bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.7554/eLife.65508

Seroconversion stages COVID19 into distinct pathophysiological states
Cited by: 36
Author(s): Matthew D. Galbraith, Kohl T Kinning, Kelly D. Sullivan, Ryan M. Baxter, Paula Araya, Kimberly R. Jordan, Seth Russell, Keith P Smith, Ross E Granrath, Jessica Shaw, Monika Dzieciątkowska, Tusharkanti Ghosh, Andrew A. Monte, Angelo D’Alessandro, Kirk C. Hansen, Tellen D Benett, Elena W.Y. Hsieh, Joaquín M. Espinosa
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.65445

Molecular characterization of projection neuron subtypes in the mouse olfactory bulb
Cited by: 16
Author(s): Sara Zeppilli, Tobias Ackels, Robin Attey, Nell Klimpert, Kimberly Ritola, Stefan Boeing, Anton Crombach, Andreas T. Schaefer, Alexander Fleischmann
Software Mentions: 8
Published: about 5 years ago

10.1186/s12859-017-1803-9

XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation
Cited by: 11
Author(s): Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson‐Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodríguez, Yidong Chen
Software Mentions: 8
Published: almost 9 years ago

10.1155/2021/9920234

Bioinformatic Analysis Reveals Central Role for Tumor-Infiltrating Immune Cells in Uveal Melanoma Progression
Cited by: 6
Author(s): Mieszko Lachota, Anton Lennikov, Karl‐Johan Malmberg, Radosław Zagożdżon
Software Mentions: 8
Published: over 5 years ago

10.1186/s12859-021-04130-7

Correlation AnalyzeR: functional predictions from gene co-expression correlations
Cited by: 35
Author(s): Henry E. Miller, Alexander J.R. Bishop
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0200925

PNPase knockout results in mtDNA loss and an altered metabolic gene expression program
Cited by: 12
Author(s): Eriko Shimada, Fasih M. Ahsan, Mahta Nili, Dian Huang, Sean Atamdede, Tara TeSlaa, Dana Case, Xiang Yu, Brian D. Gregory, Benjamin J. Perrin, Carla M. Koehler, Michael A. Teitell
Software Mentions: 8
Published: about 8 years ago

10.1186/s12864-018-4649-2

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation
Cited by: 15
Author(s): Zhisong He, Qianhui Yu
Software Mentions: 8
Published: over 8 years ago

10.7554/eLife.62208

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
Cited by: 30
Author(s): David E. Cook, Holger Kramer, David E Torres, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12859-020-3506-x

Negative binomial additive model for RNA-Seq data analysis
Cited by: 16
Author(s): Ruwei Xu, Pei Fen Kuan
Software Mentions: 8
Published: over 6 years ago

10.1038/tp.2015.169

Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain
Cited by: 56
Author(s): Aslihan Dincer, David P. Gavin, Ke Xu, B Zhang, Joel T. Dudley, Eric E. Schadt, Schahram Akbarian
Software Mentions: 8
Published: almost 11 years ago

10.1128/mSystems.00122-17

Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development
Cited by: 27
Author(s): Keaton Stagaman, Tara J Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan
Software Mentions: 8
Published: over 8 years ago

10.1371/journal.pgen.1009435

A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression
Cited by: 14
Author(s): Zachary Carico, Holden C. Stefan, Megan Justice, Askar Yimit, Jill M. Dowen
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0153782

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
Cited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: over 10 years ago

10.1186/s12864-021-07918-2

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis
Cited by: 10
Author(s): Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson A. Silva
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2019.00624

Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma
Cited by: 53
Author(s): Nitish K. Mishra, Siddesh Southekal, Chittibabu Guda
Software Mentions: 8
Published: about 7 years ago

10.3390/biology10040314

Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan)
Cited by: 6
Author(s): Nataliia Khomutovska, Asunción de los Rı́os, Marcin Syczewski, Iwona Jasser
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-020-6764-0

