Ecosyste.ms: Papers

10.3390/microorganisms9051050

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum
Cited by: 5
Author(s): Jing Zhu, Xiang Sun, Zhidong Zhang, Qi-Yong Tang, Minghong Gu, Lijuan Zhang, Min Hou, Amir Sharon, Hongli Yuan
Software Mentions: 15
Published: over 3 years ago

10.1038/s41598-020-69772-8

SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach
Cited by: 15
Author(s): Mingyi Wang, Wen Luo, Kristine Jones, Xiaopeng Bian, Russell D. Williams, Herbert Higson, Dongjing Wu, Belynda Hicks, Meredith Yeager, Bin Zhu
Software Mentions: 9
Published: over 4 years ago

10.1002/mbo3.780

Biases in the metabarcoding of plant pathogens using rust fungi as a model system
Cited by: 13
Author(s): Andreas Makiola, Ian A. Dickie, Robert J. Holdaway, Jamie R. Wood, Kate H. Orwin, Charles K. Lee, Travis R. Glare
Software Mentions: 9
Published: almost 6 years ago

10.3390/ijms22063200

Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens
Cited by: 4
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Przemysław Kołodziej, Jolanta Szymańska, Bartosz J. Płachno, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 9
Published: over 3 years ago

10.3389/fimmu.2018.00462

Analyzing Immunoglobulin Repertoires
Cited by: 77
Author(s): Neha Chaudhary, Duane R. Wesemann
Software Mentions: 8
Published: over 6 years ago

10.1038/sdata.2019.34

Global transcriptome analysis of pig induced pluripotent stem cells derived from six and four reprogramming factors
Cited by: 11
Author(s): T. Fukuda, Keiko Doi, Kenichiro Donai, Kazumasa Takahashi, Hisato Kobayashi, Takashi Hirano, Katsuhiko Nishimori, Hiroshi Yasue
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-020-67870-1

Investigating the influence of mtDNA and nuclear encoded mitochondrial variants on high intensity interval training outcomes
Cited by: 6
Author(s): Nicholas R. Harvey, Sarah Voisin, Rodney Arthur Lea, Xu Yan, Miles C. Benton, ID Papadimitriou, Jacques Michaux, Larisa M. Haupt, Kevin J. Ashton, Nir Eynon, Lyn R. Griffiths
Software Mentions: 8
Published: over 4 years ago

10.7717/peerj.4925

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
Cited by: 166
Author(s): Jonathan M. Palmer, Michelle A. Jusino, Mark T. Banik, Daniel L. Lindner
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pgen.1009094

