pypi: bwa | Projects | Ecosyste.ms: Papers

10.1186/s13073-015-0160-4

Whole genome prediction for preimplantation genetic diagnosis
Cited by: 25
Author(s): Akash Kumar, Allison Ryan, Jacob O. Kitzman, Nina Wemmer, Matthew W. Snyder, Styrmir Sigurjonsson, Choli Lee, Milena Banjevic, P.W. Zarutskie, Alexandra P. Lewis, Jay Shendure, Matthew Rabinowitz
Software Mentions: 1
Published: over 9 years ago

10.1186/s13073-015-0207-6

ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
Cited by: 6
Author(s): Jinlan Wang, Jun Liao, Jinglan Zhang, Wei‐Yi Cheng, Jörg Hakenberg, Meng Ma, Bryn D. Webb, Rajasekar Ramasamudram-chakravarthi, Lisa Karger, Lakshmi Mehta, Ruth Kornreich, George A. Diaz, Shuyu Li, Lisa Edelmann, Rong Chen
Software Mentions: 1
Published: over 9 years ago

10.1186/s13073-018-0514-9

Detection and analysis of methicillin-resistant human-adapted sequence type 398 allows insight into community-associated methicillin-resistant Staphylococcus aureus evolution
Cited by: 37
Author(s): Lei He, Hou-Feng Zheng, Yanan Wang, Katherine Y. Le, Qian Liu, Jun Shang, Yingxin Dai, Hongping Meng, Xing Wang, Tianming Li, Qianqian Gao, Juanxiu Qin, Huiying Lü, Michael Otto, Min Li
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13073-018-0523-8

Genetic risk for Alzheimer’s disease is concentrated in specific macrophage and microglial transcriptional networks
Cited by: 80
Author(s): Katherine E. Tansey, Darren Cameron, Matthew Hill
Software Mentions: 1
Published: over 6 years ago

10.1186/s13073-018-0541-6

Enabling multiplexed testing of pooled donor cells through whole-genome sequencing
Cited by: 10
Author(s): Yingleong Chan, Ying Chan, Daniel B. Goodman, Xiaoge Guo, Alejandro Chavez, Elaine T. Lim, George M. Church
Software Mentions: 1
Published: over 6 years ago

10.1186/s13073-021-00883-1

Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer
Cited by: 33
Author(s): Akihiro Fujimoto, Jing Hao Wong, Yukiko Yoshii, Shintaro Akiyama, Azusa Tanaka, Hitomi Yagi, Daichi Shigemizu, Hidewaki Nakagawa, Masashi Mizokami, Mihoko Shimada
Software Mentions: 1
Published: over 3 years ago

10.1186/2047-217X-3-12

Low coverage sequencing of two Asian elephant (Elephas maximus) genomes
Cited by: 11
Author(s): Akbar Dastjerdi, Christelle Robert, Michael Watson
Software Mentions: 1
Published: over 10 years ago

10.1186/s13742-015-0101-6

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
Cited by: 64
Author(s): Judith Risse, Marian Thomson, Sheila Patrick, Garry W. Blakely, Georgios Koutsovoulos, Mark Blaxter, Michael Watson
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41438-020-0288-2

The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant
Cited by: 52
Author(s): Jie-Dan Chen, Chao Zheng, Jianqiang Ma, Chenkai Jiang, Sezai Erċışlı, Ming-Zhe Yao, Liang Chen
Software Mentions: 1
Published: over 4 years ago

10.1093/jacamr/dlab079

Selective digestive decontamination with oral colistin plus gentamicin for persistent bacteraemia caused by non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae in a neutropenic patient
Cited by: 2
Author(s): María Spencer-Sandino, Roberto Riquelme-Neira, William C Shropshire, An Q Dinh, Gerardo González-Rocha, Paulina González-Muñoz, Alejandra Vera-Leiva, Rafael Araos, Blake Hanson, César A. Arias, José M. Munita
Software Mentions: 1
Published: over 3 years ago

10.1128/JB.00578-20

Clostridium perfringens Produces an Adhesive Pilus Required for the Pathogenesis of Necrotic Enteritis in Poultry
Cited by: 16
Author(s): Dion Lepp, Yuanyuan Zhou, Shivani Ojha, Iman Mehdizadeh Gohari, Jason Carere, Chengbo Yang, John F. Prescott, Joshua Gong
Software Mentions: 1
Published: over 3 years ago

