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1. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Author

Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., De María, Maite, Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., Gonzalez Martinez, Jose M., Hunt, Toby, Lagarde, Julien, Liang, Cindy E., Li, Haoran, Meade, Marcus Jerryd, Moraga Amador, David A., Prjibelski, Andrey D., Birol, Inanc, Bostan, Hamed, Brooks, Ashley M., Çelik, Muhammed Hasan, Chen, Ying, Du, Mei R. M., Felton, Colette, Göke, Jonathan, Hafezqorani, Saber, Herwig, Ralf, Kawaji, Hideya, Lee, Joseph, Li, Jian-Liang, Lienhard, Matthias, Mikheenko, Alla, Mulligan, Dennis, Nip, Ka Ming, Pertea, Mihaela, Ritchie, Matthew E., Sim, Andre D., Tang, Alison D., Wan, Yuk Kei, Wang, Changqing, Wong, Brandon Y., Yang, Chen, Barnes, If, Berry, Andrew E., Capella-Gutierrez, Salvador, Cousineau, Alyssa, Dhillon, Namrita, Fernandez-Gonzalez, Jose M., Ferrández-Peral, Luis, Garcia-Reyero, Natàlia, Götz, Stefan, Hernández-Ferrer, Carles, Kondratova, Liudmyla, Liu, Tianyuan, Martinez-Martin, Alessandra, Menor, Carlos, Mestre-Tomás, Jorge, Mudge, Jonathan M., Panayotova, Nedka G., Paniagua, Alejandro, Repchevsky, Dmitry, Ren, Xingjie, Rouchka, Eric, Saint-John, Brandon, Sapena, Enrique, Sheynkman, Leon, Smith, Melissa Laird, Suner, Marie-Marthe, Takahashi, Hazuki, Youngworth, Ingrid A., Carninci, Piero, Denslow, Nancy D., Guigó, Roderic, Hunter, Margaret E., Maehr, Rene, Shen, Yin, Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Au, Kin Fai, Sheynkman, Gloria M., Mortazavi, Ali, Conesa, Ana, and Brooks, Angela N.

Published
2024
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2. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Author

Jain, Shantanu, Bakolitsa, Constantina, Brenner, Steven E, Radivojac, Predrag, Moult, John, Repo, Susanna, Hoskins, Roger A, Andreoletti, Gaia, Barsky, Daniel, Chellapan, Ajithavalli, Chu, Hoyin, Dabbiru, Navya, Kollipara, Naveen K, Ly, Melissa, Neumann, Andrew J, Pal, Lipika R, Odell, Eric, Pandey, Gaurav, Peters-Petrulewicz, Robin C, Srinivasan, Rajgopal, Yee, Stephen F, Yeleswarapu, Sri Jyothsna, Zuhl, Maya, Adebali, Ogun, Patra, Ayoti, Beer, Michael A, Hosur, Raghavendra, Peng, Jian, Bernard, Brady M, Berry, Michael, Dong, Shengcheng, Boyle, Alan P, Adhikari, Aashish, Chen, Jingqi, Hu, Zhiqiang, Wang, Robert, Wang, Yaqiong, Miller, Maximilian, Wang, Yanran, Bromberg, Yana, Turina, Paola, Capriotti, Emidio, Han, James J, Ozturk, Kivilcim, Carter, Hannah, Babbi, Giulia, Bovo, Samuele, Di Lena, Pietro, Martelli, Pier Luigi, Savojardo, Castrense, Casadio, Rita, Cline, Melissa S, De Baets, Greet, Bonache, Sandra, Diez, Orland, Gutierrez-Enriquez, Sara, Fernandez, Alejandro, Montalban, Gemma, Ootes, Lars, Ozkan, Selen, Padilla, Natalia, Riera, Casandra, De la Cruz, Xavier, Diekhans, Mark, Huwe, Peter J, Wei, Qiong, Xu, Qifang, Dunbrack, Roland L, Gotea, Valer, Elnitski, Laura, Margolin, Gennady, Fariselli, Piero, Kulakovskiy, Ivan V, Makeev, Vsevolod J, Penzar, Dmitry D, Vorontsov, Ilya E, Favorov, Alexander V, Forman, Julia R, Hasenahuer, Marcia, Fornasari, Maria S, Parisi, Gustavo, Avsec, Ziga, Celik, Muhammed H, Thi, Yen Duong Nguyen, Gagneur, Julien, Shi, Fang-Yuan, Edwards, Matthew D, Guo, Yuchun, Tian, Kevin, Zeng, Haoyang, Gifford, David K, Goke, Jonathan, Zaucha, Jan, Gough, Julian, Ritchie, Graham RS, Frankish, Adam, Mudge, Jonathan M, Harrow, Jennifer, Young, Erin L, and Yu, Yao

Subjects
Biological Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Good Health and Well Being, Humans, Computational Biology, Mutation, Missense, Phenotype, Critical Assessment of Genome Interpretation Consortium, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.ResultsPerformance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.ConclusionsResults show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Published
2024

3. The status of the human gene catalogue

Author

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M., Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G., Johnson, Rory, Murphy, Terence D., Pertea, Mihaela, Pruitt, Kim D., Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A., Yandell, Mark, Carninci, Piero, and Salzberg, Steven L.

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

Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants., Comment: 14 pages

Published
2023

5. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

6. Gaps and complex structurally variant loci in phased genome assemblies

Author

Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Consortium, Human Pangenome Reference, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E, Abel, Haley J, Antonacci-Fulton, Lucinda L, Asri, Mobin, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Bourque, Guillaume, Buonaiuto, Silvia, Carroll, Andrew, Chaisson, Mark JP, Chang, Pi-Chuan, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Cody, Sarah, Colonna, Vincenza, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Doerr, Daniel, Ebler, Jana, Eizenga, Jordan M, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Feng, Xiaowen, Fischer, Christian, Flicek, Paul, Formenti, Giulio, Frankish, Adam, Fulton, Robert S, Gao, Yan, Garg, Shilpa, Garrison, Erik, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Groza, Cristian, Guarracino, Andrea, Haggerty, Leanne, Hall, Ira M, Haukness, Marina, Haussler, David, Heumos, Simon, Hoekzema, Kendra, Hourlier, Thibaut, Howe, Kerstin, Jain, Miten, Jarvis, Erich D, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Li, Heng, Liao, Wen-Wei, Lu, Shuangjia, Lu, Tsung-Yu, Lucas, Julian K, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, Markello, Charles, Martin, Fergal J, McCartney, Ann, McDaniel, Jennifer, Miga, Karen H, Mitchell, Matthew W, Monlong, Jean, Mountcastle, Jacquelyn, Munson, Katherine M, Mwaniki, Moses Njagi, Nattestad, Maria, Novak, Adam M, and Nurk, Sergey

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Humans, DNA, Satellite, Polymorphism, Genetic, Haplotypes, Segmental Duplications, Genomic, Sequence Analysis, DNA, Human Pangenome Reference Consortium, Medical and Health Sciences, Bioinformatics
Abstract

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.

Published
2023

8. Standardized annotation of translated open reading frames

Author

Mudge, Jonathan M, Ruiz-Orera, Jorge, Prensner, John R, Brunet, Marie A, Calvet, Ferriol, Jungreis, Irwin, Gonzalez, Jose Manuel, Magrane, Michele, Martinez, Thomas F, Schulz, Jana Felicitas, Yang, Yucheng T, Albà, M Mar, Aspden, Julie L, Baranov, Pavel V, Bazzini, Ariel A, Bruford, Elspeth, Martin, Maria Jesus, Calviello, Lorenzo, Carvunis, Anne-Ruxandra, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W, Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T, Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L, Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S, and van Heesch, Sebastiaan

Subjects
Molecular Sequence Annotation, Open Reading Frames, Protein Biosynthesis, Ribosomes
Published
2022

9. Harbour porpoises respond to recreational boats by speeding up and moving away from the boat path

Author

Xiuqing Hao, Héloïse Hamel, Céline Hagerup Grandjean, Ivan Fedutin, Magnus Wahlberg, Caitlin Kim Frankish, and Jacob Nabe‐Nielsen

Subjects
behavioural response, boat disturbance, drone footage, motorboat, Phocoena phocoena, recreational vessels, Ecology, QH540-549.5
Abstract

Abstract Recreational boats are common in many coastal waters, yet their effects on cetaceans and other sensitive marine species remain poorly understood. To address this knowledge gap, we used drone video footage recorded from a recreational boat to quantify how harbour porpoises (Phocoena phocoena) responded to the boat approaching at different speeds (10 or 20 knots). Furthermore, we used a hydrophone to record boat noise levels at full bandwidth (0.1–150 kHz) and at the 1/3 octave 16 kHz frequency band for both experimental speeds. The experiments were carried out in shallow waters near Funen, Denmark (55.51° N, 10.79° E) between July and September 2022. Porpoises were more likely to move further away from the path of the boat when approached at 10 knots, but not when approached at 20 knots. In contrast, they swam faster when approached at 20 knots, but not when approached at 10 knots. The recorded received sound level did not depend on how fast the boat approached, suggesting that differences in porpoise responses were related to the speed of the approaching boat rather than to sound intensity. In addition, porpoises generally reacted within close proximity (