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum
Cited by: 15
Author(s): Alice B. Dennis, Gabriel I. Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, Jan Berghöfer, Leo W. Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoé Dumas, Mohammed Errbii, Patrizia Falabella, Jean‐Luc Gatti, Elzemiek Geuverink, Joshua D. Gibson, Corinne Hertaeg, Stefanie Hartmann, Emmanuelle Jacquin‐Joly, Mark Lammers, Blas I. Lavandero, Ina Lindenbaum, Lauriane Massardier-Galatà, Camille Meslin, Nicolas Montagné, Nina Pak, Marylène Poirié, Rosanna Salvia, Chris R. Smith, Denis Tagu, Sophie Tarès, Heiko Vogel, Tanja Schwander, Jean Simon, Christian C. Figueroa, Christoph Vorburger, Fabrice Legeai, Jürgen Gadau
Software Mentions: 8
Published: over 6 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: about 6 years ago

10.3389/fcimb.2020.00194

Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections
Cited by: 2
Author(s): Malika Aïd, Daniel R. Ram, Steven E. Bosinger, Dan H. Barouch, R. Keith Reeves
Software Mentions: 8
Published: over 6 years ago

10.3389/fmicb.2020.626713

Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range
Cited by: 6
Author(s): Janneke Schreuder, Francisca C. Velkers, Alex Bossers, Ruth Bouwstra, W.F. de Boer, Pim van Hooft, J.A. Stegeman, Stephanie D. Jurburg
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-020-62354-8

Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components
Cited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pgen.1008515

Dynamic and regulated TAF gene expression during mouse embryonic germ cell development
Cited by: 15
Author(s): Megan A. Gura, Maria M. Mikedis, Kimberly A. Seymour, Dirk G. de Rooij, David C. Page, Richard N. Freiman
Software Mentions: 8
Published: over 6 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: about 8 years ago

10.1084/jem.20210615

Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung
Cited by: 63
Author(s): Davide Pisu, Lu Huang, Vipin Narang, Monique E. Theriault, Gabrielle Lê-Bury, Bernett Lee, Agnes E Lakudzala, David Mzinza, David V. Mhango, Steven C Mitini-Nkhoma, Kondwani Jambo, Amit Singhal, Henry C. Mwandumba, David G. Russell
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2019.00182

Detection of Differentially Expressed Cleavage Site Intervals Within 3′ Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs
Cited by: 9
Author(s): Benjamin J. Harrison, Juw Won Park, Cynthia Gomes, Jeffrey C. Petruska, Matthew R. Sapio, Michael J. Iadarola, Julia H. Chariker, Eric C. Rouchka
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-017-02685-1

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora
Cited by: 73
Author(s): Rachel M. Wright, Carly D. Kenkel, Carly E. Dunn, Erin N. Shilling, Line K. Bay, Mikhail V. Matz
Software Mentions: 8
Published: over 9 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: almost 11 years ago

10.1002/ece3.4894

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
Cited by: 8
Author(s): Suda Parimala Ravindran, Maike Herrmann, Mathilde Cordellier
Software Mentions: 8
Published: over 7 years ago

10.3389/fgene.2020.00041

Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
Cited by: 46
Author(s): Nicholas Lytal, Ran Di, Lingling An
Software Mentions: 8
Published: over 6 years ago

10.3389/fmolb.2021.613359

Identification of a Hypoxia-Related Signature for Predicting Prognosis and the Immune Microenvironment in Bladder Cancer
Cited by: 10
Author(s): Minxiao Jiang, Ren Lang, Yuanlei Chen, Huan Wang, Haiyang Wu, Sheng Cheng, Gonghui Li, Shicheng Yu
Software Mentions: 8
Published: over 5 years ago

10.3390/e23080945

Statistical Approach of Gene Set Analysis with Quantitative Trait Loci for Crop Gene Expression Studies
Cited by: 1
Author(s): Das S, N. Shesh
Software Mentions: 8
Published: about 5 years ago

10.1128/mSystems.00852-20

Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3
Cited by: 16
Author(s): José O. Solbiati, Ana E. Duran-Pinedo, Fernanda Godoy Rocha, Frank C. Gibson, Jorge Frias-Lopez
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12935-020-01707-9

PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer
Cited by: 13
Author(s): Li Zheng, Yaming Li, Xiaolong Wang, Qifeng Yang
Software Mentions: 8
Published: over 5 years ago

