cran: samr | Projects | Ecosyste.ms: Papers

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: almost 6 years ago

10.1186/s12859-015-0719-5

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics
Cited by: 3
Author(s): Αλέξανδρος Σακελλαρίου, George M. Spyrou
Software Mentions: 15
Published: about 9 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: almost 9 years ago

10.1038/s41396-018-0251-5

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals
Cited by: 56
Author(s): Amanda C. Perofsky, Rebecca J. Lewis, Lauren Ancel Meyers
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: almost 11 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: over 9 years ago

10.1186/1471-2105-8-457

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data
Cited by: 11
Author(s): André Fujita, João Ricardo Sato, Carlos Eduardo Ferreira, Mari Cleide Sogayar
Software Mentions: 10
Published: almost 17 years ago

10.1186/s13058-019-1148-6

Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications
Cited by: 70
Author(s): Pascal Jézéquel, Olivier Kerdraon, Hubert Hondermarck, Catherine Guérin‐Charbonnel, Hamza Lasla, Wilfried Gouraud, Jean-Luc Canon, Andrea Gombos, Florence Dalenc, Suzette Delaloge, Jérôme Lemonnier, Delphine Loussouarn, Véronique Verrièle, Mario Campone
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0095224

Two-Stage, In Silico Deconvolution of the Lymphocyte Compartment of the Peripheral Whole Blood Transcriptome in the Context of Acute Kidney Allograft Rejection
Cited by: 18
Author(s): Casey P. Shannon, Robert Balshaw, Raymond T. Ng, J. Wilson-McManus, Paul Keown, Robert McMaster, Bruce M. McManus, David Landsberg, Nicole M. Isbel, Greg Knoll, Scott J. Tebbutt
Software Mentions: 9
Published: over 10 years ago

10.1186/s13058-015-0550-y

Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response
Cited by: 223
Author(s): Pascal Jézéquel, Delphine Loussouarn, Catherine Guérin‐Charbonnel, Loı̈c Campion, Antoine Vanier, Wilfried Gouraud, Hamza Lasla, Catherine Guette, Isabelle Valo, Véronique Verrièle, Mario Campone
Software Mentions: 8
Published: over 9 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 7 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 6 years ago

10.1155/2017/5310198

Robust Significance Analysis of Microarrays by Minimum <i>β</i>-Divergence Method
Cited by: 10
Author(s): Shahjaman, Nishith Kumar, Md. Manir Hossain Mollah, Shakil Ahmed, Anjuman Ara Begum, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 7
Published: over 7 years ago

10.1186/1471-2105-15-132

Investigating perturbed pathway modules from gene expression data via structural equation models
Cited by: 19
Author(s): Daniele Pepe, Mario Grassi
Software Mentions: 7
Published: over 10 years ago

10.1186/s12859-020-03734-9

MADA: a web service for analysing DNA methylation array data
Cited by: 1
Author(s): Xinyu Hu, Li Tang, Linconghua Wang, Fang‐Xiang Wu, Min Li
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12920-015-0153-6

Gene-expression signature functional annotation of breast cancer tumours in function of age
Cited by: 4
Author(s): Pascal Jézéquel, Zein Sharif, Hamza Lasla, Wilfried Gouraud, Catherine Guérin‐Charbonnel, Loı̈c Campion, Stéphane Chrétien, Mario Campone
Software Mentions: 7
Published: almost 9 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 7 years ago

10.1186/cc11667

Identification of sepsis subtypes in critically ill adults using gene expression profiling
Cited by: 47
Author(s): David Maslove, Benjamin Tang, Anthony S. McLean
Software Mentions: 7
Published: over 12 years ago

10.1186/s12951-020-00767-3

Genomic instability-derived plasma extracellular vesicle-microRNA signature as a minimally invasive predictor of risk and unfavorable prognosis in breast cancer
Cited by: 47
Author(s): Siqi Bao, Ting Hu, Jiaqi Liu, Jianzhong Su, Jie Sun, Yue Ming, Jiaxin Li, Nan Wu, Hongyan Chen, Meng Zhou
Software Mentions: 7
Published: over 3 years ago

10.3390/medicina55060269

A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs
Cited by: 10
Author(s): Shahjaman, Rezanur Rahman, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-9-86

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Cited by: 75
Author(s): Frédéric Chalmel, Michael Primig
Software Mentions: 6
Published: over 16 years ago

