Search

Your search keyword '"Fordham, Daniel"' showing total 12 results
Start Over Author "Fordham, Daniel"
12 results on '"Fordham, Daniel"'

1. Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and its Clinical Implications

Author

Rave, Gilad, Fordham, Daniel E., Bronstein, Alex M., Silver, David H., Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Xie, Xianghua, editor, Styles, Iain, editor, Powathil, Gibin, editor, and Ceccarelli, Marco, editor

Published
2024
Full Text
View/download PDF

2. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Author

Alvarez-Ordóñez, Avelino, Alvarez, Pablo, Antonielli, Livio, Arendt, Elke, Armanini, Federica, Aubry, Aurelie, Baelum, Jacob, Barcenilla, Coral, Belanche, Alejandro, Benavent-Gil, Yaiza, Blake, Tony, Blanco-Míguez, Aitor, Bongoni, Radhika, Boyer, Mickael, Brennan, Fiona, Breselge, Samuel, Briem, Helgi, Butler, Derek, Calvete-Torre, Inés, Carballo, Omar Cristobal, Cardinal, Mireille, Carlino, Niccolò, Chervaux, Christian, Chopin, Christine, Clotaire, Natallia, Coakley, Mairead, Cobo-Díaz, José Francisco, Codd, Jim, Conroy, Stephen, Corral-Jara, Karla Fabiola, Corral-Jara, Karla-Fabiola, Cotter, Paul D., Coyne, Gerard, Creevey, Chris, Cuevas, Patricia D., Curran, Brendan, Delgado, Susana, Derde, Liesbeth, Derrien, Muriel, Ercolini, Danilo, Exposito, Ruth Gomez, López Fernández, María Mercedes, De Filippis, Francesca, Fordham, Daniel, Galy, Hubert, Gavriilidou, Asimenia, Gunnarsson, Oddur, Hanson, Buck, Hermes, Gerben, Huang, Rongcai, Huws, Sharon, Ikoyi, Israel, Jaeger, Alice, Jeffery, Ian, Jérôme, Marc, Juan, Pierre-Alexandre, Kenny, David, Kers, Annelies, Khinouche, Karim-Franck, Kirwan, Stuart, Klaassens, Eline S., Knobloch, Stephen, Kolbeinsson, Kristinn, Kolypczuk, Laetitia, Kostic, Tanja, Ledda, Fabio, Leech, John, Lehmann, Doerte, Leroi, Françoise, Lewis, Eva, Ley, Johanna, Lucic, Eva, Lynch, Kieran, Mace, Sabrina, MacLaren-Lee, Iain, Mahler de Sanchez, Lisa, Marchart, Juergen, Margolles, Abelardo, Marteinsson, Viggó Thór, Masetti, Giulia, McGovern, Fiona, McHugh, Noirin, McLoughlin, Steven, Meehan, Dara, Mølbak, Lars, Monin, Thomas, Moreno, Javier, Morgavi, Diego, Morrison, Steven, Müench, Steffen, Ramos Neves, Ana Rute, Neylon, Emma, Nyhan, Laura, O’Kelly, Rhona, O’Neil, Dominic, O’Toole, Paul, Ortiz-Chura, Abimael, Palma, Juan Manuel, Pasolli, Edoardo, Passerini, Delphine, Pastar, Milica, Pinto, Federica, Pirovano, Walter, Plans, Olga, Policht, Marion, Pop, Aurel, Pop, Bianca, Popova, Milka, Prieto, Miguel, Quijada, Narciso M., Reiss, Antje, Romero, Pedro, Ruas-Madiedo, Patricia, Rubino, Francesco, Rubio, Raul Cabrera, Ruiz, Lorena, Ryan, Angela, Ryan, Clodagh, Sabater, Carlos, Sahin, Aylin, Salaun, Cecile, Santos, Fernanda Godoy, Schneider, Carolin, Segata, Nicola, Selberherr, Evelyne, Sessitsch, Angela, Skírnisdóttir, Sigurlaug, Smidt, Hauke, Smith, Paul, Sprenger-Haussels, Markus, Tapio, Ilma, Tap, Julien, Valentino, Vincenzo, Wagner, Martin, Walsh, Aaron, Walsh, Liam, Waters, Sinead M., Willcocks, Spike, Yáñez-Ruiz, David R., Yan, Tianhai, Yap, Min, Zannini, Emanuele, Zuliani, Véronique, Punčochář, Michal, Mengoni, Claudia, Tatti, Alessia, Manghi, Paolo, Avagliano, Michele, Cabrera-Rubio, Raul, Coakley, Mairéad, Cobo-Díaz, José F., Dey, Hrituraj, Asnicar, Francesco, Fackelmann, Gloria, Heidrich, Vitor, and Rota Stabelli, Omar