10.1016/j.celrep.2018.03.075

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Cited by: 432
Author(s): Christopher J. Ricketts, Aguirre A. de Cubas, Huihui Fan, Christof C. Smith, Martin Lang, Ed Reznik, Reanne Bowlby, Ewan A. Gibb, Rehan Akbani, Rameen Beroukhim, Donald P. Bottaro, Toni K. Choueiri, Richard A. Gibbs, Andrew K. Godwin, Scott M. Haake, A. Ari Hakimi, Elizabeth P. Henske, James J. Hsieh, Thai H. Ho, Rupa S. Kanchi, Bhavani Krishnan, David J. Kwiatkowski, Wembin Lui, María J. Merino, Gordon B. Mills, Jerome Myers, Michael L. Nickerson, Victor E. Reuter, Laura S. Schmidt, Carl Simon Shelley, Hui Shen, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George V. Thomas, Benjamin G. Vincent, Cathy D. Vocke, David A. Wheeler, Lixing Yang, William Y. Kim, A. Gordon Robertson, Paul T. Spellman, W. Kimryn Rathmell, W. Marston Linehan, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila M. Reynolds, Ilya Shmulevich, Vésteinn Thórsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Ju Zhang, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin Groß, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah Phillips, Ed Reznik, Francisco Sanchez‐Vega, Chris Sander, Nikolaus Schultz, Robert P. Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul T. Spellman, Christopher C. Benz, Joshua M. Stuart, Christopher Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie Kucherlapati, Raju Kucherlapati, Stephen B. Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle R. Covington, Chad J. Creighton, Huyen Dinh, Harshavardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna M. Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Xi Liu, Fengmei Zhao, Julian M. Hess, Elizabeth L. Appelbaum, Matthew H. Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark E. Sherman, Eric M. Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall M. Corcoran, Tony Costello, Christopher M. Hovens, André Lopes Carvalho, Ana Carolina de Carvalho, José Humberto Tavares Guerreiro Fregnani, Adhemar Longatto‐Filho, Rui Manuel Reis, Cristovam Scapulatempo‐Neto, Henrique C. S. Silveira, Daniel Onofre Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia Castro, Michael Ittmann, David G. Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, А. В. Шабунин, М. М. Тавобилов, Christopher McPherson, Ronald E. Warnick, Ross S. Berkowitz, Daniel E. Cramer, Colleen M. Feltmate, Neil S. Horowitz, Adam S. Kibel, Michael G. Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz‐Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino Maria De Rose, Felice Giuliante, Marc T. Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Aleš Vícha, Tomáš Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John A. Chabot, Hanina Hibshoosh, Antonia R. Sepulveda, Tao Su, Yichen Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Román-Román, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell D. Bigner, Eric Lipp, Jeffrey R. Marks, Shannon J. McCall, Roger E. McLendon, Angeles Alvarez Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith A. Delman, Seth D. Force, Fadlo R. Khuri, Kelly R. Magliocca, Shishir K. Maithel, Jeffrey J. Olson, Taofeek K. Owonikoko, Alan Pickens, Suresh S. Ramalingam, Dong Min Shin, Gabriel L. Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad J. M. Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, J. R. Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Täubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Wung Chung, William J. Edenfield, Julie Martin, Éric Baudin, Glenn J. Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven N. Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elı́as Campo, Eva Giné, Armando López Guillermo, Nguyễn Văn Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael J. Birrer, Debra A. Bell, Mitesh J. Borad, Alan H. Bryce, Erik P. Castle, Vishal S. Chandan, John C. Cheville, John A. Copland, Michael B. Farnell, Thomas J. Flotte, Nasra H. Giama, Thai H. Ho, Michael L. Kendrick, Jean-Pierre A. Kocher, Karla Kopp, Catherine D. Moser, David M. Nagorney, Daniel J. O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia G. Que, Michael Rivera, Lewis R. Roberts, Robert C. Smallridge, Thomas C. Smyrk, Melissa L. Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell R. Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey E. Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric‐Bernstam, César A. Moran, Lois M. Ramondetta, David Rice, Anil K. Sood, Pheroze Tamboli, Timothy C. Thompson, Patricia Troncoso, Anne S. Tsao, Ignacio Wistuba, Candace Carter, Lauren E. Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina V. Long, Graham J. Mann, Michael J. Quinn, Robyn P.M. Saw, Richard A. Scolyer, Kerwin F. Shannon, Andrew J. Spillane, onathan Stretch, Maria Synott, John Thompson, James S. Wilmott, Hikmat Al‐Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor E. Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer K. Smith, Howard A. Zaren, Joong-Won Park, Nguyễn Phi Hùng, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacák, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert A. Worrell, Hannah Yang, Marc Moncrieff, Chandra V. Goparaju, Jonathan Melamed, Harvey I. Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John M.S. Bartlett, Jay Engel, Sébastien Gilbert, Jeremy Parfitt, Harman S. Sekhon, George V. Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter J. Urba, Nicholas K. Hayward, H. Th. Marc Timmers, Anna Antenucci, Francesco Facciolo, Gian Luca Grazi, Mirella Marino, Roberta Merola, Ronald R. de Krijger, Anne‐Paule Gimenez‐Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kıvanç Birsoy, Gene H. Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel P. Raymond, Cathy Schilero, Kathy Smolenski, Cecilia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl‐Friedrich Becker, Klaus‐Peter Janssen, Julia Slotta‐Huspenina, Mohamed H. Abdel‐Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James C. Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul E. Wakely, Paul Hansen, Ronald M. Lechan, James F. Powers, Arthur S. Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel M. Henderson, Sima P. Porten, Jens Waldmann, Martin Fassnacht, L. Sylvia, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark A. Nelson, Oliver F. Bathe, Peter R. Carroll, June M. Chan, Philip J. DiSaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry P. Simko, Karen Smith‐McCune, Scott R. VandenBerg, Kevin K. Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis A. Carey, Ian Forgie, Massimo Mannelli, Michael E. Carney, Brenda Hernandez, Benito Campos, Christel Herold‐Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita D. Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David G. Beer, Thomas J. Giordano, Anne‐Marie Mes‐Masson, Fred Saad, Thèrése Bocklage, Lisa M. Landrum, Robert S. Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary E. Zuna, Michael D. Feldman, Federico Valdivieso, Rajiv Dhir, James D. Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, José Sebastião dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Pretti da Cunha Tirapelli, James W.F. Catto, Kathy Agnew, Elizabeth M. Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, S. DiSean Kendall, Cassaundra Shipman, Carol R. Bradford, Thomas E. Carey, Andrea Haddad, Jeffey Moyer, Lisa A. Peterson, Mark E. Prince, Laura S. Rozek, Gregory T. Wolf, Rayleen V. Bowman, Kwun M. Fong, Ian A. Yang, Robert J. Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John F. DiPersio, Bettina F. Drake, Ramaswamy Govindan, Sharon E. Heath, Timothy J. Ley, Brian A. Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália Del Angelo Aredes, Armaz Mariamidze
Software Mentions: 8
Published: over 8 years ago