10.1074/jbc.M117.806000

CDK9 and SPT5 proteins are specifically required for expression of herpes simplex virus 1 replication-dependent late genes
Cited by: 9
Author(s): Zhiyuan Zhao, Ka‐Wei Tang, Isabella Muylaert, Tore Samuelsson, Per Elias
Software Mentions: 1
Published: about 7 years ago

10.1111/jcmm.14608

Identification of predictive genetic signatures of Cytarabine responsiveness using a 3D acute myeloid leukaemia model
Cited by: 2
Author(s): Hongwei Xu, Eric S. Muise, Sarah Javaid, Lan Chen, Răzvan Cristescu, My Sam Mansueto, Nicole E. Follmer, Jennifer Cho, Kimberley Kerr, Rachel A. Altura, Michelle R. Machacek, Benjamin Nicholson, George H. Addona, Ilona Kariv, Hongmin Chen
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.ppat.1004002

Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range
Cited by: 51
Author(s): Greg Brennan, Jacob O. Kitzman, Stefan Rothenburg, Jay Shendure, Adam P. Geballe
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.ppat.1008699

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018
Cited by: 33
Author(s): Sarah C. Hill, Renato de Souza, Julien Thézé, Ingra Morales Claro, Renato Santana Aguiar, Leandro Abade, Fabiana Cristina Pereira dos Santos, Mariana Sequetin Cunha, Juliana Silva Nogueira, Flavia Cristina Salles, Iray Maria Rocco, Adriana Yurika Maeda, Fernanda Gisele Silva Vasami, Louis du Plessis, Paola Paz Silveira, Jaqueline Góes de Jesus, Joshua Quick, Natália Coelho Couto de Azevedo Fernandes, Juliana Mariotti Guerra, Rodrigo Albergaria Réssio, Marta Giovanetti, Luiz Carlos Júnior Alcântara, Cinthya dos Santos Cirqueira, Josué Díaz‐Delgado, Fernando Luiz Lima Macedo, María do Carmo Sampaio Tavares Timenetsky, R. de Paula, Roberta Maria Fernandes Spínola, Juliana Telles de Deus, Luís Filipe Mucci, Rosa Maria Tubaki, Regiane Maria Tironi de Menezes, Patricia Ramos, André Luiz de Abreu, Laura N. Cruz, Nicholas J. Loman, Simon Dellicour, Oliver G. Pybus, Éster Cerdeira Sabino, Nuno Rodrigues Faria
Software Mentions: 1
Published: over 4 years ago

10.1073/pnas.1821543116

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient
Cited by: 65
Author(s): David B. Lowry, John T. Lovell, Li Zhang, Jason Bonnette, Philip A. Fay, Robert B. Mitchell, John Lloyd-Reilley, Arvid Boe, Yanqi Wu, F. M. Rouquette, R. L. Wynia, Xiaoyu Weng, Kathrine D. Behrman, Adam Healey, Kerrie Barry, Anna Lipzen, Diane Bauer, Aarti Sharma, Jerry Jenkins, Jeremy Schmutz, Felix B. Fritschi, Thomas E. Juenger
Software Mentions: 1
Published: over 5 years ago

10.1007/s13238-016-0260-y

Transcriptome analyses of insect cells to facilitate baculovirus-insect expression
Cited by: 12
Author(s): Kai Yu, Yanchong Yu, Xiaoyan Tang, Huimin Chen, Junyu Xiao, Xiaodong Su
Software Mentions: 1
Published: over 8 years ago

10.1186/s12977-019-0468-z

Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids
Cited by: 9
Author(s): Julia V. Halo, Amanda L. Pendleton, Abigail S. Jarosz, Robert J. Gifford, Malika L. Day, Jeffrey M. Kidd
Software Mentions: 1
Published: over 5 years ago

10.1038/srep14484

Uncovering the sources of DNA found on the Turin Shroud
Cited by: 5
Author(s): Gianni Barcaccia, Giulio Galla, Alessandro Achilli, Anna Olivieri, Antonio Torroni
Software Mentions: 1
Published: about 9 years ago

10.1038/srep18058

Co-dispersal of the blood fluke Schistosoma japonicum and Homo sapiens in the Neolithic Age
Cited by: 17
Author(s): Mingbo Yin, Hou-Feng Zheng, Jing Su, Zijian Feng, Donald P. McManus, Xiao‐Nong Zhou, Li Jin, Wei Hu
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep22850