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: over 3 years ago

10.1186/s12868-016-0283-6

25th Annual Computational Neuroscience Meeting: CNS-2016
Cited by: 71
Author(s): Tatyana O. Sharpee, Alain Destexhe, Mitsuo Kawato, Vladislav Sekulić, Frances K. Skinner, Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári, Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Krešimir Josić, Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodríguez, Pablo Varona, Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Il Kim, James T Mckenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi, James Rankin, Pamela Osborn Popp, John Rinzel, Alejandro Tabas, André Rupp, Emili Balaguer‐Ballester, Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, M. Ibbotson, Hamish Meffin, Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer, Maria Psarrou, Maria J. Schilstra, Neil Davey, Benjamin Torben‐Nielsen, Volker Steuber, Huiwen Ju, Junsheng Yu, Michael L. Hines, Liang Chen, Yuguo Yu, Jimin Kim, Will Leahy, Eli Shlizerman, Justas Birgiolas, Richard C. Gerkin, Atthaphon Viriyopase, Raoul-Martin Memmesheimer, Stan Gielen, Yuri Dabaghian, Justin DeVito, Luca Perotti, Anmo J. Kim, Lisa M. Fenk, Cheng Cheng, Gaby Maimon, Chang Zhao, Yves F. Widmer, Simon G. Sprecher, Walter Senn, Geir Halnes, Tuomo Mäki‐Marttunen, Daniel Keller, Klas H. Pettersen, Ole A. Andreassen, Gaute T. Einevoll, Yasunori Yamada, Moira L. Steyn-Ross, D. Alistair Steyn-Ross, Jorge F. Mejías, John D. Murray, Henry Kennedy, Xiaojing Wang, Alexandra Kruscha, Jan Grewe, Jan Benda, Benjamin Lindner, Laurent Badel, Kazumi Ohta, Yoshiko Tsuchimoto, Hokto Kazama, B. Kahng, Nicoladie D. Tam, Luca Pollonini, George Zouridakis, Jaehyun Soh, DaeEun Kim, Minsu Yoo, Stéphanie Palmer, Viviana Culmone, Ingo Bojak, Andrea Ferrario, Robert Merrison-Hort, Roman Borisyuk, Chang Sub Kim, T. Tezuka, Pangyu Joo, Young-Ah Rho, Shawn D. Burton, G. Bard Ermentrout, Jaeseung Jeong, Nathaniel N. Urban, Petr Maršálek, Hoon-Hee Kim, Seok-hyun Moon, Dowon Lee, Sung-beom Lee, Ji-yong Lee, Yaroslav I. Molkov, Khaldoun C. Hamade, Wondimu Teka, William Barnett, Taegyo Kim, Sergey N. Markin, Ilya A. Rybak, Csaba Forró, Harald Dermutz, László Demkó, János Vörös, Andrey Babichev, Haiping Huang, Sergio Verduzco-Flores, Filipa Santos, Péter András, Christoph Metzner, Achim Schweikard, Bartosz Zurowski, James P. Roach, Leonard M. Sander, Michał Żochowski, Quinton M. Skilling, Nicolette Ognjanovski, Sara J. Aton, Shengjun Wang, Guang Ouyang, Jing Guang, Mingsha Zhang, K. Y. Michael Wong, Changsong Zhou, P. A. Robinson, Paula Sanz‐Leon, P.M. Drysdale, Felix Fung, Romesh Abeysuriya, Chris Rennie, Xuelong Zhao, Yoonsuck Choe, Huei-Fang Yang, Yuanyuan Mi, Xinhua Lin, Si Wu, Joscha Liedtke, Manuel Schottdorf, Fred Wolf, Yuichi Yamamura, Jeffery R. Wickens, Timothy Rumbell, Julia Ramsey, Amy Reyes, Danel Draguljić, Patrick R. Hof, Jennifer I. Luebke, Christina M. Weaver, Hu He, Yang Xu, Hailin Ma, Zhiheng Xu, Yuzhe Wang, Kwangyeol Baek, Laurel Morris, Prantik Kundu, Valerie Voon, Everton J. Agnes, Tim P. Vogels, William F Podlaski, Martin A. Giese, Pradeep Kuravi, Rufin Vogels, Alexander Seeholzer, Rajnish Ranjan, Tim P. Vogels, Joaquín J. Torres, Fabiano Baroni, Roberto Latorre, Bart Gips, Eric Lowet, Mark Roberts, Peter De Weerd, Ole Jensen, Jan van der Eerden, Abdorreza Goodarzinick, M. D. Niry, Alireza Valizadeh, Aref Pariz, Shervin S. Parsi, Julia M. Warburton, Lucia Marucci, Francesco Tamagnini, Jon Brown, Krasimira Tsaneva-Atanasova, Florence I. Kleberg, Jochen Triesch, Bahar Moezzi, Nicolangelo Iannella, Natalie Schaworonkow, Lukas Plogmacher, Mitchell R. Goldsworthy, Brenton Hordacre, Mark D. McDonnell, Michael C. Ridding, Martin Zapotocky, Daniel Šmít, Isabelle Dusart, Alain Trembleau, Sakyasingha Dasgupta, Isao Nishikawa, Kazuyuki Aihara, Taro Toyoizumi, Daniel Robb, Nick Mellen, Natalia Toporikova, Rongxiang Tang, Yi‐Yuan Tang, Guangsheng Liang, Seth Kiser, James H. Howard, Julia Goncharenko, Sergej O. Voronenko, Tosif Ahamed, Greg Stephens, Pierre Yger, Baptiste Lefebvre, Giulia Lia Beatrice Spampinato, Elric Esposito, Marcel Stimberg et Olivier Marre, Hansol Choi, Min‐Ho Song, SueYeon Chung, Dan D. Lee, Haim Sompolinsky, Ryan S. Phillips, Jeffrey C. Smith, Alexandra P. Chatzikalymniou, Katie Ferguson, N. Alex Cayco Gajic, Claudia Clopath, R. Angus Silver, Padraig Gleeson, Bóris Marin, Sadra Sadeh, Adrián Quintana, Matteo Carandini, Salvador Dura‐Bernal, William W. Lytton, Andrew Davison, Luozheng Li, Wenhao Zhang, Dahui Wang, Youngjo Song, Sol Park, Ilhwan Choi, Hee‐Sup Shin, Hannah Choi, Anitha Pasupathy, Eric Shea‐Brown, Dongsung Huh, Terrence J. Sejnowski, Simon Vogt, Arvind Kumar, Robert J. Schmidt, Stephen Van Wert, Steven J. Schiff, Richard Veale, Matthias Scheutz, Sang Wan Lee, Júlia V. Gallinaro, Stefan Rotter, Leonid L. Rubchinsky, Chung Ching Cheung, Shivakeshavan Ratnadurai‐Giridharan, Safura Rashid Shomali, Majid Nili Ahmadabadi, Hideaki Shimazaki, Seyyed