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Research Articles (Genetics): Recent submissions

  • Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities 
    Van Uffelen, Alexander; Posadas, Andres; Roosens, Nancy H.C.; Marchal, Kathleen; De Keersmaecker, Sigrid C. J.; Vanneste, Kevin (Nature Research, 2024-08)
    Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation ...
  • Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini) 
    Rakotoarivelo, Andrinajoro R.; Rambuda, Thabelo; Taron, Ulrike H.; Stalder, Gabrielle; O'Donoghue, Paul; Robovsky, Jan; Hartmann, Stefanie; Hofreiter, Michael; Moodley, Yoshan (Elsevier, 2024-09)
    The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists ...
  • Poaching forensics : animal victims in the courtroom 
    Harper, Cindy Kim (Annual Reviews, 2023)
    Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is ...
  • Nanoplankton : the dominant vector for carbon export across the Atlantic Southern Ocean in spring 
    Flynn, Raquel F.; Haraguchi, Lumi; Mcquaid, Jeff; Burger, Jessica M.; Lunga, Percy Mutseka; Stirnimann, Luca; Samanta, Saumik; Roychoudhury, Alakendra N.; Fawcett, Sarah E. (American Association for the Advancement of Science, 2023-12)
    Across the Southern Ocean, large (≥20 μm) diatoms are generally assumed to be the primary vector for carbon export, although this assumption derives mainly from summertime observations. Here, we investigated carbon production ...
  • Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity 
    Shaffer, Justin P.; Nothias, Louis-Felix; Thompson, Luke R.; Sanders, Jon G.; Salido, Rodolfo A.; Couvillion, Sneha P.; Brejnrod, Asker D.; Lejzerowicz, Franck; Haiminen, Niina; Huang, Shi; Lutz, Holly L.; Zhu, Qiyun; Martino, Cameron; Morton, James T.; Karthikeyan, Smruthi; Nothias-Esposito, Melissa; Duhrkop, Kai; Bocker, Sebastian; Kim, Hyun Woo; Aksenov, Alexander A.; Bittremieux, Wout; Minich, Jeremiah J.; Marotz, Clarisse; Bryant, MacKenzie M.; Sanders, Karenina; Schwartz, Tara; Humphrey, Greg; Vasquez-Baeza, Yoshiki; Tripathi, Anupriya; Parida, Laxmi; Carrieri, Anna Paola; Beck, Kristen L.; Das, Promi; Gonzalez, Antonio; McDonald, Daniel; Ladau, Joshua; Karst, Soren M.; Albertsen, Mads; Ackermann, Gail; DeReus, Jeff; Thomas, Torsten; Petras, Daniel; Shade, Ashley; Stegen, James; Song, Se Jin; Metz, Thomas O.; Swafford, Austin D.; Dorrestein, Pieter C.; Jansson, Janet K.; Gilbert, Jack A.; Knight, Rob; The Earth Microbiome Project 500 (EMP500) Consortium; Angenant, Lars T.; Berry, Alison M.; Bittleston, Leonora S.; Bowen, Jennifer L.; Chavarria, Max; Cowan, Don A.; Distel, Dan; Girguis, Peter R.; Huerta-Cepas, Jaime; Jensen, Paul R.; Jiang, Lingjing; King, Gary M.; Lavrinienko, Anton; MacRae-Crerar, Aurora; Makhalanyane, Thulani Peter; Mappes, Tapio; Marzinelli, Ezequiel M.; Mayer, Gregory; McMahon, Katherine D.; Metcalf, Jessica L.; Miyake, Sou; Mousseau, Timothy A.; Murillo-Cruz, Catalina; Myrold, David; Palenik, Brian; Pinto-Tomas, Adrian A.; Porazinska, Dorota L.; Ramond, Jean-Baptiste; owher, Forest R.; RoyChowdhury, Taniya; Sandin, Stuart A.; Schmidt, Steven K.; Seedorf, Henning; Shade, Ashley; Shipway, J. Reuben; Smith, Jennifer E.; Stegen, James; Stewart, Frank J.; Tait, Karen; Thomas, Torsten; Tucker, Yael; U’Ren, Jana M.; Watts, Phillip C.; Webster, Nicole S.; Zaneveld, Jesse R.; Zhang, Shan (Nature Research, 2022-12)
    Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary ...
  • Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers 
    Hakkaart, Christopher; Pearson, John F.; Marquart, Louise; Dennis, Joe; Wiggins, George A.R.; Barnes, Daniel R.; Robinson, Bridget A.; Mace, Peter D.; Aittomaki, Kristiina; Andrulis, Irene L.; Arun, Banu K.; Azzollini, Jacopo; Balmana, Judith; Barkardottir, Rosa B.; Belhadj, Sami; Berger, Lieke; Blok, Marinus J.; Boonen, Susanne E.; Borde, Julika; Bradbury, Angela R.; Brunet, Joan; Buys, Saundra S.; Caligo, Maria A.; Campbell, Ian; Chung, Wendy K.; Claes, Kathleen B.M.; GEMO Study Collaborators; EMBRACE Collaborators; Collonge-Rame, Marie-Agnes; Cook, Jackie; Cosgrove, Casey; Couch, Fergus J.; Daly, Mary B.; Dandiker, Sita; Davidson, Rosemarie; De la Hoya, Miguel; De Putter, Robin; Delnatte, Capucine; Dhawan, Mallika; Diez, Orland; Ding, Yuan Chun; Domchek, Susan M.; Donaldson, Alan; Eason, Jacqueline; Easton, Douglas F.; Ehrencrona, Hans; Engel, Christoph; Evans, D. Gareth; Faust, Ulrike; Feliubadalo, Lidia; Fostira, Florentia; Friedman, Eitan; Frone, Megan; Frost, Debra; Garber, Judy; Gayther, Simon A.; Gehrig, Andrea; Gesta, Paul; Godwin, Andrew K.; Goldgar, David E.; Greene, Mark H.; Hahnen, Eric; Hake, Christopher R.; Hamann, Ute; Hansen, Thomas V.O.; Hauke, Jan; Hentschel, Julia; Herold, Natalie; Honisch, Ellen; Hulick, Peter J.; Imyanitov, Evgeny N.; SWE-BRCA Investigators; kConFab Investigators; HEBON Investigators; Isaacs, Claudine; Izatt, Louise; Izquierdo, Angel; Jakubowska, Anna; James, Paul A.; Janavicius, Ramunas; John, Esther M.; Joseph, Vijai; Karlan, Beth Y.; Kemp, Zoe; Kirk, Judy; Konstantopoulou, Irene; Koudijs, Marco; Kwong, Ava; Laitman, Yael; Lalloo, Fiona; Lasset, Christine; Lautrup, Charlotte; Lazaro, Conxi; Legrand, Clementine; Leslie, Goska; Lesueur, Fabienne; Mai, Phuong L.; Manoukian, Siranoush; Mari, Veronique; Martens, John W.M.; McGuffog, Lesley; Mebirouk, Noura; Meindl, Alfons; Miller, Austin; Montagna, Marco; Moserle, Lidia; Mouret-Fourme, Emmanuelle; Musgrave, Hannah; Nambot, Sophie; Nathanson, Katherine L.; Neuhausen, Susan L.; Nevanlinna, Heli; Yuen Yie, Joanne Ngeow; Nguyen-Dumont, Tu; Nikitina-Zake, Liene; Offit, Kenneth; Olah, Edith; Olopade, Olufunmilayo I.; Osorio, Ana; Ott, Claus-Eric; Park, Sue K.; Parsons, Michael T.; Pedersen, Inge Sokilde; Peixoto, Ana; Perez-Segura, Pedro; Peterlongo, Paolo; Pocza, Timea; Radice, Paolo; Ramser, Juliane; Rantala, Johanna; Rodriguez, Gustavo C.; Ronlund, Karina; Rosenberg, Efraim H.; Rossing, Maria; Schmutzler, Rita K.; Shah, Payal D.; Sharif, Saba; Sharma, Priyanka; Side, Lucy E.; Simard, Jacques; Singer, Christian F.; Snape, Katie; Steinemann, Doris; Stoppa-Lyonnet, Dominique; Sutter, Christian; Tan, Yen Yen; Teixeira, Manuel R.; Teo, Soo Hwang; Thomassen, Mads; Thull, Darcy L.; Tischkowitz, Marc; Toland, Amanda E.; Trainer, Alison H.; Tripathi, Vishakha; Tung, Nadine; Van Engelen, Klaartje; Jansen van Rensburg, Elizabeth; Vega, Ana; Viel, Alessandra; Weitzel, Jeffrey N.; Wevers, Marike R.; Chenevix-Trench, Georgia; Spurdle, Amanda B.; Antoniou, Antonis C. (Springer Nature, 2022-10-06)
    The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of ...