10.1371/journal.pone.0003415

Gene Expression Profiling of Two Distinct Neuronal Populations in the Rodent Spinal Cord
Cited by: 10
Author(s): Jesper Ryge, Ann-Charlotte Westerdahl, Preben Alstrøm, Ole Kiehn
Software Mentions: 6
Published: almost 16 years ago

10.7554/eLife.11491

Localized JNK signaling regulates organ size during development
Cited by: 37
Author(s): Helen Rankin Willsey, Xiaoyan Zheng, José Carlos Pastor-Pareja, A. Jeremy Willsey, Philip A. Beachy, Tian Xu
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-018-22488-2

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer
Cited by: 55
Author(s): Rogan Magee, Aristeidis G. Telonis, Phillipe Loher, Eric Londin, Isidore Rigoutsos
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2018.01634

Robust B Cell Responses Predict Rapid Resolution of Lyme Disease
Cited by: 22
Author(s): Lisa K. Blum, Julia Z. Adamska, Dale S. Martin, Alison W. Rebman, Serra E. Elliott, Richard R.L. Cao, Monica E. Embers, Mark J. Soloski, William H. Robinson
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0174602

Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data
Cited by: 1
Author(s): Yunfeng Li, Jarrett Morrow, Benjamin A. Raby, Kelan G. Tantisira, Scott T. Weiss, Wei Huang, Weiliang Qiu
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2105-15-14

Fold change rank ordering statistics: a new method for detecting differentially expressed genes
Cited by: 99
Author(s): Doulaye Dembélé, Philippe Kastner
Software Mentions: 5
Published: over 10 years ago

10.1186/s13075-015-0682-6

Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus
Cited by: 42
Author(s): D. James Haddon, Vivian K. Diep, J. M. Price, Cindy Limb, Paul J. Utz, Imelda Balboni
Software Mentions: 5
Published: over 9 years ago

10.1093/bioinformatics/btv634

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
Cited by: 54
Author(s): Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-13-26

Postmortem cardiac tissue maintains gene expression profile even after late harvesting
Cited by: 35
Author(s): Saloni Gupta, Marc K. Halushka, Gina M. Hilton, Dan E. Arking
Software Mentions: 5
Published: over 12 years ago

10.1038/srep13135

Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury
Cited by: 119
Author(s): Sara M. Camp, Ermelinda Ceco, Carrie Evenoski, Sergei M. Danilov, Tong Zhou, Eddie T. Chiang, Liliana Moreno‐Vinasco, Brandon Mapes, Jieling Zhao, Gamze Gürsoy, Mary Elizabeth Brown, Djanybek Adyshev, Shahid Siddiqui, Hector Quijada, Saad Sammani, Eleftheria Letsiou, Laleh Saadat, Mohammed Yousef, Ting Wang, Jie Liang, Joe G.N. Garcia
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0143412

Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory
Cited by: 10
Author(s): Yusuke Tanigaki, Takanobu Higashi, Kotaro Takayama, Atsushi J. Nagano, Mie N. Honjo, Hirokazu Fukuda
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0104504

Identification of Significant Features by the Global Mean Rank Test
Cited by: 17
Author(s): Martin Klammer, J. Nikolaj Dybowski, Daniel Hoffmann, Christoph Schaab
Software Mentions: 4
Published: about 10 years ago

10.26508/lsa.201900561

Refining the adipose progenitor cell landscape in healthy and obese visceral adipose tissue using single-cell gene expression profiling
Cited by: 40
Author(s): Dong Seong Cho, Bolim Lee, Jason D. Doles
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1004604

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Cited by: 77
Author(s): Andrew D. Hoffmann, Xinan Yang, Ozanna Burnicka-Turek, Joshua D. Bosman, Xiaomeng Ren, Jeffrey D. Steimle, Steven A. Vokes, Andrew P. McMahon, Vladimir V. Kalinichenko, Ivan P. Moskowitz
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.cell.2020.05.002

Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women
Cited by: 127
Author(s): Liang Liang, Marie-Louise Hee Rasmussen, Brian D. Piening, Xiaotao Shen, Songjie Chen, Hannes L. Röst, John K. Snyder, Robert Tibshirani, Line Skotte, Norman Cy Lee, Kévin Contrepois, Bjarke Feenstra, Hanyah Zackriah, M Snyder, Mads Melbye
Software Mentions: 4
Published: over 4 years ago