Human malignant mesothelioma is recapitulated in immunocompetent BALB/c mice injected with murine AB cells
Cited by: 31
Author(s): Rosanna Mezzapelle, Eltjona Rrapaj, Elena Gatti, Chiara Ceriotti, Francesco De Marchis, Alessandro Preti, Antonello E. Spinelli, Laura Perani, Massimo Venturini, Silvia Valtorta, Rosa María Moresco, Lorenza Pecciarini, Claudio Doglioni, Michela Frenquelli, Luca Crippa, Camilla Recordati, Eugenio Scanziani, Hilda de Vries, Anton Berns, Roberta Frapolli, Renzo Boldorini, Maurizio D’Incalci, Marco E. Bianchi, Massimo P. Crippa
Software Mentions: 1
Published: over 8 years ago

10.1038/srep34955

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts
Cited by: 48
Author(s): Amanda M. V. Brown, Sulochana K. Wasala, Dana K. Howe, Amy B. Peetz, Inga A. Zasada, Dee R. Denver
Software Mentions: 1
Published: about 8 years ago

10.1038/srep40873

Transcriptional profiling of olfactory system development identifies distal antenna as a regulator of subset of neuronal fates
Cited by: 10
Author(s): Scott Barish, Qingyun Li, Jia-Wern Pan, Charlie Soeder, Corbin D. Jones, Pelin Volkan
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep42222

Genotoxic Effects of Culture Media on Human Pluripotent Stem Cells
Cited by: 13
Author(s): Megha Prakash Bangalore, Syama Adhikarla, Odity Mukherjee, Mitradas M. Panicker
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-00636-4

TRPV1 temperature activation is specifically sensitive to strong decreases in amino acid hydrophobicity
Cited by: 20
Author(s): Jason O. Sosa-Pagán, Edwin S. Iversen, Jörg Grandl
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-08476-y

Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
Cited by: 11
Author(s): Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zhu Zhang, Yaping Wang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-15076-3

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
Cited by: 23
Author(s): Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A. Aaltonen, Liisa Kauppi, Kimmo Palin
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-20069-x

Long range haplotyping of paired-homologous chromosomes by single-chromosome sequencing of a single cell
Cited by: 0
Author(s): Dong Luo, Meng Zhang, Ting Liu, Wei Cao, Jiajie Guo, Caiping Mao, Yifan Li, Juanmei Wang, Weiren Huang, Daru Lu, Shuo Zhang, Zhoufang Li, Jiankui He
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-27933-w

Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant-sucking insects in agricultural and forest landscapes
Cited by: 26
Author(s): Valerio Joe Utzeri, Giuseppina Schiavo, Anisa Ribani, Silvia Tinarelli, Francesca Bertolini, Samuele Bovo
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-30918-4

A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses
Cited by: 45
Author(s): Léa François, Marion Verdenaud, Xiaopeng Fu, Darcy Ruleman, Annick Dubois, Michiel Vandenbussche, Abdelhafid Bendahmane, Olivier Raymond, Jérémy Just, Mohammed Bendahmane
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-32645-2

Urine-derived cells provide a readily accessible cell type for feeder-free mRNA reprogramming
Cited by: 31
Author(s): Anne Gaignerie, Nathalie Lefort, Morgane Rousselle, V Forest-Choquet, Léa Flippe, Valentin François-Campion, Aurore Girardeau, Amandine Caillaud, Caroline Chariau, Quentin Francheteau, Aude Derevier, Franck Chaubron, Sebastian Knöbel, Nathalie Gaborit, Karim Si‐Tayeb, Laurent David
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-32992-0

Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes
Cited by: 10
Author(s): Marco Severgnini, Barbara Lazzari, Emanuele Capra, S. Chessa, M. Luini, Roberta Bordoni, Bianca Castiglioni, M. Ricchi, Paola Cremonesi
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-35050-x

Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically–relevant faecal environment, with implications for pathogenicity
Cited by: 7
Author(s): Nigel G. Ternan, Nicola Diana Moore, Deborah J. Smyth, Gordon J. McDougall, J. William Allwood, Susan R. Verrall, Chris Gill, James Dooley, Geoffrey McMullan
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-40918-7

Genome analysis identifies the mutant genes for common industrial Silverblue and Hedlund white coat colours in American mink
Cited by: 17
Author(s): Andrey D. Manakhov, Tatiana Andreeva, О. В. Трапезов, Nikolay А. Kolchanov, Evgeny I. Rogaev
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-40660-0

DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro
Cited by: 171
Author(s): Marcha Verheijen, Matthias Lienhard, Yannick Schrooders, Olivia Clayton, Ramona Nudischer, Stefan Boerno, Bernd Timmermann, Nathalie Selevsek, Ralph Schlapbach, Hans Gmuender, Stefano Gotta, J. P. M. Geraedts, Ralf Herwig, Jos Kleinjans, Florian Caiment
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-48681-5

HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus
Cited by: 28
Author(s): Saori C. Iwase, Paola Miyazato, Hiroo Katsuya, Saiful Islam, Benjy J.Y. Tan, Jumpei Ito, Misaki Matsuo, Hiroaki Takeuchi, Takeshi Ishida, Kouki Matsuda, Kenji Maeda, Yorifumi Satou
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-49706-9

The reduction of miR146b-5p in monocytes and T cells could contribute to the immunopathogenesis of hepatitis C virus infection
Cited by: 4
Author(s): Yasuteru Kondo, Takayuki Kogure, Masashi Ninomiya, Ryo Fukuda, Norikazu Monma, Kazuho Ikeo, Yasuhito Tanaka
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-50589-z

Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
Cited by: 16
Author(s): Jugpreet Singh, Awais Khan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-52572-0

Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri
Cited by: 24
Author(s): Nicole Liechti, Nadia Schürch, Rémy Bruggmann, Matthias Wittwer
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-53611-6

Effective CRISPR interference of an endogenous gene via a single transgene in mice
Cited by: 23
Author(s): Ryan S. MacLeod, Keisha M. Cawley, Igor Gubrij, Intawat Nookaew, Melda Onal, Charles A. O’Brien
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-53937-1

Highly divergent lineage of narrow-headed vole from the Late Pleistocene Europe
Cited by: 23
Author(s): Mateusz Baca, Danijela Popović, Anna Lemanik, Katarzyna Baca, Ivan Horáček, Adam Nadachowski
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-54838-z

Comparative analysis of corrected tiger genome provides clues to its neuronal evolution
Cited by: 18
Author(s): Parul Mittal, Shubham K. Jaiswal, Nagarjun Vijay, Rituja Saxena, Vineet K. Sharma
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-56029-2

Interactions between earliest Linearbandkeramik farmers and central European hunter gatherers at the dawn of European Neolithization
Cited by: 28
Author(s): Alexey G. Nikitin, Peter F. Stadler, Nadezhda Kotova, Maria Teschler-Nicola, T. Douglas Price, Jessica Hoover, Douglas J. Kennett, Iosif Lazaridis, Nadin Rohland, Mark Lipson, David Reich
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-63102-8

Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA
Cited by: 12
Author(s): Florence Mauger, Caroline Horgues, Morgane Pierre-Jean, Nouara Oussada, Lilia Mesrob, Jean‐François Deleuze
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-67370-2

Declining genetic diversity of European honeybees along the twentieth century
Cited by: 37
Author(s): Gonçalo Espregueira Themudo, Alba Rey‐Iglesia, Lucía Robles Tascón, Annette Bruun Jensen, Rute R. da Fonseca, Paula F. Campos
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-71382-3

Currently favored sampling practices for tumor sequencing can produce optimal results in the clinical setting
Cited by: 6
Author(s): Lőrinc Sándor Pongor, Gyöngyi Munkácsy, Ildikó Vereczkey, Imre Pete, Balázs Győrffy
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-72239-5

Genome analysis of American minks reveals link of mutations in Ras-related protein-38 gene to Moyle brown coat phenotype
Cited by: 5
Author(s): Andrey D. Manakhov, Maria Yu. Mintseva, И. А. Андреев, L. I. Uralsky, Tatiana Andreeva, О. В. Трапезов, Evgeny I. Rogaev
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-76245-5

Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data
Cited by: 6
Author(s): Ngoc Hieu Tran, Thanh Binh Vo, Van Thong Nguyen, Nhat Thang Tran, Thu Huong Nhat Trinh, Hong-Anh Thi Pham, Thi Hong Thuy Dao, Như Gia Nguyễn, Yen Linh Thi Van, Vu Uyen Tran, Hoang Giang Vu, Quynh Tram Nguyen Bui, Phuong Anh Ngoc Vo, Huu Nguyen Nguyen, Quynh Tho Nguyen, Thanh Thuy Thi, Nien Vinh Lam, Phuong Cao Thi Ngoc, Dinh Kiet Truong, Hoa Nguyen, Hoa Giang, Minh-Duy Phan
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-80049-y

Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans
Cited by: 18
Author(s): Ashley N. Hall, Tychele N. Turner, Christine Queitsch
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-85100-0

Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing
Cited by: 9
Author(s): Syed Masroor Ahmed, Michelle Rudden, Sabrina M. Elias, Thomas J. Smyth, Roger Marchant, İbrahim M. Banat, James Dooley
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-86498-3

Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow
Cited by: 10
Author(s): Fernanda de Mello Malta, Deyvid Amgarten, Felipe Camilo Val, Murilo Castro Cervato, Bruna Mascaro Cordeiro de Azevedo, Marcela de Souza-Basqueira, Camila Oliveira Dos Santos Alves, Maria Soares Nóbrega, Rodrigo de Souza Reis, Pedro Henrique Sebe Rodrigues, Michel Chieregato Gretschischkin, Diego Delgado Colombo de Oliveira, Carolina Naomi Izo Nakamura, Pedro Lui Nigro Chazanas, João Renato Rebello Pinho
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-95986-5

Rapid target validation in a Cas9-inducible hiPSC derived kidney model
Cited by: 7
Author(s): Yasaman Shamshirgaran, Anna Jonebring, Anna Svensson, Isabelle Leefa, Mohammad Bohlooly‐Y, Mike Firth, Kevin J. Woollard, Alexis Hofherr, Ian Rogers, Ryan Hicks
Software Mentions: 1
Published: over 3 years ago

10.1186/s40793-017-0281-z

Genome overview of eight Candida boidinii strains isolated from human activities and wild environments
Cited by: 9
Author(s): Salvatore Camiolo, Cinzia Porru, Antonio Benítez-Cabello, Francisco Rodríguez‐Gómez, Beatríz Calero-Delgado, Andrea Porceddu, Marilena Budroni, Ilaria Mannazzu, Rufino Jiménez-Dı́az, Francisco Noé Arroyo‐López
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.stemcr.2017.02.019

Genetic Correction of SOD1 Mutant iPSCs Reveals ERK and JNK Activated AP1 as a Driver of Neurodegeneration in Amyotrophic Lateral Sclerosis
Cited by: 101
Author(s): Akshay Bhinge, Seema C. Namboori, Xiaoyu Zhang, Antonius M.J. VanDongen, Lawrence W. Stanton
Software Mentions: 1
Published: over 7 years ago

10.1186/s13287-018-0852-y

Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches
Cited by: 29
Author(s): Charlotte Saury, Aurélie Lardenois, Cindy Schleder, Isabelle Leroux, Blandine Lieubeau, Laurent David, Marine Charrier, Laëtitia Guével, Sabrina Viau, Bruno Delorme, Karl Rouger
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.02133-16

Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis
Cited by: 447
Author(s): Michael A. DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E. Long, Cara C. Boutte, Eric J. Rubín, Dirk Schnappinger, Sabine Ehrt, Sarah M. Fortune, Christopher M. Sassetti, Thomas R. Ioerger
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00128-17

RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA
Cited by: 50
Author(s): Gina C. Gordon, Jeffrey C. Cameron, Brian F. Pfleger
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00616-19

Bacterial Genome-Wide Association Identifies Novel Factors That Contribute to Ethionamide and Prothionamide Susceptibility in Mycobacterium tuberculosis
Cited by: 35
Author(s): Nathan D. Hicks, Allison F. Carey, Jian Yang, Yanlin Zhao, Sarah M. Fortune
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.01715-19

Aggregation of Nontuberculous Mycobacteria Is Regulated by Carbon-Nitrogen Balance
Cited by: 15
Author(s): William H. DePas, Megan Bergkessel, Dianne K. Newman
Software Mentions: 1
Published: about 5 years ago

10.1128/mBio.00404-20

Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism
Cited by: 9
Author(s): Samantha J. DeWerff, María A. Bautista, Matthew D. Pauly, Changyi Zhang, Rachel J. Whitaker
Software Mentions: 1
Published: over 4 years ago

10.1128/mBio.03027-20

The Bactericidal Fatty Acid Mimetic 2CCA-1 Selectively Targets Pneumococcal Extracellular Polyunsaturated Fatty Acid Metabolism
Cited by: 2
Author(s): Elisabeth Reithuber, Priyanka Nannapaneni, Olena Rzhepishevska, Åsa Lindgren, О В Ильченко, Staffan Normark, Fredrik Almqvist, Birgitta Henriques‐Normark, Peter Mellroth
Software Mentions: 1
Published: almost 4 years ago