  • Wonders of the Namib Desert 
    Cowan, Don A.; Maggs‑Kolling, Gillian (Academy of Science South Africa, 2022)
    You might think that nothing exists in a desert? Think again! The Namib Desert is teeming with life if you look closely.
  • Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe) 
    Zhang, Ticao; Qiao, Qin; Du, Xiao; Zhang, Xiao; Hou, Yali; Wei, Xin; Sun, Chao; Zhang, Rengang; Yun, Quanzheng; Crabbe, M. James C.; Van de Peer, Yves; Dong, Wenxuan (Wiley, 2022-08)
    Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosomelevel genome sequence ...
  • The neighborhood of the spike gene Is a hotspot for modular intertypic homologous and nonhomologous recombination in coronavirus genomes 
    Nikolaidis, Marios; Markoulatos, Panayotis; Van de Peer, Yves; Oliver, Stephen G.; Amoutzias, Grigorios D. (Oxford University Press, 2022-01)
    Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous ...
  • Evolution of isoform-level gene expression patterns across tissues during lotus species divergence 
    Zhang, Yue; Yang, Xingyu; Van de Peer, Yves; Chen, Jinming; Marchal, Kathleen; Shi, Tao (Wiley, 2022-11)
    Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. ...
  • Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches 
    Xu, Hui; Li, Zhen; Jiang, Peng-Fei; Zhao, Li; Qu, Chang; Van de Peer, Yves; Liu, Yan-Jing; Zeng, Qing-Yin (Wiley, 2022-04)
    Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes ...
  • In vitro dual activity of Aloe marlothii roots and its chemical constituents against Plasmodium falciparum asexual and sexual stage parasites 
    Mianda, S.M.; Invernizzi, Luke; Van der Watt, Mariette Elizabeth; Reader, Janette; Moyo, Phanankosi; Birkholtz, Lyn-Marie; Maharaj, Vinesh J. (Elsevier, 2022-10)
    Please abstract in the article.
  • New transmission-selective antimalarial agents through hit-to-lead optimization of 2-([1,1 '-Biphenyl]-4-carboxamido)benzoic acid derivatives 
    Reader, Janette; Opperman, Daniel; Van der Watt, Mariette Elizabeth; Theron, Anjo; Leshabane, Meta Kgaogelo; Da Rocha, Michelle; Turner, Jonathan; Garrabrant, Kathleen; Pina, Ivett; Mills, Catherine; Woster, Patrick M.; Birkholtz, Lyn-Marie (Wiley, 2022-11)
    Malaria elimination requires multipronged approaches, including the application of antimalarial drugs able to block humanto- mosquito transmission of malaria parasites. The transmissible gametocytes of Plasmodium ...
  • syntenet : an R/Bioconductor package for the inference and analysis of synteny networks 
    Almeida-Silva, Fabricio; Zhao, Tao; Ullrich, Kristian K.; Schranz, M. Eric; Van de Peer, Yves (Oxford University Press, 2023-01)
    Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny ...
  • By blood or by choice? On relational autonomy and the familial ties that bind us 
    Van Wyk, Tanya (Stellenbosch University, Faculty of Theology, 2022)
    This article explores the range of the construct “family” in light of the author’s experience of how the death of a congregation-member exposed the strength, persistence and immovability of the construct, “family”. Despite ...
  • Novel 3-trifluoromethyl-1,2,4-oxadiazole analogues of astemizole with multi-stage antiplasmodium activity and in vivo efficacy in a Plasmodium berghei mouse malaria infection model 
    Mambwe, Dickson; Korkor, Constance M.; Mabhula, Amanda; Ngqumba, Zama; Cloete, Cleavon; Kumar, Malkeet; Barros, Paula Ladeia; Leshabane, Meta Kgaogelo; Coertzen, Dina; Taylor, Dale; Gibhard, Liezl; Njoroge, Mathew; Lawrence, Nina; Reader, Janette; Moreira, Diogo Rodrigo; Birkholtz, Lyn-Marie; Wittlin, Sergio; Egan, Timothy J.; Chibale, Kelly (American Chemical Society, 2022-12)
    Please read abstract in the article.
  • Population genetics of a lethally managed medium-sized predator 
    Slater, K.; De Jager, Deon; Van Wyk, A.M.; Dalton, Desire Lee; Kropff, Anna S.; Du Preez, Ilse (Wiley, 2022-09)
    Globally, levels of human–wildlife conflict are increasing as a direct consequence of the expansion of people into natural areas resulting in competition with wildlife for food and other resources. By being forced into ...
