Root anatomy and soil resource capture

by Lynch, Jonathan P., Strock, Christopher F., Schneider, Hannah M., Sidhu, Jagdeep Singh, Ajmera, Ishan, Galindo-Castañeda, Tania, Klein, Stephanie P., Hanlon, Meredith T.
Published in Plant and soil

A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

by Bhosale, Rahul, Giri, Jitender, Pandey, Bipin K, Giehl, Ricardo F H, Hartmann, Anja, Traini, Richard, Truskina, Jekaterina, Leftley, Nicola, Hanlon, Meredith, Swarup, Kamal, Rashed, Afaf, Voß, Ute, Alonso, Jose, Stepanova, Anna, Yun, Jeonga, Ljung, Karin, Brown, Kathleen M, Lynch, Jonathan P, Dolan, Liam, Vernoux, Teva, Bishopp, Anthony, Wells, Darren, von Wirén, Nicolaus, Bennett, Malcolm J, Swarup, Ranjan
Published in Nature communications

Genetic Variability in Phosphorus Responses of Rice Root Phenotypes

by Vejchasarn, Phanchita, Lynch, Jonathan P., Brown, Kathleen M.
Published in Rice (New York, N.Y.)

Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

by Bhosale, Rahul, Giri, Jitender, Pandey, Bipin K, Giehl, Ricardo F H, Hartmann, Anja, Traini, Richard, Truskina, Jekaterina, Leftley, Nicola, Hanlon, Meredith, Swarup, Kamal, Rashed, Afaf, Voß, Ute, Alonso, Jose, Stepanova, Anna, Yun, Jeonga, Ljung, Karin, Brown, Kathleen M, Lynch, Jonathan P, Dolan, Liam, Vernoux, Teva, Bishopp, Anthony, Wells, Darren, von Wirén, Nicolaus, Bennett, Malcolm J, Swarup, Ranjan
Published in Nature communications

Spatiotemporal responses of rice root architecture and anatomy to drought

by Fonta, Jenna E., Giri, Jitender, Vejchasarn, Phanchita, Lynch, Jonathan P., Brown, Kathleen M.
Published in Plant and soil

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics

by Das, Abhiram, Schneider, Hannah, Burridge, James, Ascanio, Ana Karine Martinez, Wojciechowski, Tobias, Topp, Christopher N, Lynch, Jonathan P, Weitz, Joshua S, Bucksch, Alexander
Published in Plant methods

Correction to: Root anatomy and soil resource capture

by Lynch, Jonathan P., Strock, Christopher F., Schneider, Hannah M., Sidhu, Jagdeep Singh, Ajmera, Ishan, Galindo-Castaneda, Tania, Klein, Stephanie P., Hanlon, Meredith T.
Published in Plant and soil

Shovelomics root traits assessed on the EURoot maize panel are highly heritable across environments but show low genotype-by-nitrogen interaction

by Le Marié, Chantal A., York, Larry M., Strigens, Alexandre, Malosetti, Marcos, Camp, Karl-Heinz, Giuliani, Silvia, Lynch, Jonathan P., Hund, Andreas
Published in Euphytica

Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

by McFarland, Bridget A, AlKhalifah, Naser, Bohn, Martin, Bubert, Jessica, Buckler, Edward S, Ciampitti, Ignacio, Edwards, Jode, Ertl, David, Gage, Joseph L, Falcon, Celeste M, Flint-Garcia, Sherry, Gore, Michael A, Graham, Christopher, Hirsch, Candice N, Holland, James B, Hood, Elizabeth, Hooker, David, Jarquin, Diego, Kaeppler, Shawn M, Knoll, Joseph, Kruger, Greg, Lauter, Nick, Lee, Elizabeth C, Lima, Dayane C, Lorenz, Aaron, Lynch, Jonathan P, McKay, John, Miller, Nathan D, Moose, Stephen P, Murray, Seth C, Nelson, Rebecca, Poudyal, Christina, Rocheford, Torbert, Rodriguez, Oscar, Romay, Maria Cinta, Schnable, James C, Schnable, Patrick S, Scully, Brian, Sekhon, Rajandeep, Silverstein, Kevin, Singh, Maninder, Smith, Margaret, Spalding, Edgar P, Springer, Nathan, Thelen, Kurt, Thomison, Peter, Tuinstra, Mitchell, Wallace, Jason, Walls, Ramona, Wills, David, Wisser, Randall J, Xu, Wenwei, Yeh, Cheng-Ting, de Leon, Natalia
Published in BMC research notes

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

by AlKhalifah, Naser, Campbell, Darwin A, Falcon, Celeste M, Gardiner, Jack M, Miller, Nathan D, Romay, Maria Cinta, Walls, Ramona, Walton, Renee, Yeh, Cheng-Ting, Bohn, Martin, Bubert, Jessica, Buckler, Edward S, Ciampitti, Ignacio, Flint-Garcia, Sherry, Gore, Michael A, Graham, Christopher, Hirsch, Candice, Holland, James B, Hooker, David, Kaeppler, Shawn, Knoll, Joseph, Lauter, Nick, Lee, Elizabeth C, Lorenz, Aaron, Lynch, Jonathan P, Moose, Stephen P, Murray, Seth C, Nelson, Rebecca, Rocheford, Torbert, Rodriguez, Oscar, Schnable, James C, Scully, Brian, Smith, Margaret, Springer, Nathan, Thomison, Peter, Tuinstra, Mitchell, Wisser, Randall J, Xu, Wenwei, Ertl, David, Schnable, Patrick S, De Leon, Natalia, Spalding, Edgar P, Edwards, Jode, Lawrence-Dill, Carolyn J
Published in BMC research notes