Nader Rasuli, Xiaochen Zhao, Malte J. Rasch, Jens Wilting, Viola Priesemann, Anna Levina, Lucas Rudelt, Joseph T. Lizier, Richard E. Spinney, Mikail Rubinov, Michael Wibral, Ji Hyun Bak, Jonathan W. Pillow, Yuan Zaho, Il Park, J K Kang, Hae Jeong Park, Jaeson Jang, Se‐Bum Paik, Woochul Choi, Changju Lee, Min Song, Hyeonsu Lee, Youngjin Park, Ergin Yilmaz, Veli Baysal, Mahmut Özer, Daniel Saska, Thomas Nowotny, Ho Ka Chan, Alan Diamond, Christoph S. Herrmann, Micah M. Murray, Silvio Ionta, Axel Hutt, Jérémie Lefebvre, Philipp Weidel, Renato Duarte, Abigail Morrison, Jung H. Lee, Ramakrishnan Iyer, Ştefan Mihalaş, Christof Koch, Mihai A. Petrovici, Luziwei Leng, Oliver Breitwieser, David Stöckel, Ilja Bytschok, Roman Martel, Johannes Bill, Johannes Schemmel, K. Meier, Timothy B Esler, Anthony N. Burkitt, Robert R. Kerr, Bahman Tahayori, Max Nolte, Michael Reimann, Eilif Müller, Henry Markram, Antonio Parziale, Rosa Senatore, Angelo Marcelli, K. Skiker, Mounir Maouene, Samuel A. Neymotin, Alexandra H Seidenstein, Péter L. Lakatos, Terence D. Sanger, Rosemary J. Menzies, Campbell McLauchlan, Sacha J. van Albada, David J. Kedziora, Samuel A. Neymotin, Cliff C. Kerr, Benjamin A. Suter, Gordon M. Shepherd, Juhyoung Ryu, Sang-Hun Lee, Joonwon Lee, Hyang Jung Lee, Daeseob Lim, Jisung Wang, Heonsoo Lee, Nam Jung, Le Anh Quang, Seung Eun Maeng, Tae Ho Lee, Jae Woo Lee, Chang-Hyun Park, Sora Ahn, Jangsup Moon, Yun Seo Choi, Juhee Kim, Sang Beom Jun, Seungjun Lee, Hyang Woon Lee, Sumin Jo, Eunji Jun, Suin Yu, Felix Goetze, Pik‐Yin Lai, Seonghyun Kim, Jeehyun Kwag, Hyun Jae Jang, Marko Filipović, Ramón Reig, Ad Aertsen, Gilad Silberberg, Claudia Bachmann, Simone Buttler, Heidi I.L. Jacobs, Kim Dillen, Gereon R. Fink, Juraj Kukolja, Daniel Kepple, Hamza Giaffar, Dima Rinberg, Steven J. Shea, Alex Koulakov, Jyotika Bahuguna, Tom Tetzlaff, Jeanette Hellgren Kotaleski, Tim Kunze, Andre D. H. Peterson, Thomas R. Knösche, Minjung Kim, Hojeong Kim, Ji Sung Park, Ji Won Yeon, Sung-Phil Kim, Jae-Hwan Kang, Chungho Lee, Andreas Spiegler, Spase Petkoski, Matias Palva, Viktor K. Jirsa, Maria Luisa Saggio, Silvan F. Siep, William C. Stacey, Christophe Bernar, Oh-Hyeon Choung, Yong Jeong, Lee Yong-IL, Su Hyun Kim, Mir Jeong, Jeungmin Lee, Jaehyung Kwon, Jerald D. Kralik, Jaehwan Jahng, Dong‐Uk Hwang, Sang-Min Park, Seong-Kyun Kim, Hyoungkyu Kim, Pyeong Soo Kim, Sangsup Yoon, Sewoong Lim, Choongseok Park, T. Miller, Katie N Clements, Sungwoo Ahn, Eoon Hye Ji, Fadi A. Issa, Jeonghun Baek, Shigeyuki Oba, Junichiro Yoshimoto, Kenji Doya, Shin Ishii, Thiago Mosqueiro, Martin F. Strube‐Bloss, Brian E. Smith, Ramón Huerta, Michal Hadrava, Jaroslav Hlinka, Hannah Bos, Moritz Helias, Charles M. Welzig, Zachary J. Harper, Won Sup Kim, In-Seob Shin, Hyeon‐Man Baek, Seung Kee Han, René Richter, Julien Vitay, Frederick Beuth, Fred H. Hamker, Kelly Toppin, Yixin Guo, Bruce Graham, Penelope J. Kale, Leonardo L Gollo, Merav Stern, L. F. Abbott, Leonid Fedorov, Martin A. Giese, Mohammad Hovaidi Ardestani, Mohammad Javad Faraji, Kerstin Preuschoff, Wulfram Gerstner, M.J. van Gendt, Jeroen J. Briaire, Randy K. Kalkman, J.H.M. Frijns, Won Hee Lee, Sophia Frangou, Ben D. Fulcher, Patricia H. P. Tran, Alex Fornito, S. Gliske, Eugene Lim, Katherine A. Holman, Christian G. Fink, Jinseop S. Kim, Shang Mu, Kevin L. Briggman, H. Sebastian Seung, Detlef Wegener, Lisa Bohnenkamp, Udo Ernst, Anna Devor, Anders M. Dale, Glenn Terje Lines, Andy Edwards, Aslak Tveito, Espen Hagen, Johanna Senk, Markus Diesmann, Maximilian Schmidt, Rembrandt Bakker, Kelly Shen, Gleb Bezgin, Claus-Christian Hilgetag, Sacha J. van Albada, Haoqi Sun, Olga Sourina, Guang-Bin Huang, Felix Klanner, Cornelia Denk, Katharina Glomb, Adrián Ponce‐Alvarez, Matthieu Gilson, Petra Ritter, Gustavo Deco, Maria A. G. Witek, Eric Clarke, Mads Hansen, Mikkel Wallentin, Morten L. Kringelbach, Peter Vuust, Guido Klingbeil, Erik De Schutter, Wei‐Liang Chen, Yunliang Zang, Sungho Hong, Akira Takashima, Criseida Zamora, Andrew R. Gallimore, Dennis Goldschmidt, Poramate Manoonpong, Philippa J. Karoly, Dean R. Freestone, Daniel Soundry, Levin Kuhlmann, Liam Paninski, Mark Cook, Jaejin Lee, Yonatan I. Fishman, Yale E. Cohen, James A. Roberts, Luca Cocchi, Yann Sweeney, Mi Kyung Lee, Woo-Sung Jung, Youngsoo Kim, Younginha Jung, Yoon‐Kyu Song, Frédéric Chavane, Karthik Soman, Vignesh Muralidharan, V. Srinivasa Chakravarthy, Sabyasachi Shivkumar, Alekhya Mandali, Balasubramani Pragathi Priyadharsini, Hima Mehta, Catherine E. Davey, Braden A. W. Brinkman, Tyler Kekona, Fred Rieke, Michael A. Buice, Maurizio De Pittà, Hugues Berry, Nicolas Brunel, Michael Breakspear, Gary Marsat, Jordan Drew, Phillip D. Chapman, Kevin C. Daly, Samual P. Bradle, Sat Byul Seo, Jianzhong Su, Ege T. Kavalali, Justin Blackwell, LieJune Shiau, Laure Buhry, Kanishka Basnayake, Sue-Hyun Lee, Brandon A. Levy, Chris I. Baker, Timothee Leleu, Ryan T. Philips, Karishma Chhabria
Software Mentions: 7
Published: over 8 years ago