10.1016/j.celrep.2021.109118

Resident memory T cells in tumor-distant tissues fortify against metastasis formation
Cited by: 14
Author(s): Laura S. Christian, Liuyang Wang, Bryan Jian Wei Lim, Dachuan Deng, Haiyang Wu, Xiaofan Wang, Qi-Jing Li
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pgen.1006995

Environmental perturbations lead to extensive directional shifts in RNA processing
Cited by: 24
Author(s): Allison L. Richards, Donovan Watza, Anthony Findley, Adnan Alazizi, Xiaoquan Wen, Athma A. Pai, Roger Piqué-Regi, Francesca Luca
Software Mentions: 8
Published: almost 9 years ago

10.1371/journal.pone.0209200

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus
Cited by: 61
Author(s): Matthew Fuirst, Richard R. Veit, Megan Hahn, Nolwenn M. Dheilly, Lesley H. Thorne
Software Mentions: 8
Published: almost 8 years ago

10.1371/journal.pone.0249148

Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans
Cited by: 5
Author(s): Nicholas A. Kinney, Lin Kang, Harpal Bains, Elizabeth Lawson, Mesam Husain, Kumayl Husain, Inderjit Sandhu, Yongdeok Shin, Javan K. Carter, Ramu Anandakrishnan, Pawel Michalak, Harold R. Garner
Software Mentions: 8
Published: over 5 years ago

10.1128/mSystems.00917-20

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
Cited by: 7
Author(s): Matthew Chung, Ricky S. Adkins, John Mattick, Katie R. Bradwell, Amol Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0249691

Profiling DNA break sites and transcriptional changes in response to contextual fear learning
Cited by: 25
Author(s): Ryan Stott, Oleg Kritsky, Li‐Huei Tsai
Software Mentions: 8
Published: about 5 years ago