Published
2024
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10. Protocol for the development of the Chatbot Assessment Reporting Tool (CHART) for clinical advice

Author

Elizabeth Loder, Gary S Collins, Iain J Marshall, Gordon Guyatt, Per Olav Vandvik, Joerg J Meerpohl, Yaolong Chen, David Moher, An-Wen Chan, Thomas Agoritsas, Riaz Agha, Yung Lee, Alfonso Iorio, Monica Ortenzi, Farid Foroutan, Michael Berkwits, Annette Flanagin, Cynthia Lokker, Ashirbani Saha, Julio Mayol, Hugh Harvey, Stavros A Antoniou, Piyush Mathur, Carolyn Canfield, Christine Laine, Stacy Loeb, Timothy Feeney, Hugo Campos, Tyler McKechnie, Bright Huo, David Chartash, Jeremy Y Ng, Diana Samuel, Helen Frankish, Xufei Lao, Karim Ramji, Hassaan Ahmed, and Vanessa Boudreau

Subjects
Medicine
Abstract

Introduction Large language model (LLM)-linked chatbots are being increasingly applied in healthcare due to their impressive functionality and public availability. Studies have assessed the ability of LLM-linked chatbots to provide accurate clinical advice. However, the methods applied in these Chatbot Assessment Studies are inconsistent due to the lack of reporting standards available, which obscures the interpretation of their study findings. This protocol outlines the development of the Chatbot Assessment Reporting Tool (CHART) reporting guideline.Methods and analysis The development of the CHART reporting guideline will consist of three phases, led by the Steering Committee. During phase one, the team will identify relevant reporting guidelines with artificial intelligence extensions that are published or in development by searching preprint servers, protocol databases, and the Enhancing the Quality and Transparency of health research Network. During phase two, we will conduct a scoping review to identify studies that have addressed the performance of LLM-linked chatbots in summarising evidence and providing clinical advice. The Steering Committee will identify methodology used in previous Chatbot Assessment Studies. Finally, the study team will use checklist items from prior reporting guidelines and findings from the scoping review to develop a draft reporting checklist. We will then perform a Delphi consensus and host two synchronous consensus meetings with an international, multidisciplinary group of stakeholders to refine reporting checklist items and develop a flow diagram.Ethics and dissemination We will publish the final CHART reporting guideline in peer-reviewed journals and will present findings at peer-reviewed meetings. Ethical approval was submitted to the Hamilton Integrated Research Ethics Board and deemed “not required” in accordance with the Tri-Council Policy Statement (TCPS2) for the development of the CHART reporting guideline (#17025).Registration This study protocol is preregistered with Open Science Framework: https://doi.org/10.17605/OSF.IO/59E2Q.

Published
2024
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11. Author Correction: Perspectives on ENCODE

Author

Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.