10.1038/s42003-020-01174-y

Chemically induced mutations in a MutaMouse reporter gene inform mechanisms underlying human cancer mutational signatures
Cited by: 12
Author(s): Marc A. Beal, Matthew J. Meier, Danielle P. LeBlanc, Clotilde Maurice, Jason M. O’Brien, Carole L. Yauk, Francesco Marchetti
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-019-44902-z

Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome
Cited by: 12
Author(s): Jingya Wang, Sadiye Amcaoglu Rieder, Jincheng Wu, Susana Hayes, Rebecca Halpin, Melissa de los Reyes, Yashaswi Shrestha, Roland Kolbeck, Rajiv Raja
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-017-1367-z

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
Cited by: 9
Author(s): Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0195534

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis
Cited by: 34
Author(s): Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.484

The mitochondrial genome of<i>Paragonimus westermani</i>(Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)
Cited by: 29
Author(s): Devendra Kumar Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
Software Mentions: 6
Published: over 10 years ago

10.3390/jpm9020021

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
Cited by: 6
Author(s): Marín de Evsikova C, Isaac Raplee, John H. Lockhart, G Jaimes, Evsikov Av
Software Mentions: 6
Published: over 5 years ago

10.15252/embr.202050078

The actin modulator <scp>hMENA</scp> regulates <scp>GAS</scp> 6‐ <scp>AXL</scp> axis and pro‐tumor cancer/stromal cell cooperation
Cited by: 18
Author(s): Roberta Melchionna, Sheila Spada, Francesca Di Modugno, Daniel D’Andrea, Anna Di Carlo, Mariangela Panetta, Anna Maria Mileo, Isabella Sperduti, Barbara Antoniani, Enzo Gallo, Rita T. Lawlor, Lorenzo Piemonti, Paolo Visca, Michèle Milella, Gian Luca Grazi, Francesco Facciolo, Emily Chen, Aldo Scarpa, Paola Nisticò
Software Mentions: 5
Published: about 4 years ago

10.1186/s12967-019-1879-2

Clinico-pathological associations and concomitant mutations of the RAS/RAF pathway in metastatic colorectal cancer
Cited by: 11
Author(s): Edoardo Isnaldi, Anna Garuti, Gabriella Cirmena, Stefano Scabini, Edoardo Rimini, Lorenzo Ferrando, Michela Lia, Roberto Murialdo, Lucia Tixi, Enrico Carminati, Andrea Panaro, M. Gallo, Federica Grillo, Luca Mastracci, Lazzaro Repetto, Roberto Fiocca, Emanuele Romairone, Gabriele Zoppoli, Alberto Ballestrero
Software Mentions: 5
Published: over 5 years ago

10.1186/s13148-018-0580-2

Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis
Cited by: 26
Author(s): Youdinghuan Chen, David A. Armstrong, Lucas A. Salas, Haley F. Hazlett, Amanda B. Nymon, John A. Dessaint, Daniel Aridgides, Diane Mellinger, Xiaoying Li, Brock C. Christensen, Alix Ashare
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2014.00152

Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial
Cited by: 73
Author(s): Nicolas Servant, Julien Roméjon, Pierre Gestraud, Philippe La Rosa, Georges Lucotte, Séverine Lair, Virginie Bernard, Bruno Zeitouni, Fanny Coffin, Gérôme Jules-Clément, Florent Yvon, Alban Lermine, Patrick Poullet, Stéphane Liva, Stuart Pook, Tatiana Popova, Camille Barette, François D. Prud’homme, Jean Gabriel Dick, Maud Kamal, Christophe Le Tourneau, Emmanuel Barillot, Philippe Hupé
Software Mentions: 5
Published: over 10 years ago

10.1111/1755-0998.13008

Metabarcoding a diverse arthropod mock community
Cited by: 97
Author(s): Thomas Braukmann, Natalia V. Ivanova, Sean W. J. Prosser, Vasco Elbrecht, Dirk Steinke, Sujeevan Ratnasingham, Jeremy R. de Waard, Jayme E Sones, Evgeny Zakharov, Paul D. N. Hebert
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-018-0437-0

Species classifier choice is a key consideration when analysing low-complexity food microbiome data
Cited by: 56
Author(s): Aaron M. Walsh, Fiona Crispie, Órla O’Sullivan, Laura Finnegan, Marcus J. Claesson, Paul D. Cotter
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2012.00220

RNA-Seq Assembly – Are We There Yet?
Cited by: 79
Author(s): Simon Schliesky, Udo Gowik, Andreas P.M. Weber, Andrea Bräutigam
Software Mentions: 5
Published: almost 13 years ago

10.7717/peerj.8172

Exploring profile and potential influencers of vaginal microbiome among asymptomatic pregnant Chinese women
Cited by: 10
Author(s): Yining He, Yun Huang, Zhengyin Zhang, Fei Yu, Yuejie Zheng
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-63278-z

Phylogenetic Inference of H3N2 Canine Influenza A Outbreak in Ontario, Canada in 2018
Cited by: 6
Author(s): Wanhong Xu, J. Scott Weese, Davor Ojkić, Oliver Lung, Katherine Handel, Yohannes Berhane
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0160227

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers
Cited by: 19
Author(s): Stephan Pabinger, Karina Ernst, Walter Pulverer, Rainer Kallmeyer, Ana M. Valdes, Sarah Metrustry, Denis Katic, Angelo Nuzzo, Albert Kriegner, Klemens Vierlinger, Andreas Weinhaeusel
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.7788

Method for quick DNA barcode reference library construction
Cited by: 11
Author(s): Yanlei Liu, Chao Xu, Yuzhe Sun, Xun Chen, Wenpan Dong, Xiaopan Yang, Shi–Liang Zhou
Software Mentions: 4
Published: over 3 years ago

10.1038/srep43149

The hidden perils of read mapping as a quality assessment tool in genome sequencing
Cited by: 4
Author(s): Burhan Lehri, Alan M. Seddon, Andrey V. Karlyshev
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0067744

Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers
Cited by: 53
Author(s): Xinzhong Li, Andrew J. Buckton, S. Wilkinson, Shibu John, Roddy Walsh, Tomáš Novotný, Iveta Valášková, Manu Gupta, Laurence Gamé, Paul J.R. Barton, Stuart A. Cook, James S. Ware
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0237108

Comparison of microbiota in the cloaca, colon, and magnum of layer chicken
Cited by: 10
Author(s): Seo-Jin Lee, Seongwoo Cho, Tae-Min La, Hong-Jae Lee, Joong‐Bok Lee, Seung‐Yong Park, Chang‐Seon Song, In‐Soo Choi
Software Mentions: 4
Published: over 4 years ago

10.1016/j.watres.2019.06.075

Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters
Cited by: 93
Author(s): Marcos Quintela-Baluja, Mohamed Abouelnaga, Jesús L. Romalde, Jian‐Qiang Su, Yongjie Yu, Mariano Gomez-Lopez, Barth F. Smets, Yong‐Guan Zhu, David W. Graham
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-92993-4

