the expression of viral and host genes. Despite an emerging role in human diseases, a thorough…”
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Widespread macromolecular interaction perturbations in human genetic disorders by Sahni, Nidhi, Yi, Song, Taipale, Mikko, Fuxman Bass, Juan I, Coulombe-Huntington, Jasmin, Yang, Fan, Peng, Jian, Weile, Jochen, Karras, Georgios I, Wang, Yang, Kovács, István A, Kamburov, Atanas, Krykbaeva, Irina, Lam, Mandy H, Tucker, George, Khurana, Vikram, Sharma, Amitabh, Liu, Yang-Yu, Yachie, Nozomu, Zhong, Quan, Shen, Yun, Palagi, Alexandre, San-Miguel, Adriana, Fan, Changyu, Balcha, Dawit, Dricot, Amelie, Jordan, Daniel M, Walsh, Jennifer M, Shah, Akash A, Yang, Xinping, Stoyanova, Ani K, Leighton, Alex, Calderwood, Michael A, Jacob, Yves, Cusick, Michael E, Salehi-Ashtiani, Kourosh, Whitesell, Luke J, Sunyaev, Shamil, Berger, Bonnie, Barabási, Albert-László, Charloteaux, Benoit, Hill, David E, Hao, Tong, Roth, Frederick P, Xia, Yu, Walhout, Albertha J M, Lindquist, Susan, Vidal, Marc

“…How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles…”
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Viral cis-regulatory elements as sensors of cellular states and environmental cues by Rottenberg, Jaice T., Taslim, Tommy H., Soto-Ugaldi, Luis F., Martinez-Cuesta, Lucia, Martinez-Calejman, Camila, Fuxman Bass, Juan I.

“…Viruses sense cellular states and environmental signals by recruiting host transcription factors to cis-regulatory elements (CREs) in viral genomes.Viral CREs…”
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Identification of conserved skeletal enhancers associated with craniosynostosis risk genes by He(何璇), Xuan Anita, Berenson, Anna, Bernard, Michelle, Weber, Chris, Cook, Laura E, Visel, Axel, Fuxman Bass, Juan I, Fisher, Shannon

“…Abstract Craniosynostosis, defined by premature fusion of one or multiple cranial sutures, is a common congenital defect affecting more than 1/2000 infants and…”
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Theory and Application of Network Biology Toward Precision Medicine by Demchak, Barry, Kreisberg, Jason F., Fuxman Bass, Juan I.

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Comprehensive mapping of the human cytokine gene regulatory network by Santoso, Clarissa S, Li, Zhaorong, Lal, Sneha, Yuan, Samson, Gan, Kok Ann, Agosto, Luis M, Liu, Xing, Pro, Sebastian Carrasco, Sewell, Jared A, Henderson, Andrew, Atianand, Maninjay K, Fuxman Bass, Juan I

“…Abstract Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine…”
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Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors by Berenson, Anna, Lane, Ryan, Soto-Ugaldi, Luis F., Patel, Mahir, Ciausu, Cosmin, Li, Zhaorong, Chen, Yilin, Shah, Sakshi, Santoso, Clarissa, Liu, Xing, Spirohn, Kerstin, Hao, Tong, Hill, David E., Vidal, Marc, Fuxman Bass, Juan I.

“…Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these…”
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Options and Considerations When Using a Yeast One-Hybrid System by Sewell, Jared A, Fuxman Bass, Juan I

“…Comprehensive mapping of protein-DNA interactions is essential to uncover the mechanisms involved in gene regulation. However, the data generated has been…”
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A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions by Fuxman Bass, Juan I, Pons, Carles, Kozlowski, Lucie, Reece‐Hoyes, John S, Shrestha, Shaleen, Holdorf, Amy D, Mori, Akihiro, Myers, Chad L, Walhout, Albertha JM

“…Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive…”
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Therapeutic Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19 by Santoso, Clarissa S, Li, Zhaorong, Rottenberg, Jaice T, Liu, Xing, Shen, Vivian X, Fuxman Bass, Juan I

“…Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the…”
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Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters by Fuxman Bass, Juan I, Tamburino, Alex M, Mori, Akihiro, Beittel, Nathan, Weirauch, Matthew T, Reece-Hoyes, John S, Walhout, Albertha J M

“…Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in…”
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