Published
2022

13. Outcomes after surgery for children in Africa (ASOS-Paeds): a 14-day prospective observational cohort study

Author

Torborg, Alexandra, Meyer, Heidi, El Fiky, Mahmoud, Fawzy, Maher, Elhadi, Muhammed, Ademuyiwa, Adesoji O, Osinaike, Babatunde Babasola, Hewitt-Smith, Adam, Nabukenya, Mary T, Bisegerwa, Ronald, Bouaoud, Souad, Abdoun, Meriem, El Adib, Ahmed Rhassane, Kifle Belachew, Fitsum, Gebre, Meseret, Taye, Desalegn Bekele, Kechiche, Nahla, Fadalla, Tarig, Abdallah, Bareeq, Chaibou, Maman Sani, Nyarko, Mame Yaa Adobea, Ki, Kélan Bertille, Shalongo, Sarah, Mulwafu, Wakisa, Thomson, Emma, Traore, Mamadou Mour, Ndonga, Andrew, Bittaye, Mustapha, Samateh, Ahmadou Lamin, Munlemvo, Dolly M., Kalongo, Jean Jacques, Coulibaly, Yacaria, Coulibaly, Youssouf, Ravelojaona, Vaonandianina, ANDRIAMANARIVO, Lalatiana, RAHERISON, Arsitide Romain, RANDRIAMIZAO, Harifetra Mamy Richard, RAMKALAWAN, Kushal, Omar, Mohamed Abdinor, Ndikontar, Raymond, Joseph, Donamou, Dahir, Shukri, Mohamed, Mubarak, Ali Daoud, Hassan, Ndarukwa, Pisirai, OTIOBANDA, Gilbert Fabrice, Banguti, Paulin, Neil, Kara, Derbew, Miliard, Fanny, Marvin, Smalle, Isaac, Taylor, Elliott H, Duvenage, Hanel, Hardy, Anneli, Kluyts, Hyla, Pearse, Rupert, Biccard, Bruce, AARON, Olurotimi Idowu, Abd Elazeem Mohammed, Hossam Aldein Samir, Abdalkarim, Batool, Abdalla, Abubaker, Abdallah, Mohamed Abubaker Ahmed, Abdeewi, Saedah, Abdel Ghafar, Taqwa, Abdelaleem, Ali, Abdelaleem, Ibrahim Abdelmonaem, Abdelgader, Khansaa, Abdelgadir, Waffa, Abdelhafez, Mohammed, Abdelhalim, Ahmed, Abdelkabir, Mohammed, Abdelkader Osman, Mohamed, Abdelkarim, Maha, Abdelkarim, Mohamed, Abdelmohsen, Sarah Magdy, Abdelnassir, Mazin, Abdelrahman, Ahmed Saber Mohamed, Abdelwahed, Aya Elsayed, Abdelzaher, Mohamed, Abderrahim, Baba Ahmed, Abdoulaye, Touré, Abdulai, Samira, Abdulghaffar, Yunus A., Abdullah, Fatimaalzahraa, Abdullahi, Lawal Barau, Abdullahi, Muzammil, Abdulrazik, Sarah, Abdulsalam, Khalifa Ibrahim, Abdulwahed, Eman, Abdus-Salam, Rukiyat, ABE, TOLUSHE, Abera Mulugeta, Gersam, Aboelghait, Aml Ali, Abol Oyoun, Nariman, Aboubekr, Boumediene, Abraham, Meera, Abu, Mohammed, Abuagila, Ahlam ali, Abubakar, Maimuna, Abugilah, Mohammed, Abuzeid, Issa A, Achouri, Djelloul, Acquah, Serwah Akua, Adam, Nusiba Bushra Ahmed, ADAMU, AUWAL, Adamu, Kabir Musa, ADAMU, MUHAMMAD, ADAMU, Sani, Adane, Samuel Gashu, Adeaga, Mojolaoluwa, Adebayo, Sikiru, Adedire, Adejare, Adegoke, Paul Aderemi, Adeniyi, Adebayo Augustine, Adeoye, Ibukunoluwa, Aderibigbe, Gbenga, ADEROUNMU, Azeezat, ADEYEMI, WILLIAMS, ADEYEMO, Adekunle, Adigun, Tinuola, Adika, Enoch Delad, ADISA, Adewale O, Adjei, Esther, Adjepong-Tandoh, Ernest Kwame, Ads, Alaa Mohamed, ADUMAH, Dr Collins Chijioke, ADUMAH, Lilian ogechi, Adzamli, Innocent, Afari, Jonas, Afedo, Wisdom, Affan, Abubaker, AFOLAYAN, Ayodeji Olawale, Agaba, Stuart, Agbeno, Evans, Agbonrofo, Peter, Aghadi, Ifeanyi, AGU, EDITH, Agyen, Thomas, Agyen-Mensah, Kwasi, Ahensan, Daasebre, Ahmad, Misbahu Haruna, AHMED, Awrayit, Ahmed, Linda, Ahmed, Nidal Youseef Altaher Aboh, Ahmed, Rubaa, Ahmed Jroush, Mohamed, ahmed maghur, Hasan, AHOGNI, G.N. Geofroid, Ait Yahia, Smain, Aji, Narjiss, Aji, Sani Ali, Akerele, William, Akhideno, Irene, Akinmokun, Israel, AKINNIYI, Akin Taofeek, Akinniyi, Ayodeji, AKINYEMI, Samuel, Akitoye, Olumide Adeleke, AKPAETTE, Iniofon Clement, Akuma, Terungwa Jacob, Akuokor, Daniel, Akwei, Clement Nii-Akwei, Al Bashir, Rayan Badran Hamed, Al Gharyani, Mohamed Fathi, al Islam ben Jouira, Rayet, Aladelusi, Timothy, Alakaloko, Felix, Alameen, Hind, Alameen Moheyaldeen, Mohammed, Alaogaly, Mona, Alarabi, Rehab, Alawami, Milud, Alazabi, Basma Masaud, Alazabi, Mona, Albakosh, Bashir Abobaker, ALBDULRRAZIQ, HUSAYN MOHAMMED ElFEETOURI, Aldieb, Asmma, Aldressi, Wafa, Alegbeleye, Godwin E., Alfa, Yakubu, Alhadad, Qamrah, Alhaddad, Arwa R, Alhaddad, Hayfa Faraj, Alhadi, Aliya, Alhamali, Aya, Alharam, Abtisam, Alhlafi, Majduldeen, Alhouwasi, Basmah, Alhudhairy, Sara, Ali, Abdallah Motasim Ahmed, Ali, Ahmed Jama, Ali, Almuaz, Ali, Asma, Ali, Enas, Ali, Mutwakil, Ali, Salem, Ali, Yunusa Y., Ali Ahmed, Abdelbaset, Aliozor, Sampson, Aljamal, Sarah, Alkaseek, Akram, Alkhalifa, Elmustafa, Alkoni, Samah, Allie, Abbaas, Almelyan, Khawla, Almugaddami, Ayman, Almujreesi, Asmaa, Alqady, Eithar, Alragheai, Alaa Ahmed, Alshareea, Entisar, Alshareef, Abulnasir, Alsori, Mohamed, Altomy, Seham Ahmed, Al-Touny, Aiman, Al-Touny, Shimaa A., Alum Aguma, Rachel, Alwaer, Nuha Miftah, Al-zletni, Hadeel, Alzwai, Marwa, Amaambo, Nelago, Amah, Christopher C, Amary, Marwa, Amengle, Ludovic Albert, Amesho, Shiwana Lineekela Omwene, Ametepe, Mawuli, Amkhatirah, Emad, Amnaina, Mohamed Gamal, Amoah, Benjamin, Amoah, Joseph Kofi, Amo-Aidoo, Nana Adjoa Simitsewa, Amoako-Boateng, Mabel, Ampong, Jude, Anane-Fenin, Betty, Anarfi, Samuel, Andriamanarivo, Mamy Lalatiana, Aniakwo, Luke, Aniteye, Ernest, Ankrah, Levi Nii-Ayi, Anno, Audrey, Anyanwu, Lofty-John Chukwuemeka, Anyigba, Edem, Appeadu-Mensah, William, Appiah-Thompson, Peter, Apraku-Peprah, Ewuarabena Lydia, Aremu, Shuaib Kayode, Arinaitwe, Moses, Armah, Ralph, Arthur, Augustine, Arthur, Douglas, Asah-Opoku, Kwaku, Asante, Mabel, Asante-Asamani, Alvin, Asare, Angbo, Asasira, Lausa, Ashfersh, Mohamed, ASHINDOITIANG, John A., Ashong, Joycelyn, Ashraf Salah, Mohamed, Asiedu, Charles, Asiedu, Isaac, Asiyanbi, Kolawole, Asla, Amir, Asman, Wilfred, Asoegwu, Emeka J., Assalhi, Mohamed, Assim, Claudia, Asudo, Felicia Dele, Atai, Alice Gertrude, Ateeqa, Sara Bin, Atim, Terkaa, Atindama, Solomon, ATIQUI, IJLAL, Atrih, Zoubir, Attah, Raphael Avidime, Awad, Ahmed K, Awedew, Atalel Fentahun, Aween, Husayn, Awere-Kyere, Lawrence, Awindaogo, Joseph, Awori Achani, Margaret, Ayad, Kusay, Azab, Ahmed, Azas, Alberta, Aziza, Bochra, Azize, Diallo Abdoul, AZOUI, Abdelkrim, Azouz, Jomana, Baba, Suleiman, Babalola, Olakunle Fatai, Babiker, Mona, Baddoo, Daniel, Badi, Aml, BADMUS, Sarat Abolore, Badr, Helmy, Bah, Abdoulie, Bah, Fatoumata Yakhie, Bah, Kajali, Bah, Marma Tumaneh, Bahroun, Sumayyah, Baidoo, Ebikela, Baidoo, Kenneth, Baidoo, Richard, Bakare, Adewumi, Bakeer, Hiba