10.3389/fmicb.2018.00570

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments
Cited by: 37
Author(s): Nicholas D. Youngblut, Samuel E. Barnett, Daniel H. Buckley
Software Mentions: 8
Published: over 8 years ago

10.3389/fgene.2019.01331

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing
Cited by: 50
Author(s): Tian Mou, Wenjiang Deng, Fengyun Gu, Yudi Pawitan, Trung Nghia Vu
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0232271

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data
Cited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: over 6 years ago

10.1186/s12935-020-01661-6

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Cited by: 6
Author(s): R. Adam, Sanne M. van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E. de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen
Software Mentions: 8
Published: almost 6 years ago

10.3390/ijms21114014

Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in Zebrafish
Cited by: 6
Author(s): Sophia Murat El Houdigui, Christelle Adam-Guillermin, Olivier Armant
Software Mentions: 8
Published: over 6 years ago

10.1016/j.stem.2020.03.005

GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells
Cited by: 42
Author(s): Alexandra Gunne-Braden, Adrienne E. Sullivan, Borzo Gharibi, Rahuman S. Malik Sheriff, Alok Kumar Maity, Yi Fang Wang, A. Edwards, Ming Jiang, Michael Howell, Robert Goldstone, Roy Wollman, Philip East, Silvia Santos
Software Mentions: 8
Published: over 6 years ago

10.17179/excli2015-168

Data- and knowledge-based modeling of gene regulatory networks: an update.
Cited by: 24
Author(s): Jörg Linde, Sylvie Schulze, Sebastian Henkel, Reinhard Guthke
Software Mentions: 8
Published: over 11 years ago

10.1038/s41598-021-93570-5

Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles
Cited by: 18
Author(s): Emily J. Ross, Emily R. Gordon, Hanna Sothers, Roshan Darji, Oakley Baron, Dustin W. Haithcock, Balabhaskar Prabhakarpandian, Kapil Pant, R Myers, Sara J. Cooper, Nancy J. Cox
Software Mentions: 8
Published: about 5 years ago

10.1093/molbev/msab029

Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes
Cited by: 56
Author(s): Hanpeng Liao, Xi Li, Qiue Yang, Yudan Bai, Peng Cui, Chang Wen, Chen Liu, Zhi Chen, Jiahuan Tang, Jiangang Che, Zhen Yu, Stefan Geisen, Shungui Zhou, Ville‐Petri Friman, Yong‐Guan Zhu
Software Mentions: 8
Published: over 5 years ago

10.1038/srep44736

Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
Cited by: 5
Author(s): Jian Yu, Constance Ciaudo
Software Mentions: 8
Published: over 9 years ago

10.1111/pbi.12919

An epigenetic breeding system in soybean for increased yield and stability
Cited by: 63
Author(s): Sunil Kumar Kenchanmane Raju, Mon‐Ray Shao, Robersy Sánchez, Ying-Zhi Xu, Ajay Sandhu, George L. Graef, Sally A. Mackenzie
Software Mentions: 8
Published: over 8 years ago

10.3389/fgene.2020.573515

SETDB1 Overexpression Sets an Intertumoral Transcriptomic Divergence in Non-small Cell Lung Carcinoma
Cited by: 8
Author(s): Yong‐Kook Kang, Byungkuk Min
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-021-98966-x

Identification of immune-related subtypes of colorectal cancer to improve antitumor immunotherapy
Cited by: 4
Author(s): Xiangkuo Zheng, Yong Gao, Chunhua Yu, Guiquan Fan, Pengwu Li, Ming Zhang, Jian Yu, Mingqing Xu
Software Mentions: 8
Published: almost 5 years ago

10.3389/fmicb.2020.01780

Response of Soil Bacterial Community Diversity and Composition to Time, Fertilization, and Plant Species in a Sub-Boreal Climate
Cited by: 5
Author(s): Honghong Li, Petri Penttinen, Anu Mikkonen, Frederick L. Stoddard, Kristina Lindström
Software Mentions: 8
Published: about 6 years ago

10.1371/journal.pone.0125000

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Cited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Software Mentions: 8
Published: over 11 years ago