Whole genome sequencing of nearly isogenic WMI and WLI inbred rats identifies genes potentially involved in depression and stress reactivity
Cited by: 5
Author(s): Tristan V de Jong, Panjun Kim, Victor Guryev, Megan K. Mulligan, Robert W. Williams, Eva E. Redei, Hao Chen
Software Mentions: 4
Published: over 3 years ago

10.1186/s40246-016-0068-0

A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis
Cited by: 18
Author(s): Isaac Akogwu, Nan Wang, Chaoyang Zhang, Ping Gong
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.11724

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
Cited by: 11
Author(s): Zeeshan Ahmed, Eduard Gibert Renart, Saman Zeeshan
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0067539

Choosing a Benchtop Sequencing Machine to Characterise Helicobacter pylori Genomes
Cited by: 25
Author(s): Timothy T. Perkins, Chin Yen Tay, Fanny Thirriot, Barry J. Marshall
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0181463

DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing
Cited by: 49
Author(s): Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0121701

A Next Generation Semiconductor Based Sequencing Approach for the Identification of Meat Species in DNA Mixtures
Cited by: 58
Author(s): Francesca Bertolini, Marco Ciro Ghionda, Enrico D’Alessandro, Calogero Geraci, Vincenzo Chiofalo, Luca Fontanesi
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-14-675

Efficient and accurate whole genome assembly and methylome profiling of E. coli
Cited by: 40
Author(s): Jason Powers, Victor Weigman, Jenny Shu, John Pufky, Donald Cox, Patrick Hurban
Software Mentions: 4
Published: almost 12 years ago

10.3390/microorganisms7100393

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?
Cited by: 15
Author(s): Léa Siegwald, Ségolène Caboche, Gaël Even, Éric Viscogliosi, Christophe Audebert, Magali Chabé
Software Mentions: 4
Published: about 5 years ago

10.3389/fphys.2016.00606

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Cited by: 30
Author(s): Alejandra Contreras, Benjamin Cocom-Chan, Georgina Hernández-Montes, Tobías Portillo-Bobadilla, Osbaldo Resendis‐Antonio
Software Mentions: 4
Published: almost 8 years ago

10.1186/2042-5783-3-2

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
Cited by: 109
Author(s): D.J. Edwards, Kathryn E. Holt
Software Mentions: 4
Published: over 11 years ago

10.1111/1751-7915.12006

Tips and tricks for the assembly of aCorynebacterium pseudotuberculosisgenome using a semiconductor sequencer
Cited by: 12
Author(s): Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Siomar de Castro Soares, Anderson Santos, Síntia Almeida, Luís Carlos Guimarães, Flávia Figueira, Eudes Guilherme Vieria Barbosa, Andreas Tauch, Vasco Azevedo, Artur M. S. Silva
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pcbi.1003031

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
Cited by: 255
Author(s): Lauren M. Bragg, Graham N. Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson
Software Mentions: 4
Published: over 11 years ago

10.3390/genes11111303

Mitochondrial Sequencing of Missing Persons DNA Casework by Implementing Thermo Fisher’s Precision ID mtDNA Whole Genome Assay
Cited by: 19
Author(s): Daniela Cuenca, Jessica Battaglia, Michelle Halsing, Sandra Sheehan
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0124671

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Cited by: 158
Author(s): Dáithí C. Murray, Megan L. Coghlan, Michael Bunce
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-017-4011-0

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
Cited by: 54
Author(s): Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Young Ho Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug, Gregory R. Grant
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-34430-7

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing
Cited by: 27
Author(s): Marie-Amélie Forin-Wiart, Marie-Lazarine Poulle, Sylvain Piry, Jean‐François Cosson, Claire Larose, Maxime Galan
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.3757

Genotyping strategy matters when analyzing hypervariable major histocompatibility complex‐Experience from a passerine bird
Cited by: 15
Author(s): Silje L. Rekdal, Jarl Andreas Anmarkrud, Arild Johnsen, Jan T. Lifjeld
Software Mentions: 3
Published: almost 7 years ago

10.1093/femsle/fny069

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies
Cited by: 15
Author(s): Ainsley Beaton, Cédric Lood, Edward Cunningham-Oakes, Alison Macfadyen, Alex J. Mullins, Walid E.l. Bestawy, João Botelho, Sylvie Chevalier, Shannon R. Coleman, Chloe Dalzell, Stephen K. Dolan, Alberto Faccenda, Maarten G. K. Ghequire, Steven A. Higgins, Alexander Kutschera, Jordan Murray, Martha L. Redway, Talal Sabhan Salih, Ana C. da Silva, Brian A. Smith, Nathan Smits, R. P.M. Thomson, Stuart Daniel Woodcock, Martin Welch, Pierre Cornélis, Rob Lavigne, Vera van Noort, Nicholas P. Tucker
Software Mentions: 3
Published: over 6 years ago

10.1186/s12985-019-1223-8

Sequencing of animal viruses: quality data assurance for NGS bioinformatics
Cited by: 10
Author(s): Gianpiero Zamperin, Pierrick Lucas, Irene Cano, David Ryder, Miriam Abbadi, David M. Stone, Argelia Cuenca, Estelle Vigouroux, Yannick Blanchard, Valentina Panzarin
Software Mentions: 3
Published: about 5 years ago

10.1186/s12879-015-0902-3

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities
Cited by: 55
Author(s): Jacob Moran-Gilad, Vitali Sintchenko, Susanne Karlsmose Pedersen, William J. Wolfgang, James B. Pettengill, Errol Strain, René S. Hendriksen
Software Mentions: 3
Published: over 9 years ago

10.1007/s10549-018-4798-7

FFPE breast tumour blocks provide reliable sources of both germline and malignant DNA for investigation of genetic determinants of individual tumour responses to treatment
Cited by: 6
Author(s): Anna Wilkins, Ritika Chauhan, Alistair G. Rust, Alex Pearson, Frances Daley, Floriana Manodoro, Kerry Fenwick, Judith Bliss, John Yarnold, Navita Somaiah
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0067129