10.1128/mSphere.00486-18

Discovery of mcr-1 -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage
Cited by: 42
Author(s): Brian M. Forde, Hosam M. Zowawi, Patrick N A Harris, Leah W. Roberts, Emad Ibrahim, Nissar Shaikh, Anand Deshmukh, Mazen A. Sid Ahmed, Muna Al Maslamani, Kyra Cottrell, Ella Trembizki, Lana Sundac, Heidi H. Yu, Jian Li, Mark A. Schembri, David M. Whiley, David L. Paterson, Scott A. Beatson
Software Mentions: 1
Published: about 6 years ago

10.1128/mSphere.00412-18

The Genetic Transformation of Chlamydia pneumoniae
Cited by: 23
Author(s): Kensuke Shima, Maximilian Wanker, Rachel J. Skilton, Lesley T. Cutcliffe, Christiane Schnee, Thomas A. Kohl, Stefan Niemann, Javier Geijo, Matthias Klinger, Peter Timms, Thomas Rattei, Konrad Sachse, Ian N. Clarke, Jan Rupp
Software Mentions: 1
Published: about 6 years ago

10.1128/mSphere.00389-21

Overlapping of Independent SARS-CoV-2 Nosocomial Transmissions in a Complex Outbreak
Cited by: 8
Author(s): Laura Pérez‐Lago, Helena Martínez-Lozano, José Antonio Pajares-Díaz, Arantxa Díaz-Gómez, Marina Machado, Pedro J. Sola‐Campoy, Marta Herránz, Maricela Valerio, María Olmedo, Julia Suárez‐González, Víctor Quesada-Cubo, Maria Del Mar Gómez-Ruiz, Nieves López‐Fresneña, Ignacio Sánchez-Arcilla, Iñaki Comas, Fernando Gónzález-Candelas, Sonia García de San José, Rafael Bañares, Pilar Catalán, Patricia Muñóz, Darı́o Garcı́a de Viedma
Software Mentions: 1
Published: about 3 years ago

10.1093/hmg/ddv033

Mosaic structural variation in children with developmental disorders
Cited by: 51
Author(s): Dan King, Wendy D. Jones, Yanick J. Crow, Anna F. Dominiczak, Nicola A. Foster, Tom R. Gaunt, Jade Harris, Stephen Hellens, Tessa Homfray, Josie Innes, Elizabeth A. Jones, Shelagh Joss, Abhijit Kulkarni, Sahar Mansour, Andrew D. Morris, Michael Parker, David J. Porteous, Hashem A. Shihab, Blair H. Smith, Katrina Tatton‐Brown, John Tolmie, Maciej Trzaskowski, Pradeep Vasudevan, Emma Wakeling, Michael J. Wright, Robert Plomin, Nicholas J. Timpson, Matthew E. Hurles
Software Mentions: 1
Published: almost 10 years ago

10.1002/humu.23375

An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice
Cited by: 21
Author(s): Gillian Ellison, Miika J. Ahdesmäki, Sally Luke, Paul Waring, Andrew Wallace, Ronnie Wright, Benno Röthlisberger, Katja Ludin, Sabine Merkelbach‐Bruse, Carina Heydt, Marjolijn J. L. Ligtenberg, Arjen R. Mensenkamp, David González de Castro, Thomas R. Jones, Ana Vivancos, Olga Kondrashova, Patrick Pauwels, Christine Weyn, Eric Hahnen, Jan Hauke, Richie Soong, Zhongwu Lai, Brian Dougherty, T. Hedley Carr, Justin Johnson, John Mills, J. Carl Barrett
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41396-021-00911-3

Host genotype and genetic diversity shape the evolution of a novel bacterial infection
Cited by: 16
Author(s): Alice K. E. Ekroth, Michael Gerth, Emily Stevens, Suzanne A. Ford, Kayla C. King
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41396-020-00879-6

Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems
Cited by: 11
Author(s): Samriti Midha, Daniel J. Rigden, Stefanos Siozios, Gregory D. D. Hurst, Andrew P. Jackson
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13046-017-0591-4

High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods
Cited by: 62
Author(s): Dan Su, Dadong Zhang, Kaiyan Chen, Jing Lü, Junzhou Wu, Xi Cao, Ying Liu, Qihuang Jin, Yizhou Ye, Zhenghua Xie, Lei Xiong, Weimin Mao, Fugen Li
Software Mentions: 1
Published: about 7 years ago