10.1371/journal.pone.0187722

Plasma microRNA profiling: Exploring better biomarkers for lymphoma surveillance
Cited by: 47
Author(s): Drirh Khare, Neta Goldschmidt, Aya Bardugo, Devorah Gur‐Wahnon, Iddo Z. Ben‐Dov, Batia Avni
Software Mentions: 8
Published: almost 9 years ago

10.7717/peerj.8522

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells
Cited by: 8
Author(s): Phongsakorn Chuammitri, Soulasack Vannamahaxay, Benjaporn Sornpet, Kidsadagon Pringproa, Prapas Patchanee
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0234537

Prairie plants harbor distinct and beneficial root-endophytic bacterial communities
Cited by: 0
Author(s): Boahemaa Adu-Oppong, Scott A. Mangan, Cláudia Stein, Christopher P. Catano, Jonathan A. Myers, Gautam Dantas
Software Mentions: 8
Published: about 6 years ago

10.1186/s40168-016-0208-8

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
Cited by: 124
Author(s): Jonathan Thorsen, Asker Brejnrod, Martin Steen Mortensen, Morten Arendt Rasmussen, Jakob Stokholm, Waleed Abu Al‐Soud, Søren J. Sørensen, Hans Bisgaard, Johannes Waage
Software Mentions: 8
Published: almost 10 years ago

10.3389/fphys.2021.662132

Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability
Cited by: 10
Author(s): Austin E. Gillen, Rui Fu, Kent Riemondy, Jennifer Jager, Bin Fang, Mitchell A. Lazar, Sandra L. Martin
Software Mentions: 8
Published: over 5 years ago

10.3390/v13061019

Human Retrotransposons and the Global Shutdown of Homeostatic Innate Immunity by Oncolytic Parvovirus H-1PV in Pancreatic Cancer
Cited by: 2
Author(s): Matthias Neulinger-Muñoz, Dominik Schaack, Svetlana Grekova, Andrea S. Bauer, Thomas Giese, Gabriel Alexander Salg, Elisa Espinet, Barbara Leuchs, Anette Heller, Jürg P. F. Nüesch, Miriam Schenk, Michael Volkmar, Nathalia A. Giese
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-018-34019-0

Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status
Cited by: 4
Author(s): Yu Hasegawa, Britni Curtis, Vernon Yutuc, Megan Rulien, Kelly Morrisroe, Kristin Watkins, Clayton Ferrier, Chris English, Laura Hewitson, Carolyn M. Slupsky
Software Mentions: 8
Published: almost 8 years ago

10.3389/fpls.2018.01632

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus
Cited by: 22
Author(s): Ruijuan Li, Kwangju Jeong, John Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin Maloof
Software Mentions: 8
Published: almost 8 years ago

10.1128/mBio.01369-21

HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 + T Cells Early Postinfection
Cited by: 6
Author(s): Hélène Bauby, Christopher Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Software Mentions: 8
Published: about 5 years ago

10.1186/s40168-018-0434-3

Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing
Cited by: 20
Author(s): Ellen L. Young, Manus Carey, Andrew A. Meharg, Caroline Meharg
Software Mentions: 8
Published: over 8 years ago

10.1038/s41598-019-40503-y

Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions
Cited by: 23
Author(s): Quen J. Cheng, Faraz Behzadi, Supriya Sen, Sho Ohta, Roberto Spreafico, Rosane M. B. Teles, Robert L. Modlin, Alexander Hoffmann
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-021-89065-y

Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity
Cited by: 24
Author(s): Jake M. Robinson, Christian Cando‐Dumancela, Rachael E. Antwis, Ross Cameron, Craig Liddicoat, Ravin Poudel, Philip Weinstein, Martin F. Breed
Software Mentions: 8
Published: over 5 years ago

10.3389/fimmu.2021.649551

TSPAN1, TMPRSS4, SDR16C5, and CTSE as Novel Panel for Pancreatic Cancer: A Bioinformatics Analysis and Experiments Validation
Cited by: 11
Author(s): Yi-Jun Hua, Tiandong Li, Hua Wang, Jinyu Wu, Chuncheng Yi, Jianxiang Shi, Peng Wang, Chunhua Song, Liping Dai, Guozhong Jiang, Yuguang Huang, Yu Ye, Jitian Li
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 5 years ago