Baliad, Baky Fahmy, Mohamed A, Balogun, James, Bamigboye, Babatunde, Bankah, Patrick, Banson, Mabel, Barhouma, Yehia Emad, Barongo, Mugisha, BASHIR RABIU, MOHAMMED, Bassem, Adham, Bedair, Mohamed Adel Ali, Beeharry, Hemanshu Rambojan, Beeharry, Shanjugsing, Bekele, Sintayehu, Belie, Orimisan, Belkhair, Abdulmunem, Ben Ahmed, Yosra, Ben Ashur, Abir, Ben Hamida, Bahaeddin, Benade, Christia, BENMANSEUR, Sawsen, Bensebti, Amina Amel, BERDAI, Mohamed Adnane, Beyuo, Vera, Biala, Marwa, Bilson-Amoah, Estella, Bin wali, Salema Subhi, Binnawara, Muhannud, Birlie Chekol, Wubie, Birqeeq, Ghada, Biyase, Thuli, Blankson, Paa Kwesi, Boakye, Benedict, Boakye-Acheampong, Kwame, Boakye-Yiadom, Kwaku, Boateng, Joseph, Bobaker, Salem, Bode, Christopher, Bogoslovskiy, Alexander, Bolarinwa, Eniola Sefiu, Boretti, Lorenzo, Botchway, Maame Tekyiwa, Botha, Christo, BOUDA, B. David, BOURENANE, Haithem, BOUZBID, Sabiha, Boye, Jeffrey, Branny, Mthelebofu, Brown, George Darko, Brown, Warren, Bua, Emmanuel, BWALA, KEFAS JOHN, Camara, Bakary, Camara, M'mah Lamine, Carol, Tisana, Ceesay, Winston, Chafee, Karim, Chaklie Agegnehu, Bewuketu, Chamir, Congo, Chaziya, Peter YC, Chellan, Chantal, Cheniki, Narimane, Chennouf, Sarra, Chepkoech, Eglah, Chilango, Creamy, Chinda, John Yola, Chokwe, Thomas M., Choutri, Hichem, Christian, Nana Ama, Chukwu, Isaac, Chummun, Girish, Cilliers, Celeste, Cloete, Estie, Collison, Carol, Cronje, Larissa, Daary, Dennis, DAD, Bouzid, Daddy, Hadjara, Dahilo, Enoch Auta, Dairam, Jenitha, Dalaf, Manar Salim, Damson, Pempho, Daneji, Sulaiman Muhammad, Daniel, Adekunle, Daoud, Asmaa, Daoud, Hassan, Darat, Tarik Darat, Darko, Kwadwo Opoku, Darko, Kwame, Davidson, Kerryn, Davies, Abigail, Dawang, Yusuf Davou, Dayal, Kishan, Dayie, Makafui, de Goede, Adele, Deelawar, Bibi Waardanaaz, Derwish, Khawla, Desalu, Ibironke, Dessalegn Beza, Andinet, Dhege, Celestino, Dhilraj, Deepika, Diallo, Thierno Sadou, Diaw, Mbaye, Diaw Diop, Amadou, DIENE, Mansour, Dieng, Mactar, Dippenaar, Tinus, Djagbletey, Robert, Djedid, Nihel Klouche, Djouonang, Kamga Telly, Dominique, Shep, Drammeh, Basiru, Drissi, Hajer, du Bruyn, Aritha, Dube, Thandeka, Dufe, Rebecca, Dung, Dido, Earl, Ettiene, Ebrahem, Osama Khalifa Ali, Ebrahim, Zahier, Edena, Morrison E., Effa Ngono, Rosa, Egbuchulem, Kelvin, Egdeer, Amin, Eguma, Stella A., Ehimhantie, Martins, EJIOFOR, Ogochukwu Chidi, Ejuma, Lucy O., Ekenze, Sebastian, Ekhmaj, Reyad Almokhtar, Ekor, Oluwayemisi, EKPA, Sifonobong, Ekpemo, Chidi Samuel, Ekudo, Joseph, Ekwunife, Okechukwu Hyginus, El Koraichi, Alae, El Magrahi, Hamida, El Mejrab, Mohsen, El Sadek, Rania, El YOUBI, Haitam, Eladani, Oman, Elamesh, Sara Abdel Hamid, Elamien, Mohanad, Elamin Elnour, Moheyaldien Ahmed, Elbadawy, Merihan A, Elbaseet, Hesham, Elderwy, Ahmad A., Elebute, Olumide, Elgamal, Mostafa, Elgenidy, Anas, Elghareeb, Ahmed, Elgherwi, Laila, Elhadad, Rasha, Elhadi, Ahmed, Elhassan, Mohamed, Elkhouly, Abdallah Mohamed, Ellebedy, Mohamed, ELMAJRI, MOHAMED FUAD, Elmandouh, Omar, Elmandouh, Reem, Elmorsi, Rami, ELOMBILA, Marie, Elsadek, Menan, Elsalhawy, Shady, Elsayem, Karam, Elshafiey, Mahmoud, El-Sharkawi, Mohammad, Elshazly, Mohamed, Eltaub, Darine, Eltayeb, Almoutaz A, Eltayeb, Mohammed Eltayeb Zainelabdean, Eltegani Abdalla, Abeer, ElWakeel, Mai, Embu, Henry, Emoru, Arthur, Enicker, Basil, Enti, Donald, Entsua-Mensah, Kow, Eseile, Samuel Ideyonbe, Essuman, Vera Adobea, Et-taghy, Hiba, Etwire, Victor, Eyaman, Kuba Daniel, Ezbeida, Mabroukah, EZEKIEL, ANTHONY SABO, Ezidiegwu, Stanley Ugochukwu, Ezomike, Uchechukwu Obiora, FABOYA, Omolara, Fadlalmola, Hammad.A., FAGBAYIMU, Oluwatobiloba Micheal, Faida, Hamza, FALL, Khady, Farahat, Sherif, Faraj, Ali, Faraj, Noora, Farghaly, Amal, Farhat, Karima Omar Ahmed, Farinyaro, Aliyu Umar, Fathi Bani, Ghada, Fattah, Ahmed, Fening, Nana, Fentahun Emrie, Assefa, Fidieley, Melody, Fikadu Keneni, Dame, Fischer, Monique, Flint, Margot, Fodo, Naledi, Fofana, Naby, Fokeerah, Nitish, Folami, Emmanuel, Folokwe, Siyasanga, Fonternel, Doors, Fosi Kamga, Gacelle, Fotso, Luc Kamga, Fourtounas, Maria, Frankish, Leanne, Gabier, Ilhaam, Gacii, Vernon M., Gaffoor, M Sheik, Gagara, Moussa, GALADIMA, Hajara Aminu, Gamubaka, Richard, Ganey, Mike, Ganiyu, Oseni Oyediran, Gasa, Nompumelelo, Gatheru, Antony P., Gawu, Victoria Sena, Gaya, Subha Shita Devi, GAYE, Ibrahima, Gebremichael Ganta, Ashagre, Gelaw, Kassahun Girma, Geldenhuys, Lieze, Getachew Tegegn, Ayenachew, Ghemmied, Malak, Ghmagh, Reem, GILES, AHEREZA, Ginsburg, Ricky Ginsburg, Girma, Kassahun, Gjam, Fatima, Glover-Addy, Hope, Gobin, Veekash, Gomeh, Patricia, Gomez, Dimingo, Gorelyk, Alexandro, Gossaye, Abay, Govender, Veneshree, Grant, Jenny, Grayson, Britney L., Grobbelaar, Mariette, Gueye, Khadim Rassoul, GUIRO, Habibou, Gumede, Simphiwe, Gurure, Desire, Gusibat, Anwar, Gyeke-Boafo, Nana Kwame, HACHEMI, Sihem, Haddis, Kullehe, Haidar, Arwa, Haif, Assia, Hameed-Ikram, Sarwat, Hamid, Haytham, Hamukwaya, Dilona, Hanson, Nana Andoh, Hanzi, Joseph, Hardcastle, Timothy, Harissou, Adamou, Hasan, Ameerah, Hasan, Hayat Ben, Hasan, Najat Ben, Hashi, Abdullahi Said, Hashish, Amel A, Hassaan, Ibrahim, Hassan, Sadiq, Hassan, Sakariye Abdullaahi, Hassan, Tasneem, Hassan, Zeinab, Hassane, Maman Lawal, Hassanein, Mohamed, Hawu, Yoli, Haywood, David, Heelan, Halima, Hendricks, Natalie, Hillah, Ayayi, Hlela, Qinisile, HMAMOUCHI, Badreddine, Hoko, Zanele, Honny, Dorothy, Honore, Samba, Houidi, Senda, Human, Thys, Hussain, Eiman, Hussain Kona, Moataz Hashim, Hussein, Yara, Ibekwe, Titus Sunday, Ibiyemi, Akeem, IBIYEYE, TAIBAT, Ibrahim, Ibrahim Ali, Ibrahim, Lawal Ibrahim, Ibrahim, Soaleh, Ibrahim Abubakar, Amina, Ibrahim Alain, Traore, Idipo, Frieda, Idoko, Godwin, Idowu, Olusola, Idris, Mohammad El-Amin, Igaga, Elizabeth Namugaya, Iindongo, Etuuva, IITULA, Petrus, IKOTUN, Oluwafunmilayo, ILLE, Gloria, Imposo, Desire Hubert, Invernizzi, Jonathan, Irungu, Eric, Isbayqah, Areej Mohammed, Isbayqah, Eenas Mohammed, Ismael, Guibla, Ismail, Ali M, Itambi, Asoh Maxwell, Jabang, John