Preliminary Assessment of Microbiome Changes Following Blood-Feeding and Survivorship in the Amblyomma americanum Nymph-to-Adult Transition using Semiconductor Sequencing
Cited by: 72
Author(s): Arturo C. Menchaca, David K. Visi, Otto F. Strey, Pete D. Teel, Kevin Kalinowski, Michael S. Allen, Phillip Williamson
Software Mentions: 3
Published: over 11 years ago

10.3390/v12070782

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Cited by: 4
Author(s): Sílvia Inês Sardi, Renata Carvalho, Luis Gustavo Carvalho Pacheco, João Fernando Lourenço de Almeida, Emilia M M D A Belitardo, Carina S. Pinheiro, Gúbio Soares Campos, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0081468

Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data
Cited by: 62
Author(s): Yoji Kukita, Junji Uchida, Shigeyuki Oba, Kazumi Nishino, Toru Kumagai, Koki Taniguchi, Takako Okuyama, Fumio Imamura, Kikuya Kato
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-15-673

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
Cited by: 10
Author(s): Ikuko N. Motoike, Mitsuyo Matsumoto, Inaho Danjoh, Fumiki Katsuoka, Kazuyuki Kojima, Naoki Nariai, Yukuto Sato, Yumi Yamaguchi-Kabata, Itó S, Hisaaki Kudo, Ichiko Nishijima, Satoshi Nishikawa, Xiaoqing Pan, Rumiko Saito, Sakae Saitō, Tomo Saito, Matsuyuki Shirota, Kaoru Tsuda, Junji Yokozawa, Kazuhiko Igarashi, Naoko Minegishi, Osamu Takahashi, Nobuo Fuse, Masao Nagasaki, Kengo Kinoshita, Jun Yasuda, Masayuki Yamamoto
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0247041

16S rRNA gene sequencing of rectal swab in patients affected by COVID-19
Cited by: 32
Author(s): Antonio Mazzarelli, Maria Letizia Giancola, Anna Farina, Luisa Marchioni, Martina Rueca, Cesare Ernesto Maria Gruber, Barbara Bartolini, Tommaso Ascoli Bartoli, Gaetano Maffongelli, Maria Rosaria Capobianchi, Giuseppe Ippolito, Antonino Di, Emanuele Nicastri, Valerio Pazienza
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-13-341

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
Cited by: 1,666
Author(s): Michael A. Quail, Miriam E. Smith, Paul Coupland, Thomas D. Otto, Simon R. Harris, Thomas R. Connor, Anna Bertoni, Harold Swerdlow, Yong Gu
Software Mentions: 3
Published: almost 13 years ago

10.1128/mSphere.00833-19

Fecal Viral Community Responses to High-Fat Diet in Mice
Cited by: 28
Author(s): Anjelique Schulfer, Tasha M. Santiago-Rodríguez, Melissa Ly, Joshua M. Borin, Jessica Chopyk, Martin J. Blaser, David T. Pride
Software Mentions: 3
Published: over 4 years ago

10.1128/mSphere.00410-18

Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products
Cited by: 41
Author(s): Zhengyao Xue, Mary E. Kable, Maria L. Marco
Software Mentions: 3
Published: about 6 years ago

10.1186/s40246-019-0220-8

Next-generation sequencing in liquid biopsy: cancer screening and early detection
Cited by: 262
Author(s): M Chen, Hongyu Zhao
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0155459

Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology
Cited by: 12
Author(s): Sabiha Shaik, Narender Kumar, Aditya Kumar Lankapalli, Sumeet K. Tiwari, Ramani Baddam, Niyaz Ahmed
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-015-0840-5

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform
Cited by: 17
Author(s): Andy Kilianski, Patrick Carcel, Shijie Yao, Pierce A. Roth, Josh Schulte, Greg B. Donarum, Ed Fochler, Jessica M. Hill, Alvin T. Liem, Michael R. Wiley, Jason T. Ladner, Bradley P. Pfeffer, Oliver Elliot, Alexandra Petrosov, Dereje D. Jima, Tyghe G. Vallard, Melanie C. Melendrez, Evan W. Skowronski, Phenix‐Lan Quan, W. Ian Lipkin, Henry S. Gibbons, David L. Hirschberg, Gustavo Palacios, C. Nicole Rosenzweig
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0210356

Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome
Cited by: 27
Author(s): Víctor M. Guerrero-Sánchez, Ana M. Maldonado‐Alconada, Francisco Amil-Ruíz, Andrea Antonio Verardi, Jesús V. Jorrín‐Novo, María‐Dolores Rey
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-43336-x

A highly flexible and repeatable genotyping method for aquaculture studies based on target amplicon sequencing using next-generation sequencing technology
Cited by: 28
Author(s): Mana Sato, S. Hosoya, Sota Yoshikawa, Shun Ohki, Yuki Kobayashi, Takuya Itou, Kiyoshi Kikuchi
Software Mentions: 3
Published: over 5 years ago

10.1038/srep37563

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Cited by: 21
Author(s): Marcus Davidsson, Paula Díaz-Fernández, Oliver D. Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33773-5

Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease
Cited by: 12
Author(s): Mangesh V. Suryavanshi, Shrikant Bhute, Rahul P. Gune, Yogesh S. Shouche
Software Mentions: 3
Published: about 6 years ago

10.1038/s41597-019-0225-0

A multi-modal data resource for investigating topographic heterogeneity in patient-derived xenograft tumors
Cited by: 8
Author(s): Satwik Rajaram, Maike A. Roth, Julia Malato, Scott R. VandenBerg, Byron Hann, Chloé E. Atreya, Steven J. Altschuler, Lani F. Wu
Software Mentions: 3
Published: about 5 years ago