Published
2024
Full Text
View/download PDF

3. Development of a biosensor using aptamer/antigen interactions

Author

Fordham, Daniel George and McClellan, James Alexander

Subjects
610.28, Biology
Abstract

The use of aptamers acting within novel biosensors as molecular recognition elements is well documented with a wide variety of techniques being adapted to take advantage of the benefits of oligonucleotide detection. A continuing barrier to the commercial use of ssDNA or RNA aptamers remains the lack of a high-throughput system that confers reliable selection and description of suitable species. Here we describe simple methodologies that utilise fusion proteins, modified affinity chromatography, HPLC, and, nanopore assays, along with other techniques to isolate novel aptamers to well-characterised proteins. These methods have yielded novel aptamers to the HsdR, and HsdS subunits of type I restrictionmodification system EcoR124I and to the human rhinovirus 3C protease, along with an enriched libraries for nitrotyrosine. In addition to the isolation of novel aptamer species, methods for the characterisation of the binding capabilities of candidate aptamers are presented. The techniques of SPR, EMSA, and dot blotting are evaluated and utilised in the appraisal of the novel aptamer sequences.

Published
2011

4. Embryologist agreement when assessing blastocyst implantation probability: is data-driven prediction the solution to embryo assessment subjectivity?

Author

Fordham, Daniel E, primary, Rosentraub, Dror, additional, Polsky, Avital L, additional, Aviram, Talia, additional, Wolf, Yotam, additional, Perl, Oriel, additional, Devir, Asnat, additional, Rosentraub, Shahar, additional, Silver, David H, additional, Gold Zamir, Yael, additional, Bronstein, Alex M, additional, Lara Lara, Miguel, additional, Ben Nagi, Jara, additional, Alvarez, Adrian, additional, and Munné, Santiago, additional

Published
2022
Full Text
View/download PDF

7. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author

Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., Jarvis, Erich D., Kirschel, Alexander N. G., Digby, Andrew, Veale, Andrew, Bronikowski, Anne, Murphy, Bob, Robertson, Bruce, Baker, Clare, Mazzoni, Camila, Balakrishnan, Christopher, Lee, Chul, Mead, Daniel, Teeling, Emma, Aiden, Erez Lieberman, Todd, Erica, Eichler, Evan, Naylor, Gavin J. P., Zhang, Guojie, Smith, Jeramiah, Wolf, Jochen, Touchon, Justin, Delmore, Kira, Jakobsen, Kjetill, Komoroske, Lisa, Wilkinson, Mark, Genner, Martin, Pšenička, Martin, Fuxjager, Matthew, Stratton, Mike, Liedvogel, Miriam, Gemmell, Neil, Minias, Piotr, Dunn, Peter O., Sudmant, Peter, Morin, Phil, Ayub, Qasim, Kraus, Robert, Vernes, Sonja, Smith, Steve, Lama, Tanya, Edwards, Taylor, Smith, Tim, Gilbert, Tom, Marques-Bonet, Tomas, Einfeldt, Tony, Venkatesh, Byrappa, Johnson, Warren, Warren, Wes, Bukhman, Yury, Formenti, Giulio [0000-0002-7554-5991], and Apollo - University of Cambridge Repository

Subjects
Vertebrate, Research, Assembly, Sequencing, Duplications, Long reads, Repeats, Mitochondrial DNA
Abstract

Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

Published
2021

8. Additional file 8 of Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author

Formenti, Giulio, Arang Rhie, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Woori Kwak, Korlach, Jonas, Arkarachai Fungtammasan, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., and Jarvis, Erich D.

Abstract

Additional file 8: Supplementary Note 1. Relationship between mtDNA sequencing, coverage and genome size.

Published
2021
Full Text
View/download PDF

9. Additional file 12 of Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author

Formenti, Giulio, Arang Rhie, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Woori Kwak, Korlach, Jonas, Arkarachai Fungtammasan, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., and Jarvis, Erich D.

Abstract

Additional file 12. Review history.

Published
2021
Full Text
View/download PDF

11. Syncope and undifferentiated shock

Author

Trotzky, Daniel, primary, Amer, Ali, additional, Fraij, Salha, additional, Fordham, Daniel E., additional, Granovsky, Gregory, additional, Aizik, Uri, additional, Carady, Natali, additional, Cohen, Aya, additional, Fuchs, Shmuel, additional, Mengesha, Bethlehem, additional, Burgsdorf, Oleg, additional, Yofik, Inna, additional, Naimark, Ari, additional, Baruch, Inbal, additional, Barac, Yaron D., additional, and Pachys, Gal, additional

Published
2021
Full Text
View/download PDF

12. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.

Author

Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, and Jarvis ED

Subjects
Animals, Computational Biology methods, Computational Biology standards, Evolution, Molecular, High-Throughput Nucleotide Sequencing, Gene Duplication, Genome, Mitochondrial, Genomics methods, Repetitive Sequences, Nucleic Acid, Vertebrates genetics
Abstract

Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly., Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization., Conclusions: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results