Nute, Jaga, Rudhir, Jaganath, Ushir, Jaiteh, Lamin, Jallow, Cherno S, James, Olutayo, Javed, Sayed, Jithoo, Sandhya, Jlidi, Said, Joel, Lessan, Johnson, Marianne, JONES, TAIWO, Jooma, Zainub, Joomye, Shehzaad, Joosab, Mehboob, JOUINI, Riadh, Jubail, Mohamed J, Juggoo, Chaya, Jumbi, Timothy Mwai, Kaabar, Nejib, Kabirou, Mourtala, Kabiru, Abdulkadir Muhammad, Kabre, B. Yvette, Kache, Stephen, Kacimi, Salah Eddine Oussama, KADAS, ABUBAKAR SAIDU, KAHANSIM, Barminas, Kalipa, Mandisa, Kalongo, Jean Jacques Kabuley, Kalu, Nmesomachi Enyidiya, Kamate, Benoi, Kamwangen, Gracia Mitonga, Kandjimi, Matti, Kanjana-Zondo, Nokuzola, Kankpeyeng, Lawrence, Kapalamula, Tiyamike, Karadji, Souleymane, Kargbo, Mohamed Alieu, Karghul, Mohamed, Kaskar, Razeena, Kasker, Razeena, Kasobya, Faith, Kassem, Ossama, Kateregga, George, Kayima, Peter, Kedwany, Ahmed M., Ken-Amoah, Sebastian, Kenneth, Tomanya Kakura, KERISSE, Amina Nour El-Houd, KERKENI, Yosra, Khairi, Rania, Khaled, Mohamed, Khalifa, Eissa, Khalifa, Marwa Suliman, Khalil, Mohamed Kamal, Khattab, Mohamed S I, Khodary, Ahmed Refaat, Khumalo, Bridget Florence, Khumalo, Phindile, Kigayi, Jean Pierre, Kimutai, Timothy Kiprotich, KINDO, Bassirou, KIRFI, ABDULLAHI MUSA, Koggoh, Patience, Koko, Alshaima A, Kopieniak, Marcin, Kotagiri, Chandra, Kotey, Emily, Kouicem, Aya Tinhinane, Kpangkpari, Richard, Kudoh, Vincent, Kufonya, Norman, Kuhn, Warren, Kutor, Jasper, Kwakye, Akosua, Kynes, J. Matthew, Lambrechts, Lelanie, Lamiri, Rachida, LANRE, OLOKO NASIRUDEEN, Larvie, Prince, Lateef, Azeez Kehinde, LATRECHE, Samir, Lawal, Taiwo, Leballo, Gontse, Lebereki, Simon, Lee, Dorinda, Leeb, Gregory, Leonard, Tristan, LEYONO-MAWANDZA, Peggy Dalliah Gallou, Likongo, Ted Botawaosenge, Limalia, Ziyaad, LIMAN, HARUNA USMAN, Loae, Nada, Lompoli, Beinvenue Nkoy Ena, Lusungu, Dodo, M.Mokhtar, Fatma AL-Zahraa, Madany, Mohie El-Din Mostafa, Maddy, Reginald Jeff, Madombwe, Gladmore, Mafabi, Solomon, Magashi, Mahmoud Kawu, Maharaj, Sanvir, Mahfouz, Shaimaa Mahmoud, Mahlare, Korowe Rose Voncil, Mahmoud, Fathia, Maikassoua, Mamane, Maison, Patrick, Maiwald, Dela, Makhoba, Philisiwe, Makinita, Sewela Grace, Makou epse Tolefac, Myriam, Malau, Thomas Kefas, Mamathuntsha, Tshilidzi Godfrey, Mamo, Tihitena Negussie, Mamuda, Atiku, Mandundzo, Paidamoyo, Mangray, Hansie, Mani, Salma, Manneh, Ebrima K, Mansour, Noureldin Mohamed, Manyere, DV, Mapurisa, Amarylis, Mare, Pieter, Martin, Mogammad Ebrahim, Mashaal, Abdelhafeez, Mashaya, Sonela, Masilela, Patience Busisiwe, Mathebula, Ruth, Mathinya, Tlhapane, Matlala, Tumelo Kwena, Matlou, Mabitsela, Matos-Puig, Roel, Matoug, Salmin, Maudarbocus, Mohammad Jeelani, Mavesere, Haziel Pindukai, Mavila, Jackson, Mayet, Shafeeqa, Maygag, Mohamed, Mbatha, Nonhlanhla, Mbatudde, Rita, Mbiya Kapinga, Anne, Mbuyamba, Jojo, Mbuyi, Ali T, Mdlalose, Nkosinathi, Prowling, Megan, Mejeni, Nathalie, Mekonnen Ejigu, Yayehyirad, Merghani, Safa, Metogo, Junette Epse Njoki, Mhiri, Riadh, Mhone, Lyness, Michael, Afieharo, Miko, Abdullahi Mustapha, Milad, Ahmed, Mishra, Ravi, Mjadu, Londiwe, Mkhontwana, Nokonwaba, Mlambo, Nompilo, Mncwango, Zama, Mngoma, Gcina, Mnguni, Mzamo, Modekwe, Victor Ifeanyichukwu, Mogane, Palesa, Moghazy, Rama, Mogotsi, Kena, Mohalal, Mohamed Salah, Mohamed, Amin Awad Alamin, Mohamed, Maria, Mohamed, Molhema Eltaib Elamin, Mohamed, Suleyman Abdullahi, Mohamedkheir, Mohamed Abdelmoneim, Mohammad, Ahmad Lofty, Mohammad, Alhassan Datti, Mohammad, Aminu Mohammad, Mohammed, Abdulrahman, Mohammed, Muhanned, Mohammed, Rabiu Isah, Mohammed, Rehab, Mohammed, Taha Salah Abdelmaksaod, Mohammedosman, Doaa, Mohsen, Siham Moftah, Molla Getahun, Amsalu, Moloisi, Makwati, Monib, Fatma A, Moodley, Kirushin, Moopanar, Manogran, Morgan, Fatma, Moris, Baluku, Morna, Martin, Moses, Vaughn, Mostafa, Mahmoud Mohamed, Motiang, Mammie, Motseoile, Toni, Motshabi, Palesa, MOUSSAOUI, Nassima, Mpoto, Dany Bolimo, MPOY EMY MONKESSA, Christ Mayick, MRARA, BUSISIWE, Mshelbwala, Philip Mari, Msherghi, Ahmed, Msibi, Trevor, Mubunda, Raphael Kapend, Muhammad, Abubakar Bala, Muhammad, Saminu, Muhanguzi, Joshua, Muhindo, Ruth, Mukenga, Martin Mamba, Mukuna, Patrick Miteo, Mulewa, Deogracias, Munanzvi, Kudzayi Sarah, Mungur, Luckshmanraj, Munubi, Aziz, Munyalo, Francisca Syovata, Muriithi, Julius M., Musa, Abdullahi Aliyu, Musa, Kareem, Musa, Mosaab Abdelhafiz Ebrahim, Musana, Fred, Musewu, Tongo Douglas, Musiitwa, Albino Kiboonwa, Mwangi, Caroline M., Mwepu, Idesbald Mwebe, Mwepu, Michel Ilunga, Mwika, Peter Mwirichia, Mwiti, Timothy M., Myeni, Physician, Mzoneli, Nosisi, Naana, Reyam, Nabukenya, Gladys, Nabunya, Susan, Naidoo, Alishka, Naidoo, Verushka, Naidu, Priyanka, Nakyanzi, Caroline, Nambi, Esther, Nampawu, Mary Juliet, Nampiina, Gorret, Namutebi, Hasifah, Nana, Benedict, Nanda, Joëlle Sandra Youssa, Nanimambi, Juliana, Nantongo, Betty, Napolitano, Luisa, Naser, Alg, Nassar, Ahmad Sammy, Nassar, Muhammad Sammy, Nasser, Nadine, Nawezo, Jacob Gerald, NDIAYE, Alain, NDIAYE, Cheikh Ahmed Tidiane, Ndiaye, Françoise, Ndibarekera, Sarah Harriet, Ndjoko, Sylvie Mishondo, Ndlovu, Msizi, Nduwayezu, Richard, Negash, Samuel, Nehema, Sarah, Neizer, Margaret, NEJMI, Sifeddine, Nezam-Parast, Masoud, Ng How Tseung, Kenny, Ngcelwane, Thandokazi, Ngene, Ikenna, Nghidinwa, Hilka, Ngissah, Reuben, Ngock, George Farrar Fola Ngock, Ngouane, Diane, Ngumi, Zipporah, Nibret, Yonas, NIENGO OUTSOUTA, Gilles, Njie, Masirending, NJOKANMA, Rapheal Azuka, Nkhata, Lister, Nkhuna, Nyajane Thomas, Nkosi, Nobuhle, Nkosi, Sebenzile, Nkwembe, Christophe Mualuka, Nnaji, Chimaobi, Nneji-Akazie, Tochukwu, Nongqo, Nezisa, Nortey, Michael, Noutakdie Tochie, Joel, Nsaful, Josephine, Nsimire, Berthe Barhayiga, Nte, Stanley K., Ntshingila, Cebile, Ntsie, Nthabiseng Precious, Ntsoane, David, Ntumy, Michael Yao, Nuer-Allornuvor, Gloria, Nuhu, Samuel, Nutsuklo, Prudence, Nwachukwu, Callistus Uchenna, NWAFULUME, NNAEMEKA, Nwangwu, Emmanuel, Nwankwo, Elochukwu P, Nyame, Clement Agyekum, Nyamekye, Evelyn, Nyankah, Eunice, Nyoka-Mokgalong, Cecilia, Oase, Divine, Obande, Joseph Orinya, Obbeng, Ambe, Obeng-Adjei, Grace-Imelda, Obianyo, Ijeoma, Obianyo, Nene