10.3390/jof7010054

Paracoccidioides brasiliensis Isolated from Nine-Banded Armadillos (Dasypus novemcinctus) Reveal Population Structure and Admixture in the Amazon Basin
Cited by: 3
Author(s): Eduardo Bagagli, Daniel R. Matute, Hans Garcia Garces, Bernardo Guerra Tenório, Adalberto Garcia Garces, Lucas Gomes de Brito Alves, Danielle Hamae Yamauchi, Marluce Francisca Hrycyk, Bridget M. Barker, Marcus de Melo Teixeira
Software Mentions: 1
Published: almost 4 years ago

10.1093/jhered/esab003

A Reference Genome Assembly of American Bison,Bison bison bison
Cited by: 13
Author(s): Jonas Oppenheimer, Benjamin D. Rosen, Michael P. Heaton, B. L. Vander Ley, Wade R Shafer, Fred T Schuetze, Brad Stroud, L. A. Kuehn, Jennifer C. McClure, Jennifer P. Barfield, Harvey D. Blackburn, Theodore S. Kalbfleisch, Derek M. Bickhart, Kimberly M Davenport, Kristen L. Kuhn, Edward Green, Beth Shapiro, Timothy P. L. Smith
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41388-019-0780-z

Dissecting mechanisms of resistance to targeted drug combination therapy in human colorectal cancer
Cited by: 25
Author(s): Paul A. Clarke, Toby Roe, Kate Swabey, Steve Hobbs, Craig McAndrew, Kathy Tomlin, Isaac M. Westwood, Rosemary Burke, Robert van Montfort, Paul Workman
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.43606

Long-term balancing selection drives evolution of immunity genes in Capsella
Cited by: 60
Author(s): Daniel Koenig, Jörg Hagmann, Rachel Li, Felix Bemm, Tanja Slotte, Barbara Neuffer, Stephen I. Wright, Detlef Weigel
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.49258

Extensive impact of low-frequency variants on the phenotypic landscape at population-scale
Cited by: 37
Author(s): Téo Fournier, Omar Abou Saada, Jing Hou, Jackson Peter, Elodie Caudal, Joseph Schacherer
Software Mentions: 1
Published: about 5 years ago

10.7554/eLife.59683

A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes
Cited by: 109
Author(s): François Kroll, Gareth T. Powell, Marcus Ghosh, Gaia Gestri, Paride Antinucci, Timothy J. Hearn, Hande Tunbak, Sumi Lim, Harvey W Dennis, Joseph Fernandez, David Whitmore, Elena Dreosti, Stephen W. Wilson, Ellen J. Hoffman, Jason Rihel
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.49212

Rare variants contribute disproportionately to quantitative trait variation in yeast
Cited by: 60
Author(s): Joshua S. Bloom, James Boocock, Sebastian Treusch, Meru J. Sadhu, Laura Day, Holly Oates-Barker, Leonid Kruglyak
Software Mentions: 1
Published: about 5 years ago

10.7554/eLife.51481

Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa
Cited by: 48
Author(s): Camilo Barbosa, Roderich Römhild, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 1
Published: about 5 years ago

10.7554/eLife.41769

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Cited by: 186
Author(s): Jeffrey M. Alexander, Juan Guan, Bingkun Li, Lenka Maliskova, Michael Song, Yin Shen, Bo Huang, Stavros Lomvardas, Orion D. Weiner
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.53734

A small protein encoded by a putative lncRNA regulates apoptosis and tumorigenicity in human colorectal cancer cells
Cited by: 34
Author(s): Xiao Ling Li, Lőrinc Sándor Pongor, Wei Tang, Sudipto Das, Bruna Rodrigues Muys, Michael R. Jones, Sarah B. Lazar, Emily A. Dangelmaier, Corrine Corrina R Hartford, Ioannis Grammatikakis, Qinyu Hao, Qinyu Sun, Aaron J. Schetter, Jennifer L. Martindale, Binwu Tang, Lisa M. Miller Jenkins, Ana I. Robles, Robert L. Walker, Stefan Ambs, Raj Chari, Svetlana A. Shabalina, Myriam Gorospe, Perwez Hussain, Curtis C. Harris, Paul S. Meltzer, Kannanganattu V. Prasanth, Mirit I. Aladjem, Þorkell Andrésson, Ashish Lal
Software Mentions: 1
Published: about 4 years ago