10.1038/srep25255

Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota
Cited by: 193
Author(s): Christophe Audebert, Gaël Even, Amandine Cian, Dima El Safadi, Gabriela Certad, Laurence Delhaès, Bruno Pereira, Céline Nourrisson, Philippe Poirier, Ivan Wawrzyniak, Frédéric Delbac, Christelle Morelle, Patrick Bastien, Laurence Lachaud, Anne‐Pauline Bellanger, Françoise Botterel, Ermanno Candolfi, Guillaume Désoubeaux, Florent Morio, Christelle Pomarès, Méja Rabodonirina, Alexandre Loywick, Sophie Merlin, Éric Viscogliosi, Magali Chabé
Software Mentions: 3
Published: over 8 years ago

10.1186/gb-2013-14-5-r51

Characterizing and measuring bias in sequence data
Cited by: 708
Author(s): Michael G. Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J. Lennon, Ryan Hegarty, Chad Nusbaum, David B. Jaffe
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12882-020-01805-w

The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature
Cited by: 49
Author(s): Jordan Stanford, Karen E Charlton, Anita Stefoska‐Needham, Rukayat Ibrahim, Kelly Lambert
Software Mentions: 3
Published: over 4 years ago

10.3390/genes11121398

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples
Cited by: 18
Author(s): Marta Diepenbroek, Birgit Bayer, Kristina Schwender, Roberta Schiller, Jessica Lim, Robert Lagacé, Katja Anslinger
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-020-03726-9

IonCRAM: a reference-based compression tool for ion torrent sequence files
Cited by: 2
Author(s): Moustafa Shokrof, Mohamed Abouelhoda
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0107534

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity
Cited by: 22
Author(s): Masanori Fujimoto, Gregory A Moyerbrailean, Sifat Noman, Jason P. Gizicki, Michal L. Ram, Phyllis A. Green, Jeffrey L. Ram
Software Mentions: 3
Published: about 10 years ago

10.1590/1678-4685-GMB-2018-0351

A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines
Cited by: 1
Author(s): Gabriela P. Branco, Renan Valieris, Lucas Venezian Povoa, Luíza Ferreira de Araújo, Gustavo Ribeiro Fernandes, Jorge Estefano Santana de Souza, María Galli de Amorim, Elisa Napolitano Ferreira, Israel Tojal da Silva, Diana Noronha Nunes, Emmanuel Dias-Neto
Software Mentions: 3
Published: almost 5 years ago

10.1111/jam.13590

16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria
Cited by: 41
Author(s): George S. Watts, Ken Youens‐Clark, Marvin J. Slepian, Donna M. Wolk, Marc M. Oshiro, Gregory S. Metzger, Dalia Dhingra, Lee D. Cranmer, Bonnie Hurwitz
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2016.01407

Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge
Cited by: 106
Author(s): Jayeeta Sarkar, Sufia K. Kazy, Abhishek Gupta, Avishek Dutta, Balaram Mohapatra, Ajoy Roy, Paramita Bera, Adinpunya Mitra, Pinaki Sar
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.201

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing
Cited by: 173
Author(s): Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M. Nair, Maksym Kremenskoy, Baby Joseph, Igor V. Kurochkin
Software Mentions: 3
Published: about 11 years ago

10.7717/peerj.9085

Fast sequence-based microsatellite genotyping development workflow
Cited by: 24
Author(s): Olivier Lepais, Émilie Chancerel, Christophe Boury, Franck Salin, Aurélie Manicki, Laura Taillebois, Cyril Dutech, Abdeldjalil Aissi, Cecile F. E. Bacles, Françoise Daverat, Sophie Launey, Erwan Guichoux
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2016.01781

The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges
Cited by: 18
Author(s): Jon Thomassen Hestetun, Helge K. Dahle, Steffen Leth Jørgensen, Bernt Rydland Olsen, Hans Tore Rapp
Software Mentions: 3
Published: about 8 years ago

10.1038/sdata.2017.81

Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization
Cited by: 8
Author(s): Léa Siegwald, Christophe Audebert, Gaël Even, Éric Viscogliosi, Ségolène Caboche, Magali Chabé
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.18910

Integrated analysis of the molecular action of Vorinostat identifies epi-sensitised targets for combination therapy
Cited by: 3
Author(s): Jodie Hay, Katrina M. Lappin, Fabio G. Liberante, Laura M. Kettyle, Kyle B. Matchett, Alexander Thompson, Ken Mills
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2020.544162

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance
Cited by: 37
Author(s): Aquillah M. Kanzi, James Emmanuel San, Benjamin Chimukangara, Eduan Wilkinson, Maryam Fish, Veron Ramsuran, Túlio de Oliveira
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2019.01226

Rapid Multiplex Genotyping of 20 HLA-A*02:01 Restricted Minor Histocompatibility Antigens
Cited by: 6
Author(s): Dmitrii Romaniuk, Anna Postovskaya, Alexandra Khmelevskaya, Dmitry B. Malko, Grigory A. Efimov
Software Mentions: 2
Published: over 5 years ago

10.3390/life10100228

The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers
Cited by: 21
Author(s): Soyeon Kim, Joo Won Lee, Young‐Seok Park
Software Mentions: 2
Published: about 4 years ago

10.3389/fcimb.2020.527102

The Most Frequently Used Sequencing Technologies and Assembly Methods in Different Time Segments of the Bacterial Surveillance and RefSeq Genome Databases
Cited by: 25
Author(s): Bo Segerman
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2018.03185

TCR Repertoire Analysis Reveals Mobilization of Novel CD8+ T Cell Clones Into the Cancer-Immunity Cycle Following Anti-CD4 Antibody Administration
Cited by: 20
Author(s): Hatsuo Aoki, Satoshi Ueha, Shigeyuki Shichino, Haru Ogiwara, Shin Ichi Hashimoto, Kazuhiro Kakimi, Satoru Ito, Kouji Matsushima
Software Mentions: 2
Published: almost 6 years ago