E, Obiechina, Sylvester, OBRI, Abraham I., ODI, TEMITOPE, Odingo, Jonathan, Oelofsen, Siobhan, Ofori, Emmanuel, Ofori-Adjei, Dziffa, Ogaji, Idoko Monday, Ogundoyin, Olakayode Olaolu, OGUNLEYE, OLABISI, OGUNS, Abayomi, Ogunsua, Oluseyi, Ohemeng-Mensah, Elvis, Ojediran, Olubukola, Ojediran, Oluwabukade, Ojewuyi, Abiodun, Ojewuyi, Olufemi, Ojo, Adedoyin, OJO, Olugbenga Olalekan, Ojo, Omotayo, Okedare, Amos, Okenwa, Samuel C., Oko, Adariku Godwin, Okojie, Nkechi, Okonkwo, Leonard Nduka, Okoth, Peter, Okunlola, Abiodun Idowu, Okunlola, Cecilia Kehinde, Okurut, Mathew, Oladimeji, Motunrayo, Oladiran, Ajibola, Olagunju, Ganiyat R., Olajide, Abdul-Rahman Lukman, Olajide, Adewale. Timothy, Olang, Patrick R., Olayinka, Oluwakemi, Olori, Samson, Olulana, Dare, Olulana, Dare Isaac, Olusanya, Bolutife, Omar, Duaa Eisa, Onakpoya, Uvie, ONeil, Matthew, Onen, Hudson, ONYEKA, Chinonso, Oosthuizen, Alexis, Opandoh, Isabella, Opiyo, Sophy, Oppong, Jonathan, Orewole, Tesleem Olayinka, Orji, Mathias, Osagie, Olabisi, Osagie, Osasumwen T., Osaheni, Osayomwanbo, Osama Sleem, Adham, Osawa, Francis Omondi, Osei, Fred, Osei-Nketiah, Samuel, Osei-Poku, Dorcas, Osman, Alaa, Osman Ahmed, Mohammed, Osman Suliman, Sarah Omer, Otchere, Kofi, Othman, Amani Alsayd Abdulsalam, Othman, Eman, Othman, May, Otim, Paul, Otim, Tonny, Otman, Rema Hassan, Otoki, Violet, OUDJHIH, Messa, OUEDRAOGO, Issaka, OUEDRAOGO, P. Justin, Ousmane Hamady, Issa, Ouyahia, Amel, OWOJUYIGBE, Afolabi, Owoo, Christian, Owoo, Precious, Owusu Boamah, Matthew, Oyedele, Abisola, Oyedepo, Olanrewaju, Oyegbola, Christianah, Panday, Juniata, Parker, Ewomazino U. Evi, Parker, Ilyas, Parker, Robert K., Pembe, Julie Ndjondo, Percivale, Beatrice, Pereko, Janet, Pérez, Mariela, Perumal, Neville, Pillay, Leresse, Pretorius, Robyn, Prinsloo, Roz, Pryce, Charles, Puryag, Ashveen, QUADRI, Oladeji Raheem, Quansah, Kofi, Quarcoopome, Cornelia, Quarshie, Amanda, Quartson, Elizabeth, Quashie-Sam, James, Rabiu, Ayuba, Rabiu, Taofeek, Rahma, Manal, Rahman, Ganiyu Adebisi, Rais, Mounira, Rajah, Chantal, Rakotondrainibe, Aurélia, Ramakrishnan, Rema, Ramatou, Sabo, Ramdawon, Brinda, Ramdhani, Kirthi, Ramkaun, Yeswant, RAPHAEL, OSELE, Raslan, Hani Mohammed Ahmed, Redelinghuys, Cara, Riffi, Omar, Rikhotso, Hundzukani, Roberts, Charles AP, Robertson, Caroline, Roland, Nchufor, Roos, John, S. Abdalgadir, Esra, Saad, Alshaimaa, Saad, Mahmoud M., Saad El-Tanekhy, Aalaa, Saadi, Cyrine, Saadu, Tasiu, Saber, Mohamed, Sabir Yassin, Fatima Mohammed, Sabo, Vinishe Yakubu, Sabra, Tarek Abdelazem, Saeid, Dawoud Amhimmid, Safar, Amna, Sagboze, Sandra, Sahnoun, Lassaad, Salahu, Babangida Mohammed, Salami, Kelvin, Salawu, Adedayo Idris, Saleh, Hawazen, Saleh, Ismail Ali, Saleh, Khetam Mohamed, Salele, Aliyu Mohammed, Salem, Fatima, Salem, Osama, Salih, Mohammed Ali Ismael Alamin, Salisu, Ibrahim, Sall, Mouhamedoun, SAMB, Cheikh Fall, Sangak, Isam A, Sanoussi, Nanzir Moctar, Sanya, Douglas, Sanyang, Anaumana B, Sarpong, Pokua, SARR, Joseph Niame, Schnaubelt, Romy, Searyoh, Kafui, SECK, Ndèye Fatou, Secka, Abdoulie Sering, Seif, Mohamed, Seilbea, Yvonne, Semret Hailu, Berhe, Sepenu, Perez, Sewlall, Janice, Seyi-Olajide, Justina, Shai, Shiluva, Shalaby, Abdullah Mohamad Omar, SHAPHAT, IBRAHIM, Shava, Garai, Sheidu Owuda, Abdullahi, Sheshe, Abdurrahman Abba, Shetiwy, Mosab, Shezi, Nomusa, Shihab, Maryam Husam, Shitakumuna, Helena, Shitaye, Nebiyu, Shitta, Andrew H., Sholadoye, Tunde Talib, Shouasha, Princely, Shu'aibu, Naziru Garba, Shuiap, Nouran musbah, Sibeko, Bongekile, Sikhakhane, Sebe, Sikwete, Guigui, Sime Gizaw, Habtamu, Simelane, Nhlanhlenhle, Simon, Edwina, Singh, Usha, SIRAJALDIN, Abdulla, Siriboe, Esme, Siyothula, Thozama, Siyotula, Thozama, Smart-Yeboah, Awo, SMITH, Saidat, Solala, Sivuyisiwe, Soliman, Eman A., Solo, Corinne Eulalie, Sombéwendin Charles, Ilboudo, Sonaike, Monisola, Songden, David Zumnan, Sottie, Daniel, Soualili, Zineddine, Soula, Enas, Souleymane, Sidibe, SOWANDE, Oludayo Adedapo, Spytko, Alex, Srir, Daria Omar M, Ssebuguzi, Lawrence, Stegmann, George Frederik, Strauss, Lindsey, Struwig, Estee, Succi, Marcello, Suleiman, Abdul-Rasheed, Suliman, Mazin, Swartz, Mikhail, Taha, Taha M., Takai, Idris Usman, Takou, Bougoue Horline, Takrouney, Mohammed Hamada, Takure, Augustine, TALABI, Ademola Olusegun, Tall, Mamadou, Taute, Carla, Tawfik, Mohamed, Taylor, Jenna, Tembe, Dias Salomao, Temesgen, Fissha, Tesfaye, Emnet, Theko, Dineo, Thiart, Mari, Thompson, Ruary, Thuer, Linda, Tientcheu Fabrice, Tim, Tilahun, Zekaryas Belete, Tilahun Woldetsadik, Tsion, Timo, Manuella, Timotews, Namene, Tjiyokola, David, Tolani, Musliu Adetola, TOUABTI, Souhem, Traoré, Diakaridia, Tsegha, Livingfaith Jighjigh, Tseli, Mbeki, Tumuhimbise, Christine, Tumukunde, Janat, Tunkara, Salihu F S, Turshan, Laila, Turton, Edwin, Uchendu, Chukwudi Chukwuemeka, UDIE, Gabriel U., UDOSEN, Joseph E., Ugalahi, Mary, Ugwu, Euphemia M., UGWU, Ikechukwu Ethelbert, Ugwu, Jideofor Okechukwu, Ugwunne, Chuka A, Ukpabio, Ukpabio E.I., Umar, Aminu Muhammed, UMEH, Chizoba Linda, Ungen, Rowena, Usang, Usang, Usenbo, T, Usman, Mustapha Ibrahim, UWAYESU, Roda, Van Aswegen, Benjamin, van der Byl, Ashley, van der Linde, Pieter, van der Walt, Stephan, van Schalkwyk, Hendrik Petrus, van Tonder, Charme, van Vuuren, Suleen, van Wyk, Janri, van Zyl, Sudene, Wabule, Agnes, Wacays, Abdirahman, Waheed Mowafy, Ghada, Waisiko, Bethleen, Walawah, David, Walithandia, Eziron, Wamwaki, John, Wataaka, Nicholas, Wessels, Nelia, Williams, Emmanuel, WILLIAMS, Omolara, Woldegiorgis, Abel, Wolfaardt, George, Wondossen, Mekete, Woodun, Ritish, Workineh, Saleamlak Tigabie, Wubetu, Solomon, Yahia, Mohamed, Yakubu, Hamisu, Yakubu, Saidu Yusuf, Yalewu, Dawit Zerihun, YAMEOGO, T. Azer-Clovis, Yeboah, Francis, YENYI AHUKA LONGOMBE, Thérèse, Younes, Eman, Young, Chad, Younis, Nageia, Younus, Tarig Yousuf Ibrahim, YUSUF, STEPHEN, Zaki, Fatima, Zbida, Ibrahim, Zenda, Thubelihle, ZERIZER, Yassine, Zingoni, Kudzai, Zitouni, Hayett, ZONGO, P. Valentin, Zubi, Abdalrahem, Zulu, Nonhlanhla, and Zulu, Nqobile