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis

by Smith, Byron J, Piceno, Yvette, Zydek, Martin, Zhang, Bing, Syriani, Lara Aboud, Terdiman, Jonathan P, Kassam, Zain, Ma, Averil, Lynch, Susan V, Pollard, Katherine S, El-Nachef, Najwa
Published in Scientific reports

Mutational signatures of ionizing radiation in second malignancies

by Behjati, Sam, Gundem, Gunes, Wedge, David C, Roberts, Nicola D, Tarpey, Patrick S, Cooke, Susanna L, Van Loo, Peter, Alexandrov, Ludmil B, Ramakrishna, Manasa, Davies, Helen, Nik-Zainal, Serena, Hardy, Claire, Latimer, Calli, Raine, Keiran M, Stebbings, Lucy, Menzies, Andy, Jones, David, Shepherd, Rebecca, Butler, Adam P, Teague, Jon W, Jorgensen, Mette, Khatri, Bhavisha, Pillay, Nischalan, Shlien, Adam, Futreal, P Andrew, Badie, Christophe, McDermott, Ultan, Bova, G Steven, Richardson, Andrea L, Flanagan, Adrienne M, Stratton, Michael R, Campbell, Peter J
Published in Nature communications

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

by Alioto, Tyler S, Buchhalter, Ivo, Derdak, Sophia, Hutter, Barbara, Eldridge, Matthew D, Hovig, Eivind, Heisler, Lawrence E, Beck, Timothy A, Simpson, Jared T, Tonon, Laurie, Sertier, Anne-Sophie, Patch, Ann-Marie, Jäger, Natalie, Ginsbach, Philip, Drews, Ruben, Paramasivam, Nagarajan, Kabbe, Rolf, Chotewutmontri, Sasithorn, Diessl, Nicolle, Previti, Christopher, Schmidt, Sabine, Brors, Benedikt, Feuerbach, Lars, Heinold, Michael, Gröbner, Susanne, Korshunov, Andrey, Tarpey, Patrick S, Butler, Adam P, Hinton, Jonathan, Jones, David, Menzies, Andrew, Raine, Keiran, Shepherd, Rebecca, Stebbings, Lucy, Teague, Jon W, Ribeca, Paolo, Giner, Francesc Castro, Beltran, Sergi, Raineri, Emanuele, Dabad, Marc, Heath, Simon C, Gut, Marta, Denroche, Robert E, Harding, Nicholas J, Yamaguchi, Takafumi N, Fujimoto, Akihiro, Nakagawa, Hidewaki, Quesada, Víctor, Valdés-Mas, Rafael, Nakken, Sigve, Vodák, Daniel, Bower, Lawrence, Lynch, Andrew G, Anderson, Charlotte L, Waddell, Nicola, Pearson, John V, Grimmond, Sean M, Peto, Myron, Spellman, Paul, He, Minghui, Kandoth, Cyriac, Lee, Semin, Zhang, John, Létourneau, Louis, Ma, Singer, Seth, Sahil, Torrents, David, Xi, Liu, Wheeler, David A, López-Otín, Carlos, Campo, Elías, Campbell, Peter J, Boutros, Paul C, Puente, Xose S, Gerhard, Daniela S, Pfister, Stefan M, McPherson, John D, Hudson, Thomas J, Schlesner, Matthias, Lichter, Peter, Eils, Roland, Jones, David T W, Gut, Ivo G
Published in Nature communications

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

by Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Getz, Gad, Morris, Quaid D, Stein, Lincoln D
Published in Nature communications

Integrative pathway enrichment analysis of multivariate omics data

by Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Reimand, Jüri
Published in Nature communications

Divergent mutational processes distinguish hypoxic and normoxic tumours

by Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C
Published in Nature communications

Sex differences in oncogenic mutational processes

by Li, Constance H, Prokopec, Stephenie D, Sun, Ren X, Yousif, Fouad, Schmitz, Nathaniel, Boutros, Paul C
Published in Nature communications

Genomic footprints of activated telomere maintenance mechanisms in cancer

by Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Brors, Benedikt, Rippe, Karsten, Jones, David T W, Feuerbach, Lars
Published in Nature communications

Pathway and network analysis of more than 2500 whole cancer genomes

by Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven P C, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose M G, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Reimand, Jüri, Stuart, Joshua M, Raphael, Benjamin J
Published in Nature communications

The clinical features of the overlap between COPD and asthma

by Hardin, Megan, Silverman, Edwin K, Barr, R Graham, Hansel, Nadia N, Schroeder, Joyce D, Make, Barry J, Crapo, James D, Hersh, Craig P
Published in Respiratory research