Search Results - "Mahmoud, Medhat"

Structural variant calling: the long and the short of it by Mahmoud, Medhat, Gobet, Nastassia, Cruz-Dávalos, Diana Ivette, Mounier, Ninon, Dessimoz, Christophe, Sedlazeck, Fritz J

“…Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases,…”
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Chromosome-scale, haplotype-resolved assembly of human genomes by Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., Li, Heng

“…Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for…”
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Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data by Liu, Yunxi, Kearney, Joshua, Mahmoud, Medhat, Kille, Bryce, Sedlazeck, Fritz J., Treangen, Todd J.

“…Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host…”
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PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation by Mahmoud, Medhat, Doddapaneni, Harshavardhan, Timp, Winston, Sedlazeck, Fritz J

“…Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV,…”
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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study by Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., Mason, Christopher E.

“…Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of…”
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Genomic variant benchmark: if you cannot measure it, you cannot improve it by Majidian, Sina, Agustinho, Daniel Paiva, Chin, Chen-Shan, Sedlazeck, Fritz J, Mahmoud, Medhat

“…Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing…”
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MethPhaser: methylation-based long-read haplotype phasing of human genomes by Fu, Yilei, Aganezov, Sergey, Mahmoud, Medhat, Beaulaurier, John, Juul, Sissel, Treangen, Todd J., Sedlazeck, Fritz J.

“…The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step…”
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Role of right ventricular–pulmonary arterial coupling assessed by echocardiography to predict adverse outcomes in patients with acute pulmonary embolism by Mostafa, Amir, Medhat, Mahmoud, Alhosary, Hossam, Amin, Wassim

“…Background Pulmonary embolism (PE) is a lethal type of venous thromboembolic disease. Right ventricular (RV) failure is not an uncommon complication of PE…”
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The perceptual saliency of fearful eyes and smiles: A signal detection study by Elsherif, Mahmoud Medhat, Sahan, Muhammet Ikbal, Rotshtein, Pia

“…Facial features differ in the amount of expressive information they convey. Specifically, eyes are argued to be essential for fear recognition, while smiles…”
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Ghat: an R package for identifying adaptive polygenic traits by Mahmoud, Medhat, Tost, Mila, Ha, Ngoc-Thuy, Simianer, Henner, Beissinger, Timothy

“…Abstract Identifying selection on polygenic complex traits in crops and livestock is important for understanding evolution and helps prioritize important…”
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FixItFelix: improving genomic analysis by fixing reference errors by Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F, Farek, Jesse, Soto, Daniela C, Parker, Stephen C J, Smith, Albert V, Dennis, Megan Y, Zook, Justin M, Sedlazeck, Fritz J

“…The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed…”
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Towards a culture of open scholarship: the role of pedagogical communities by Azevedo, Flávio, Liu, Meng, Pennington, Charlotte R, Pownall, Madeleine, Evans, Thomas Rhys, Parsons, Sam, Elsherif, Mahmoud Medhat, Micheli, Leticia, Westwood, Samuel J

“…The UK House of Commons Science and Technology Committee has called for evidence on the roles that different stakeholders play in reproducibility and research…”
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Correction: The perceptual saliency of fearful eyes and smiles: A signal detection study by Elsherif, Mahmoud Medhat, Sahan, Muhammet Ikbal, Rotshtein, Pia

“…[This corrects the article DOI: 10.1371/journal.pone.0173199.]…”
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Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study by Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., Mason, Christopher E.

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Determinants of Renewable Energy Production in Egypt New Approach: Machine Learning Algorithms by Alhendawy, Hamdy Ahmad Aly, Abdallah Mostafa, Mohammed Galal, Elgohari, Mohamed Ibrahim, Mohamed, Ibrahim Abdalla Abdelraouf, Mahmoud, Nabil Medhat Arafat, Mater, Mohamed Ahmed Mohamed

“…The production of renewable energy has become one of the important elements in the pursuit of sustainable and environmentally friendly economic development,…”
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Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk by Behera, Sairam, Belyeu, Jonathan R, Chen, Xiao, Paulin, Luis F, Nguyen, Ngoc Quynh H, Newman, Emma, Mahmoud, Medhat, Menon, Vipin K, Qi, Qibin, Joshi, Parag, Marcovina, Santica, Rossi, Massimiliano, Roller, Eric, Han, James, Onuchic, Vitor, Avery, Christy L, Ballantyne, Christie M, Rodriguez, Carlos J, Kaplan, Robert C, Muzny, Donna M, Metcalf, Ginger A, Gibbs, Richard A, Yu, Bing, Boerwinkle, Eric, Eberle, Michael A, Sedlazeck, Fritz J

“…The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN)…”
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Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing by Alvarez Jerez, Pilar, Daida, Kensuke, Grenn, Francis P., Malik, Laksh, Miano-Burkhardt, Abigail, Makarious, Mary B., Ding, Jinhui, Gibbs, J. Raphael, Moore, Anni, Reed, Xylena, Nalls, Mike A., Shah, Syed, Mahmoud, Medhat, Sedlazeck, Fritz J., Dolzhenko, Egor, Park, Morgan, Iwaki, Hirotaka, Casey, Bradford, Ryten, Mina, Blauwendraat, Cornelis, Singleton, Andrew B., Billingsley, Kimberley J.

“…Parkinson’s disease (PD) is a common neurodegenerative disorder with a significant risk proportion driven by genetics. While much progress has been made, most…”
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Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance by Mahmoud, Medhat, Gracz-Bernaciak, Joanna, Żywicki, Marek, Karłowski, Wojciech, Twardowski, Tomasz, Tyczewska, Agata

“…To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two L. lines traditionally bred in…”
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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms [version 1; peer review: 1 approved, 3 approved with reservations] by Walker, Kimberly, Kalra, Divya, Lowdon, Rebecca, Chen, Guangyi, Molik, David, Soto, Daniela C., Dabbaghie, Fawaz, Khleifat, Ahmad Al, Mahmoud, Medhat, Paulin, Luis F, Raza, Muhammad Sohail, Pfeifer, Susanne P., Agustinho, Daniel Paiva, Aliyev, Elbay, Avdeyev, Pavel, Barrozo, Enrico R., Behera, Sairam, Billingsley, Kimberley, Chong, Li Chuin, Choubey, Deepak, De Coster, Wouter, Fu, Yilei, Gener, Alejandro R., Hefferon, Timothy, Henke, David Morgan, Höps, Wolfram, Illarionova, Anastasia, Jochum, Michael D., Jose, Maria, Kesharwani, Rupesh K., Kolora, Sree Rohit Raj, Kubica, Jędrzej, Lakra, Priya, Lattimer, Damaris, Liew, Chia-Sin, Lo, Bai-Wei, Lo, Chunhsuan, Lötter, Anneri, Majidian, Sina, Mendem, Suresh Kumar, Mondal, Rajarshi, Ohmiya, Hiroko, Parvin, Nasrin, Peralta, Carolina, Poon, Chi-Lam, Prabhakaran, Ramanandan, Saitou, Marie, Sammi, Aditi, Sanio, Philippe, Sapoval, Nicolae, Syed, Najeeb, Treangen, Todd, Wang, Gaojianyong, Xu, Tiancheng, Yang, Jianzhi, Zhang, Shangzhe, Zhou, Weiyu, Sedlazeck, Fritz J, Busby, Ben

“…In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural…”
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A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved] by Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A, Markello, Charles J, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R, Lin, Michael F, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L, Sagayaradj, Sagayamary, Novak, Adam M, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T, Zeng, Qiandong, Zook, Justin M, Paten, Benedict, Busby, Ben

“…In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics…”
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