Published
2024
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14. The ape that made up its mind: Human intelligence must guide technological evolution

Author

Frankish, Keith

Subjects
An Artificial History of Natural Intelligence: Thinking with Machines from Descartes to the Digital Age (Nonfiction work) -- Bates, David W., Books -- Book reviews, Literature/writing
Abstract

AN ARTIFICIAL HISTORY OF NATURAL INTELLIGENCE Thinking with machines from Descartes to the digital age DAVID W. BATES 408pp. University of Chicago Press. 36 [pounds sterling] (US $45). There is [...]

Published
2024

16. Movement ecology and fisheries bycatch risk of albatross and large petrel species from Bird Island, South Georgia

Author

Frankish, Caitlin, Manica, Andrea, and Phillips, Richard A.

Subjects
333.95, Movement, Seabird, Ecology, Biologging, Fisheries bycatch
Abstract

Recording animal movements is essential for understanding the distribution of species over time, with far-reaching consequences for fitness, population dynamics and conservation. Oceanic seabirds are some of the most mobile and threatened species on Earth, mainly because of incidental mortality (bycatch) in fisheries. Tracking these birds has improved our knowledge of how the environment and individual traits shape specific foraging and migratory strategies; however, this research is biased towards adult life-stages, which are easier to track. In particular, juveniles remain understudied, even though they are likely to differ in their critical habitats and overlap with fisheries, and hence bycatch risk, with implications for population trajectories. In this thesis, I capitalize on recent advances in tracking technology and the wealth of data collected on threatened albatross and large petrel species breeding at Bird Island, South Georgia, to investigate variation in spatial ecology and fisheries bycatch risk across multiple life-stages and species. In Chapter 1, I introduce the main topics of this thesis. In Chapters 2-4, I investigate how wind and resource availability shape divergent movement patterns between juveniles and adult life-stages, and identify age-specific bycatch risk. As high juvenile mortality is likely to result in an ageing population, in Chapter 5 I examine senescence in foraging behaviour, and consider the ramifications for population recovery. In Chapter 6, I then assess the effectiveness of existing fisheries bycatch mitigation measures by investigating the diving capabilities of the most bycaught species in the Southern Ocean. Finally, I conclude with a general discussion summarizing my main findings and suggesting future work. Overall, my results provide new insight into the capacity and motivation for movement in wide-ranging animals; highlighting the diversity of extrinsic and intrinsic processes shaping movements over the lifespans of individuals, and with implications for focusing conservation efforts in time and space.

Published
2021
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18. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

Author

Sweeney, Blake A, Petrov, Anton I, Ribas, Carlos E, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Seemann, Stefan E, Gorodkin, Jan, Cannone, Jamie J, Gutell, Robin R, Kay, Simon, Marygold, Steven, dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M, Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P, Lowe, Todd M, Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Volders, Pieter-Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J, Kalvari, Ioanna, Nawrocki, Eric P, Petrov, Anton S, Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M, Hoksza, David, Lovering, Ruth C, Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, and Weinberg, Zasha

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Animals, Apicomplexa, Base Sequence, Betacoronavirus, Databases, Nucleic Acid, Fungi, Gene Ontology, Humans, Internet, Molecular Sequence Annotation, Nucleic Acid Conformation, RNA, Untranslated, Sequence Analysis, RNA, Software, RNAcentral Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

Published
2021

19. Beyond #FeesMustFall: Understanding the Inclusion Role of Social Media during Students' Protests in South Africa

Author

Olagunju, Anu, Frankish, Tarryn, and Wade, Jean Philippe

Abstract

Studies have shown how social media, including Facebook and Twitter, are reshaping communication, news, and information. It is therefore important to explore the role social media plays in student protests and campaigns in order to determine to what extent social media allows participation and audience inclusion during #FeesMustFall and other contemporary discussions among students. This study also looks at how audience inclusion in Facebook and Twitter is increasingly shaping the "News" habits of young South African students. The study used a qualitative, exploratory, and interpretive approach. Thirteen students were interviewed (audio-recorded) one-on-one using a semi-structured interview guide. The findings indicate that students find recourse in social media as an avenue for inclusion and participation on social issues surrounding the youths during and beyond the #FeesMustFall campaign.

Published
2022
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20. Interval colorectal cancers after negative faecal immunochemical test in the New Zealand Bowel Screening Pilot

Author

Paul Frankish, Ian Bissett, Susan Parry, Kai Sheng Saw, Kerry Sexton, and Mike Hulme-Moir

Subjects
Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Objective Evaluate the diagnostic performance of faecal immunochemical test (FIT), identify risk factors for FIT-interval colorectal cancers (FIT-IC) and describe long-term outcomes of participants with colorectal cancers (CRC) in the New Zealand Bowel Screening Pilot (BSP).Design From 2012 to 2017, the BSP offered eligible individuals, aged 50–74 years, biennial screening using a quantitative FIT with positivity threshold of 15 µg haemoglobin (Hb)/g faeces. Retrospective review of prospectively maintained data extracted from the BSP Register and New Zealand Cancer Registry identified any CRC reported in participants who returned a definitive FIT result. Further details were obtained from hospital records. FIT-ICs were primary CRC diagnosed within 24 months of a negative FIT. Factors associated with FIT-ICs were identified using logistic regression.Results Of 387 215 individuals invited, 57.4% participated with 6.1% returning positive FIT results. Final analysis included 520 CRC, of which 111 (21.3%) met FIT-IC definition. Overall FIT sensitivity for CRC was 78.7% (95% CI=74.9% to 82.1%), specificity was 94.1% (95% CI=94.0% to 94.2%). In 78 (70.3%) participants with FIT-IC, faecal Hb was reported as undetectable. There were no significant associations between FIT-IC and age, sex, ethnicity and deprivation. FIT-ICs were significantly associated with proximal tumour location, late stage at diagnosis, high-grade tumour differentiation and subsequent round screens. Median follow-up time was 74 (2–124) months. FIT-IC had significantly poorer overall survival.Conclusion FIT sensitivity in BSP compared favourably to published data. FIT-ICs were more likely to be proximal tumours with poor long-term outcomes. Further lowering of FIT threshold would have minimal impact on FIT-IC.

Published
2023
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21. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., and Weissman, Tsachy

Published
2023
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22. Perspectives on ENCODE

Author

Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, Animals, Binding Sites, Chromatin, DNA Methylation, Databases, Genetic, Gene Expression Regulation, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Molecular Sequence Annotation, Quality Control, Regulatory Sequences, Nucleic Acid, Transcription Factors, ENCODE Project Consortium, General Science & Technology
Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Published
2020

23. Perspectives on ENCODE.

Author

ENCODE Project Consortium, Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, Chromatin, Animals, Humans, Mice, Histones, Transcription Factors, Genomics, DNA Methylation, Gene Expression Regulation, Binding Sites, Regulatory Sequences, Nucleic Acid, Genome, Genome, Human, Quality Control, Databases, Genetic, Molecular Sequence Annotation, Human Genome, Vaccine Related, Biotechnology, Genetics, Immunization, Vaccine Related (AIDS), Prevention, 1.1 Normal biological development and functioning, Generic health relevance, General Science & Technology
Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Published
2020

39. SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility

Author

Silvennoinen, Katri, Gawel, Kinga, Tsortouktzidis, Despina, Pitsch, Julika, Alhusaini, Saud, van Loo, Karen M. J., Picardo, Richard, Michalak, Zuzanna, Pagni, Susanna, Martins Custodio, Helena, Mills, James, Whelan, Christopher D., de Zubicaray, Greig I., McMahon, Katie L., van der Ent, Wietske, Kirstein-Smardzewska, Karolina J., Tiraboschi, Ettore, Mudge, Jonathan M., Frankish, Adam, Thom, Maria, Wright, Margaret J., Thompson, Paul M., Schoch, Susanne, Becker, Albert J., Esguerra, Camila V., and Sisodiya, Sanjay M.

Published
2022
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40. RNAcentral: a hub of information for non-coding RNA sequences

Author

Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley JF, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, and Williams, Kelly P

Subjects
Biological Sciences, Environmental Sciences, Chemical Sciences, The RNAcentral Consortium, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Published
2019

41. The CD40 agonist HERA-CD40L results in enhanced activation of antigen presenting cells, promoting an anti-tumor effect alone and in combination with radiotherapy

Author

Jamie Frankish, Debayan Mukherjee, Erminia Romano, Katharina Billian-Frey, Matthias Schröder, Karl Heinonen, Christian Merz, Mauricio Redondo Müller, Christian Gieffers, Oliver Hill, Meinolf Thiemann, Jamie Honeychurch, Tim Illidge, and Jaromir Sykora

Subjects
CD40, HERA-CD40L, TNFRSF, TRAF2, tumor micro environment (TME), antigen presenting cells, Immunologic diseases. Allergy, RC581-607
Abstract

IntroductionThe ability to modulate and enhance the anti-tumor immune responses is critical in developing novel therapies in cancer. The Tumor Necrosis Factor (TNF) Receptor Super Family (TNFRSF) are potentially excellent targets for modulation which result in specific anti-tumor immune responses. CD40 is a member of the TNFRSF and several clinical therapies are under development. CD40 signaling plays a pivotal role in regulating the immune system from B cell responses to myeloid cell driven activation of T cells. The CD40 signaling axis is well characterized and here we compare next generation HERA-Ligands to conventional monoclonal antibody based immune modulation for the treatment of cancer.Methods & resultsHERA-CD40L is a novel molecule that targets CD40 mediated signal transduction and demonstrates a clear mode of action in generating an activated receptor complex via recruitment of TRAFs, cIAP1, and HOIP, leading to TRAF2 phosphorylation and ultimately resulting in the enhanced activation of key inflammatory/survival pathway and transcription factors such asNFkB, AKT, p38, ERK1/2, JNK, and STAT1 in dendritic cells. Furthermore, HERA-CD40L demonstrated a strong modulation of the tumor microenvironment (TME) via the increase in intratumoral CD8+ T cells and the functional switch from pro-tumor macrophages (TAMs) to anti-tumor macrophages that together results in a significant reduction of tumor growth in a CT26 mouse model. Furthermore, radiotherapy which may have an immunosuppressive modulation of the TME, was shown to have an immunostimulatory effect in combination with HERA-CD40L. Radiotherapy in combination with HERA-CD40L treatment resulted in an increase in detected intratumoral CD4+/8+ T cells compared to RT alone and, additionally, the repolarization of TAMs was also observed, resulting in an inhibition of tumor growth in a TRAMP-C1 mouse model.DiscussionTaken together, HERA-CD40L resulted in activating signal transduction mechanisms in dendritic cells, resulting in an increase in intratumoral T cells and manipulation of the TME to be pro-inflammatory, repolarizing M2 macrophages to M1, enhancing tumor control.