10.3390/life11040340

Cross-Validation of Next-Generation Sequencing Technologies for Diagnosis of Chromosomal Mosaicism and Segmental Aneuploidies in Preimplantation Embryos Model
Cited by: 6
Author(s): Anıl Biricik, Ettore Cotroneo, Maria Giulia Minasi, Pierfrancesco Greco, Sara Bono, Matteo Surdo, Federica Lecciso, Mariateresa Sessa, Francesco Fiorentino, Francesca Spinella, Ermanno Greco
Software Mentions: 2
Published: over 3 years ago

10.15252/embr.201949248

Small‐molecule inhibition of aging‐associated chromosomal instability delays cellular senescence
Cited by: 24
Author(s): Monika Barroso-Vilares, Joana Catarina Macedo, Mário Reis, Jessica D Warren, Duane A. Compton, Elsa Logarinho
Software Mentions: 2
Published: over 4 years ago

10.3389/fcimb.2021.555072

Microbiota Detection Patterns Correlate With Presence and Severity of Barrett’s Esophagus
Cited by: 4
Author(s): Ikenna Okereke, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Clark R. Andersen, Richard B. Pyles
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-S5-S7

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
Cited by: 16
Author(s): Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Ion Măndoiu, Alexander Zelikovsky
Software Mentions: 2
Published: over 10 years ago

10.3390/cells8080902

Deep Sequencing Reveals Central Nervous System Compartmentalization in Multiple Transmitted/Founder Virus Acute HIV-1 Infection
Cited by: 15
Author(s): Sodsai Tovanabutra, Rujipas Sirijatuphat, Phuc Pham, Lydia Bonar, Elizabeth A. Harbolick, Meera Bose, Hongshuo Song, David C. Chang, Celina Oropeza, Anne Marie O’Sullivan, Joyce Balinang, Eugène Kroon, Donn Colby, Carlo Sacdalan, Joanna Hellmuth, Phillip Chan, Peeriya Prueksakaew, Suteeraporn Pinyakorn, Linda L. Jagodzinski, Duanghathai Sutthichom, Suwanna Pattamaswin, Mark de Souza, Robert A. Gramzinski, Jerome H. Kim, Nelson L. Michael, Merlin L. Robb, Nittaya Phanuphak, Jintanat Ananworanich, Victor Valcour, Gustavo H. Kijak, Eric Sanders‐Buell, Serena Spudich, Mhrp Viral Sequencing Core, Search Study Team
Software Mentions: 2
Published: over 5 years ago

10.1016/j.dib.2017.11.049

Complete genome sequence of native Bacillus cereus strains isolated from intestinal tract of the crab Ucides sp.
Cited by: 8
Author(s): João Costa Filho, Sérgio Jorge, Frederico Schmitt Kremer, Natasha Rodrigues de Oliveira, Vinícius Farias Campos, Luciano da Silva Pinto, Odir A. Dellagostin, Rubens Galdino Feijó, Francisca Gleire Rodrigues de Menezes, Oscarina Viana de Sousa, Rodrigo Maggioni, Luís Fernando Marins
Software Mentions: 2
Published: almost 7 years ago

10.3390/biomedicines9020142

Novel Ex Vivo Model to Examine the Mechanism and Relationship of Esophageal Microbiota and Disease
Cited by: 4
Author(s): Samuel Cass, Catherine Hamilton, Aaron L. Miller, Daniel C. Jupiter, Kamil Khanipov, Adam L. Booth, Richard B. Pyles, Timothy Krill, Gabriel Reep, Ikenna Okereke
Software Mentions: 2
Published: almost 4 years ago

10.3390/cancers11070998

BRAF Mutation Status in Circulating Tumor DNA from Patients with Metastatic Colorectal Cancer: Extended Mutation Analysis from the AGEO RASANC Study
Cited by: 19
Author(s): Léo Mas, Jean‐Baptiste Bachet, Valérie Taly, Olivier Bouché, Julien Taieb, Romain Cohen, Aurélia Meurisse, Claudine Normand, Jean–Marc Gornet, Pascal Artru, Samy Louafi, Anne Thirot-Bidault, Isabelle Baumgaertner, Romain Coriat, David Tougeron, Thierry Lecomte, Florence Mary, Thomas Aparicio, Lysiane Marthey, Hélène Blons, Déwi Vernerey, Pierre Laurent‐Puig
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12092490

Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer
Cited by: 25
Author(s): Tania Rossi, Giulia Gallerani, Davide Angeli, Claudia Cocchi, Erika Bandini, Pietro Fici, Michele Gaudio, Giovanni Martinelli, Andrea Rocca, Roberta Maltoni, Francesco Fabbri
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0051263

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes
Cited by: 14
Author(s): Agnès Dettaı̈, Cyril Gallut, Sophie Brouillet, Joël Pothier, Guillaume Lecointre, Régis Debruyne
Software Mentions: 2
Published: almost 12 years ago

10.3390/cancers10040088

Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients
Cited by: 12
Author(s): Simon Heeke, Paul Hofman, Élodie Long-Mira, Virginie Lespinet, Salomé Lalvée, Olivier Bordone, Camille Ribeyre, Virginie Tanga, Jonathan Benzaquen, Sylvie Leroy, Charlotte Cohen, Jérôme Mouroux, Charles Hugo Marquette
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers11121895

Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma
Cited by: 16
Author(s): H Winter, Pamela J. Kaisaki, Joe Harvey, Edoardo Giacopuzzi, Matteo P. Ferla, Melissa M Pentony, Samantha J. L. Knight, Ricky A. Sharma, Jenny C. Taylor, James McCullagh
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13000-020-01011-0

The decisive role of molecular pathology in presumed somatic metastases of type II testicular germ cell tumors: report of 2 cases
Cited by: 3
Author(s): Mariëtte E.G. Kranendonk, Wenzel M. Hackeng, G. Johan A. Offerhaus, Folkert H.M. Morsink, G. N. Jonges, Gerard Groenewegen, Pieter-Jaap Krijtenburg, Heinz‐Josef Klümpen, Wendy W.J. de Leng, Leendert Looijenga, Lodewijk A.A. Brosens
Software Mentions: 2
Published: over 4 years ago