10.18632/oncotarget.10827

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA
Cited by: 25
Author(s): Mathias Stiller, Antje Sucker, Klaus G. Griewank, Daniela E. Aust, Gustavo Baretton, Dirk Schadendorf, Susanne Horn
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.14926

Detection fidelity of AR mutations in plasma derived cell-free DNA
Cited by: 19
Author(s): Alexa Goldstein, Patricia Valda Toro, Justin Lee, John L. Silberstein, Mary Nakazawa, Ian Waters, Karen Cravero, David Chu, Rory L. Cochran, Min‐Soo Kim, Daniel Shinn, Samantha Torquato, Robert M. Hughes, Aparna Pallavajjala, Michael A. Carducci, Channing J. Paller, Samuel R. Denmeade, Bruce Kressel, Bruce J. Trock, Mario A. Eisenberger, Emmanuel S. Antonarakis, Ben Ho Park, Paula J. Hurley
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.20764

Subependymal giant cell astrocytomas in Tuberous Sclerosis Complex have consistent TSC1/TSC2 biallelic inactivation, and no BRAF mutations
Cited by: 45
Author(s): Anika Bongaarts, Κρινιώ Γιαννίκου, Roy J. Reinten, Jasper J. Anink, James D. Mills, Floor E. Jansen, G M Wim Spliet, Wilfred F. A. den Dunnen, Roland Coras, Ingmar Blümcke, Werner Paulus, Theresa O. Scholl, Martha Feucht, Katarzyna Kotulska, Sergiusz Jóźwiak, Anna Maria Buccoliero, Chiara Caporalini, Flavio Giordano, Lorenzo Genitori, Figen Söylemezoğlu, José Pimentel, Mark Nellist, Antoinette Y. N. Schouten–van Meeteren, Anwesha Nag, Angelika Mühlebner, David J. Kwiatkowski, Eleonora Aronica
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.22560

Integrative molecular network analysis identifies emergent enzalutamide resistance mechanisms in prostate cancer
Cited by: 10
Author(s): Carly J. King, Josha Woodward, Jacob Schwartzman, Daniel J. Coleman, Robert Lisac, Nicholas J. Wang, Kathryn Van Hook, Lina Gao, Joshua A. Urrutia, Mark Dane, Laura M. Heiser, Joshi J. Alumkal
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.24567

Analysis of the 9p21.3 sequence associated with coronary artery disease reveals a tendency for duplication in a CAD patient
Cited by: 5
Author(s): Natalay Kouprina, Mikhail Liskovykh, Nathan Lee, Vladimir N. Noskov, Joshua J. Waterfall, Robert L. Walker, Paul S. Meltzer, Eric J. Topol, Vladimir Larionov
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.27954

Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection
Cited by: 6
Author(s): Josephine Dubois, Jacqueline Rueger, Bernhard Haubold, Rosel Kretschmer‐Kazemi Far, Georg Sczakiel
Software Mentions: 1
Published: over 3 years ago

10.3390/jpm9010010

VARIFI—Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data
Cited by: 0
Author(s): Milica Krunic, Peter Venhuizen, Leonhard Müllauer, Bettina Kaserer, Arndt von Haeseler
Software Mentions: 1
Published: almost 6 years ago

10.1186/1750-1172-9-12

The supposed tumor suppressor gene WWOX is mutated in an early lethal microcephaly syndrome with epilepsy, growth retardation and retinal degeneration
Cited by: 68
Author(s): Ghada M.H. Abdel-Salam, Michaela Thoenes, Hanan H. Afifi, Friederike Körber, Daniel Swan, Hanno J. Bolz
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13023-016-0514-z

Viable phenotype of ILNEB syndrome without nephrotic impairment in siblings heterozygous for unreported integrin alpha3 mutations
Cited by: 19
Author(s): E. Colombo, Luigina Spaccini, L. Volpi, Gloria Negri, Davide Cittaro, Dejan Lazarevic, Salvatore Zirpoli, Andrea Farolfi, Cristina Gervasini, Maria Vittoria Cubellis, Lidia Larizza
Software Mentions: 1
Published: about 8 years ago

10.1186/s13023-020-01361-4

Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta
Cited by: 9
Author(s): Kristofer Andersson, B. Malmgren, Eva Albrecht, Ann Nordgren, Fulya Taylan, Göran Dahllöf
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: bwa

Papers Mentioning bwa 989