10.3389/fmicb.2021.632935

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events
Cited by: 19
Author(s): Benjamin Zwirzitz, Stefanie U. Wetzels, Emmanuel D. Dixon, Svenja Fleischmann, Evelyne Selberherr, Sarah Thalguter, Narciso M. Quijada, Monika Dzieciol, Martin Wagner, Beatrix Stessl
Software Mentions: 8
Published: over 5 years ago

10.1186/s40168-021-01078-x

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
Cited by: 85
Author(s): Fei Xie, Wei Jin, Huazhe Si, Yuan Yuan, Ye Tao, Junhua Liu, Xiaoxu Wang, Chengjian Yang, Qiushuang Li, Xiu-Tian Yan, Limei Lin, Qian Jiang, Lei Zhang, Chang Guo, Chris Greening, Rasmus Heller, Le Luo Guan, Phillip B. Pope, Zhiliang Tan, Weiyun Zhu, Min Wang, Qiang Qiu, Zhipeng Li, Shengyong Mao
Software Mentions: 8
Published: over 5 years ago

10.1093/gigascience/giz004

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches
Cited by: 103
Author(s): Darshan B. Dhakan, Abhijit Maji, Ashok Sharma, Rituja Saxena, Joby Pulikkan, Tony Grace, Andrés Gómez, Joy Scaria, Katherine R. Amato, Vineet K. Sharma
Software Mentions: 8
Published: over 7 years ago

10.1016/j.csbj.2021.05.024

Machine learning applied to serum and cerebrospinal fluid metabolomes revealed altered arginine metabolism in neonatal sepsis with meningoencephalitis
Cited by: 12
Author(s): Peng Zhang, Zhangxing Wang, Huixian Qiu, Wenhao Zhou, Mingbang Wang, Guoqiang Cheng
Software Mentions: 8
Published: over 5 years ago

10.3389/fcvm.2020.575275

Reactivation of Atrium Genes Is a Primer for Heart Infarction or Regeneration
Cited by: 1
Author(s): Yang Zhen
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pcbi.1006907

Ten quick tips for effective dimensionality reduction
Cited by: 164
Author(s): Linh P. Nguyen, Susan Holmes
Software Mentions: 8
Published: over 7 years ago

10.3389/fonc.2021.640881

Exploration of an Integrative Prognostic Model of Radiogenomics Features With Underlying Gene Expression Patterns in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Yeqian Huang, Hao Zeng, Linyan Chen, Yuling Luo, Xuelei Ma, Ye Zhao
Software Mentions: 8
Published: over 5 years ago

10.1038/s41380-020-0844-z

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids
Cited by: 66
Author(s): Tomoyo Sawada, Thomas E. Chater, Yohei Sasagawa, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J.M. Benjamin, Apuã C.M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Takeshi Kato
Software Mentions: 8
Published: about 6 years ago

10.7554/eLife.58331

An essential role for MEF2C in the cortical response to loss of sleep in mice
Cited by: 19
Author(s): Theresa E. Bjorness, Ashwinikumar Kulkarni, Volodymyr Rybalchenko, Ayako Suzuki, Catherine Bridges, Adam J. Harrington, Christopher W. Cowan, Joseph S. Takahashi, Genevieve Konopka, Robert Greene
Software Mentions: 8
Published: about 6 years ago

10.1093/gigascience/giz147

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
Cited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 7 years ago

10.1038/s41598-019-45193-0

Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
Cited by: 7
Author(s): Polina Drozdova, Daria Bedulina, Ekaterina Madyarova, Lorena Rivarola-Duarte, S Schreiber, Peter F. Stadler, Till Luckenbach, Maxim A. Timofeyev
Software Mentions: 8
Published: over 7 years ago

10.3389/fmicb.2021.654108

Gut Microbiota of Drosophila subobscura Contributes to Its Heat Tolerance and Is Sensitive to Transient Thermal Stress
Cited by: 22
Author(s): Angélica Jaramillo, Luis E. Castañeda
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0246052

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection
Cited by: 10
Author(s): Aleksandra Boba, Kamil Kostyń, Bartosz Kozak, Iwan Zalewski, Jan Szopa, Anna Kulma
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.44036

Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific loci
Cited by: 38
Author(s): Sonia Sen, Sachin Chanchani, Tony D. Southall, Chris Q. Doe
Software Mentions: 8
Published: over 7 years ago

10.1080/19490976.2021.1966263

Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium
Cited by: 28
Author(s): Mareike Neumann, Alex Steimle, Erica T. Grant, Mathis Wolter, Amy Parrish, Stéphanie Willième, Dirk Brenner, Eric C. Martens, Mahesh S. Desai
Software Mentions: 8
Published: over 5 years ago

10.3389/fcell.2021.651575

An N6-Methyladenosine-Related Gene Set Variation Score as a Prognostic Tool for Lung Adenocarcinoma
Cited by: 8
Author(s): Huijuan Zhang, Jing Hu, Aina Liu, Huajun Qu, Fenge Jiang, Congcong Wang, Steven Mo, Ping Sun
Software Mentions: 8
Published: about 5 years ago

10.3390/v12090956

Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival
Cited by: 17
Author(s): Allison R. Kolbe, Matthew L. Bendall, Alexander T. Pearson, Doru Paul, Douglas F. Nixon, Marcos Pérez‐Losada, Keith A. Crandall
Software Mentions: 8
Published: about 6 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 5 years ago

10.18632/oncotarget.16961

RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature
Cited by: 24
Author(s): Ryne C. Ramaker, Brittany N. Lasseigne, Andrew A. Hardigan, Laura Palacio, David S. Gunther, R Myers, Sara J. Cooper
Software Mentions: 8
Published: over 9 years ago

10.1128/mSphere.00916-19

Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities
Cited by: 15
Author(s): Charlotte De Rudder, Marta Calatayud, Sarah Lebeer, Tom Van de Wiele
Software Mentions: 8
Published: over 6 years ago

10.3389/fcell.2021.704242

Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients
Cited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: about 5 years ago

10.1080/19490976.2021.1903289

Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota
Cited by: 9
Author(s): Mariia Taguer, Ben Shapiro, Corinne F. Maurice
Software Mentions: 8
Published: over 5 years ago

10.18632/oncotarget.10834

Dysregulated long intergenic non-coding RNA modules contribute to heart failure
Cited by: 15
Author(s): Lin Pang, Jing Hu, Guanxiong Zhang, Xiang Li, Xinxin Zhang, Fulong Yu, Yujia Lan, Jiu Hua Xu, Bo Pang, Dong Han, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 10 years ago

10.3389/fcvm.2019.00167

SS-31 Peptide Reverses the Mitochondrial Fragmentation Present in Fibroblasts From Patients With DCMA, a Mitochondrial Cardiomyopathy
Cited by: 21
Author(s): Pranav Machiraju, Xuemei Wang, Rasha Sabouny, Joshua Huang, Tian Zhao, Fatima Iqbal, Melissa A. King, Dimple Prasher, A Lodha, Nerea Jimenez-Tellez, Amir Ravandi, Bob Argiropoulos, David S. Sinasac, Aneal Khan, Timothy E. Shutt, Steven C. Greenway
Software Mentions: 8
Published: almost 7 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: about 5 years ago

10.18632/oncotarget.24506

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data
Cited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: over 8 years ago

10.3389/fonc.2020.574939

Identification of an Immune-Related Gene Signature Based on Immunogenomic Landscape Analysis to Predict the Prognosis of Adult Acute Myeloid Leukemia Patients
Cited by: 19
Author(s): Ruiqi Zhu, Huishan Tao, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 8
Published: almost 6 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: almost 8 years ago

10.18632/oncotarget.12122

Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis
Cited by: 37
Author(s): Jing Hu, Jiu Hua Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Xu Chun, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 10 years ago

10.7554/eLife.68312

A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma
Cited by: 12
Author(s): Dayana C Farhat, Matthew W. Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed‐Ali Hakimi, Christopher Swale
Software Mentions: 8
Published: about 5 years ago

10.1186/s12864-021-07898-3

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events
Cited by: 4
Author(s): Ümit Akköse, Veysel Oğulcan Kaya, Laura A. Lindsey-Boltz, Zeynep Karagöz, Adam D. Brown, Peter A. Larsen, Anne D. Yoder, Aziz Sancar, Ogün Adebali
Software Mentions: 8
Published: about 5 years ago

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Papers Mentioning DESeq2 9,583