  • Sapwood mycobiome varies across host, plant compartment and environments in Nothofagus forests from Northern Patagonia 
    Molina, Lucia; Rajchenberg, Mario; De Errasti, Andres; Vogel, Braian; Coetzee, Martin Petrus Albertus; Aime, Mary Catherine; Pildain, Maria Belen (Wiley, 2023-12)
    Global forests are increasingly being threatened by altered climatic conditions and increased attacks by pests and pathogens. The complex ecological interactions among pathogens, microbial communities, tree hosts and the ...
  • The predictive ability of the 313 variant–based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant 
    Lakeman, Inge M.M.; Van den Broek, Alexandra J.; Vos, Julien A.M.; Barnes, Daniel R.; Adlard, Julian; Andrulis, Irene L.; Arason, Adalgeir; Arnold, Norbert; Arun, Banu K.; Balmana, Judith; Barrowdale, Daniel; Benitez, Javier; Borg, Ake; Caldes, Trinidad; Caligo, Maria A.; Chung, Wendy K.; Claes, Kathleen B.M.; GEMO Study Collaborators; EMBRACE Collaborators; Collee, J. Margriet; Couch, Fergus J.; Daly, Mary B.; Dennis, Joe; Dhawan, Mallika; Domchek, Susan M.; Eeles, Ros; Engel, Christoph; Evans, D. Gareth; Feliubadalo, Lidia; Foretova, Lenka; Friedman, Eitan; Frost, Debra; Ganz, Patricia A.; Garber, Judy; Gayther, Simon A.; Gerdes, Anne-Marie; Godwin, Andrew K.; Goldgar, David E.; Hahnen, Eric; Hake, Christopher R.; Hamann, Ute; Hogervorst, Frans B.L.; Hooning, Maartje J.; Hopper, John L.; Hulick, Peter J.; Imyanitov, Evgeny N.; OCGN Investigators; HEBON Investigators; KconFab Investigators; Isaacs, Claudine; Izatt, Louise; Jakubowska, Anna; James, Paul A.; Janavicius, Ramunas; Jensen, Uffe Birk; Jiao, Yue; John, Esther M.; Joseph, Vijai; Karlan, Beth Y.; Kets, Carolien M.; Konstantopoulou, Irene; Kwong, Ava; Legrand, Clementine; Leslie, Goska; Lesueur, Fabienne; Loud, Jennifer T.; Lubinski, Jan; Manoukian, Siranoush; McGuffog, Lesley; Miller, Austin; Gomes, Denise Molina; Montagna, Marco; Mouret-Fourme, Emmanuelle; Nathanson, Katherine L.; Neuhausen, Susan L.; Nevanlinna, Heli; Yuen Yie, Joanne Ngeow; Olah, Edith; Olopade, Olufunmilayo I.; Park, Sue K.; Parsons, Michael T.; Peterlongo, Paolo; Piedmonte, Marion; Radice, Paolo; Rantala, Johanna; Rennert, Gad; Risch, Harvey A.; Schmutzler, Rita K.; Sharma, Priyanka; Simard, Jacques; Singer, Christian F.; Stadler, Zsofia; Stoppa-Lyonnet, Dominique; Sutter, Christian; Tan, Yen Yen; Teixeira, Manuel R.; Teo, Soo Hwang; Teule, Alex; Thomassen, Mads; Thull, Darcy L.; Tischkowitz, Marc; Toland, Amanda E.; Tung, Nadine; Janse van Rensburg, Elizabeth (Elsevier, 2021-06-10)
    PURPOSE : To evaluate the association between a previously published 313 variant–based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant ...
  • The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences 
    Fang, Yuhan; Qin, Xing; Liao, Qinggang; Du, Ran; Luo, Xizhi; Zhou, Qian; Li, Zhen; Chen, Hengchi; Jin, Wanting; Yuan, Yaning; Sun, Pengbo; Zhang, Rui; Zhang, Jiao; Wang, Li; Cheng, Shifeng; Yang, Xueyong; Yan, Yuehong; Zhang, Xingtan; Zhang, Zhonghua; Bai, Shunong; Van de Peer, Yves; Lucas, William John; Huang, Sanwen; Yan, Jianbin (Nature Research, 2022-09)
    Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. ...