Published
2023
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42. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

Author

Morales, Joannella, Pujar, Shashikant, Loveland, Jane E., Astashyn, Alex, Bennett, Ruth, Berry, Andrew, Cox, Eric, Davidson, Claire, Ermolaeva, Olga, Farrell, Catherine M., Fatima, Reham, Gil, Laurent, Goldfarb, Tamara, Gonzalez, Jose M., Haddad, Diana, Hardy, Matthew, Hunt, Toby, Jackson, John, Joardar, Vinita S., Kay, Michael, Kodali, Vamsi K., McGarvey, Kelly M., McMahon, Aoife, Mudge, Jonathan M., Murphy, Daniel N., Murphy, Michael R., Rajput, Bhanu, Rangwala, Sanjida H., Riddick, Lillian D., Thibaud-Nissen, Françoise, Threadgold, Glen, Vatsan, Anjana R., Wallin, Craig, Webb, David, Flicek, Paul, Birney, Ewan, Pruitt, Kim D., Frankish, Adam, Cunningham, Fiona, and Murphy, Terence D.

Published
2022
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43. SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB

Author

Neufeldt, Christopher J., Cerikan, Berati, Cortese, Mirko, Frankish, Jamie, Lee, Ji-Young, Plociennikowska, Agnieszka, Heigwer, Florian, Prasad, Vibhu, Joecks, Sebastian, Burkart, Sandy S., Zander, David Y., Subramanian, Baskaran, Gimi, Rayomand, Padmanabhan, Seetharamaiyer, Iyer, Radhakrishnan, Gendarme, Mathieu, El Debs, Bachir, Halama, Niels, Merle, Uta, Boutros, Michael, Binder, Marco, and Bartenschlager, Ralf

Published
2022
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44. Technology and the Human Minds

Author

Frankish, Keith, Piccinini, Gualtiero, Series Editor, Brogaard, Berit, Editorial Board Member, Craver, Carl, Editorial Board Member, Machery, Edouard, Editorial Board Member, Shagrir, Oron, Editorial Board Member, Sprevak, Mark, Editorial Board Member, Clowes, Robert W., editor, Gärtner, Klaus, editor, and Hipólito, Inês, editor

Published
2021
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45. SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB

Author

Christopher J. Neufeldt, Berati Cerikan, Mirko Cortese, Jamie Frankish, Ji-Young Lee, Agnieszka Plociennikowska, Florian Heigwer, Vibhu Prasad, Sebastian Joecks, Sandy S. Burkart, David Y. Zander, Baskaran Subramanian, Rayomand Gimi, Seetharamaiyer Padmanabhan, Radhakrishnan Iyer, Mathieu Gendarme, Bachir El Debs, Niels Halama, Uta Merle, Michael Boutros, Marco Binder, and Ralf Bartenschlager

Subjects
Biology (General), QH301-705.5
Abstract

Neufeldt et al. evaluate transcriptional and cytokine secretion profiles of cells and patient sera following SARS-CoV-2 infection and detect distinct upregulation of inflammatory cytokines. They also demonstrate that this upregulation is mediated by cGAS-STING and NF-κB signalling, which could provide a potential avenue for the development of future therapies against SARS-CoV-2.

Published
2022
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46. P539: Fostering a common language in clinical genomics: MANE Select as a universal standard to report clinical variants

Author

Shashikant Pujar, Jane Loveland, Alex Astashyn, Ruth Bennett, Andrew Berry, Eric Cox, Claire Davidson, Olga Ermolaeva, Catherine Farrell, Reham Fatima, Tamara Goldfarb, Jose Gonzalez, Diana Haddad, Matthew Hardy, Toby Hunt, John Jackson, Vinita Joardar, Michael Kay, Vamsi Kodali, Kelly McGarvey, Jonathan Mudge, Michael Murphy, Sanjida Rangwala, Françoise Thibaud-Nissen, Anjana Vatsan, Wallin Craig, Webb David, Adam Frankish, Fiona Cunningham, and Terence Murphy

Subjects
Genetics, QH426-470, Medicine
Published
2023
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47. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Author

Lilue, Jingtao, Doran, Anthony G, Fiddes, Ian T, Abrudan, Monica, Armstrong, Joel, Bennett, Ruth, Chow, William, Collins, Joanna, Collins, Stephan, Czechanski, Anne, Danecek, Petr, Diekhans, Mark, Dolle, Dirk-Dominik, Dunn, Matt, Durbin, Richard, Earl, Dent, Ferguson-Smith, Anne, Flicek, Paul, Flint, Jonathan, Frankish, Adam, Fu, Beiyuan, Gerstein, Mark, Gilbert, James, Goodstadt, Leo, Harrow, Jennifer, Howe, Kerstin, Ibarra-Soria, Ximena, Kolmogorov, Mikhail, Lelliott, Chris J, Logan, Darren W, Loveland, Jane, Mathews, Clayton E, Mott, Richard, Muir, Paul, Nachtweide, Stefanie, Navarro, Fabio CP, Odom, Duncan T, Park, Naomi, Pelan, Sarah, Pham, Son K, Quail, Mike, Reinholdt, Laura, Romoth, Lars, Shirley, Lesley, Sisu, Cristina, Sjoberg-Herrera, Marcela, Stanke, Mario, Steward, Charles, Thomas, Mark, Threadgold, Glen, Thybert, David, Torrance, James, Wong, Kim, Wood, Jonathan, Yalcin, Binnaz, Yang, Fengtang, Adams, David J, Paten, Benedict, and Keane, Thomas M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Animals, Animals, Laboratory, Chromosome Mapping, Genetic Loci, Genome, Haplotypes, Mice, Mice, Inbred BALB C, Mice, Inbred C3H, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Inbred DBA, Mice, Inbred NOD, Mice, Inbred Strains, Molecular Sequence Annotation, Phylogeny, Polymorphism, Single Nucleotide, Species Specificity, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.

Published
2018

48. Beyond #FeesMustFall: Understanding the inclusion role of social media during students’ protests in South Africa

Author

Anu Olagunju, Tarryn Frankish, and Jean Philippe Wade

Subjects
Audience inclusion, Facebook, Twitter, Social media, University students, #FeesMustFall, Education (General), L7-991
Abstract

Studies have shown how social media, including Facebook and Twitter, are reshaping communication, news, and information. It is therefore important to explore the role social media plays in student protests and campaigns in order to determine to what extent social media allows participation and audience inclusion during #FeesMustFall and other contemporary discussions among students. This study also looks at how audience inclusion in Facebook and Twitter is increasingly shaping the “News” habits of young South African students. The study used a qualitative, exploratory, and interpretive approach. Thirteen students were interviewed (audio-recorded) one-on-one using a semi-structured interview guide. The findings indicate that students find recourse in social media as an avenue for inclusion and participation on social issues surrounding the youths during and beyond the #FeesMustFall campaign.

Published
2022
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49. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Author

Lambourne, Luke, primary, Mattioli, Kaia, additional, Santoso, Clarissa, additional, Sheynkman, Gloria, additional, Inukai, Sachi, additional, Kaundal, Babita, additional, Berenson, Anna, additional, Spirohn-Fitzgerald, Kerstin, additional, Bhattacharjee, Anukana, additional, Rothman, Elisabeth, additional, Shrestha, Shaleen, additional, Laval, Florent, additional, Yang, Zhipeng, additional, Bisht, Deepa, additional, Sewell, Jared A., additional, Li, Guangyuan, additional, Prasad, Anisa, additional, Phanor, Sabrina, additional, Lane, Ryan, additional, Campbell, Devlin M., additional, Hunt, Toby, additional, Balcha, Dawit, additional, Gebbia, Marinella, additional, Twizere, Jean-Claude, additional, Hao, Tong, additional, Frankish, Adam, additional, Riback, Josh A., additional, Salomonis, Nathan, additional, Calderwood, Michael A., additional, Hill, David E., additional, Sahni, Nidhi, additional, Vidal, Marc, additional, Bulyk, Martha L., additional, and Fuxman Bass, Juan I., additional

Published
2024
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