10.1186/gm551

Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia
Cited by: 28
Author(s): Miriam Sonnet, Rainer Claus, Natália Becker, Manuela Zucknick, Jana Petersen, Daniel B. Lipka, Christopher C. Oakes, Mindaugas Andrulis, Amelie Lier, Michael D. Milsom, Tania Witte, Lei Gu, Soo Zin Kim-Wanner, Peter Schirmacher, Michael Wulfert, Norbert Gattermann, Michael Lübbert, Frank Rosenbauer, Michael Rehli, Lars Bullinger, Dieter Weichenhan, Christoph Plass
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1009164

The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition
Cited by: 7
Author(s): Gloria González Curto, Audrey Der Vartanian, Youcef El-Mokhtar Frarma, Line Manceau, Lorenzo Baldi, Selene Prisco, Nabila Elarouci, Frédéric Causeret, Daniil Korenkov, Muriel Rigolet, Frédéric Auradé, Aurélien de Reyniès, Vincent Contremoulins, Frédéric Relaix, Orestis Faklaris, James Briscoe, Pascale Gilardi-Hebenstreit, Vanessa Ribes
Software Mentions: 4
Published: almost 4 years ago

10.1186/1752-0509-4-121

Gene set analysis exploiting the topology of a pathway
Cited by: 62
Author(s): M. Sofia Massa, Monica Chiogna, Chiara Romualdi
Software Mentions: 4
Published: about 14 years ago

10.1186/gb-2008-9-11-r164

Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Cited by: 50
Author(s): Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, Frédéric Devaux
Software Mentions: 4
Published: over 16 years ago

10.1371/journal.pgen.1002604

Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions
Cited by: 52
Author(s): Xiaojing Yang, Houtan Noushmehr, Han Han, Claudia Andreu-Vieyra, Gangning Liang, Peter A. Jones
Software Mentions: 4
Published: over 12 years ago

10.1038/srep13364

Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases
Cited by: 26
Author(s): Yao Lu, Zhong Li, Huan Teng, Hongke Xu, Songnan Qi, Jianan He, Dayong Gu, Qijun Chen, Hongwei Ma
Software Mentions: 4
Published: about 9 years ago

10.1186/1471-2105-8-446

Novel definition files for human GeneChips based on GeneAnnot
Cited by: 110
Author(s): Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sérgio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato
Software Mentions: 4
Published: almost 17 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-019-2683-y

RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets
Cited by: 17
Author(s): Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo, Claudia Coronnello
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-13-355

Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding
Cited by: 7
Author(s): Zhou Zhu, Minmin Shi, Wenyue Hu, Heather Estrella, Jon Engebretsen, Tim Nichols, David M. Briere, Natilie Hosea, Gerrit Los, Paul A. Rejto, Andrea Fanjul
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-14-514

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data
Cited by: 15
Author(s): Leandro Hermida, Carine Poussin, Michael Stadler, Sylvain Gubian, Alain Sewer, Dimos Gaidatzis, Hans-Rudolf Hotz, Florian Martin, Vincenzo Belcastro, Stéphane Cano, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2350-13-25

Systems analysis of inflammatory bowel disease based on comprehensive gene information
Cited by: 7
Author(s): Satoru Suzuki, Takako Toda, Yutaka Fukuoka, Dennis P. Wall, Hiroshi Tanaka, Peter J. Tonellato
Software Mentions: 3
Published: over 12 years ago

10.1186/1755-8794-3-32

A sequence-based approach to identify reference genes for gene expression analysis
Cited by: 39
Author(s): Raj Chari, Kim M. Lonergan, Larissa A. Pikor, Bradley P. Coe, Chang-Qi Zhu, Tommy H.T. Chan, Calum MacAulay, Ming‐Sound Tsao, Stephen Lam, Raymond T. Ng, Wan L. Lam
Software Mentions: 3
Published: about 14 years ago

10.1186/1752-0509-8-S1-S5

Detection of type 2 diabetes related modules and genes based on epigenetic networks
Cited by: 6
Author(s): Liu Hui, Tongtong Wang, Hongbo Liu, Yanjun Wei, Guofeng Zhao, Jianzhong Su, Qiong Wu, Hong Qiao, Yan Zhang
Software Mentions: 3
Published: over 10 years ago

10.1186/s12934-019-1185-y

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Cited by: 12
Author(s): Sarada Raghavan, Sharon Chee, Juntao Li, Jérémie Poschmann, Niranjan Nagarajan, Siau Jia Wei, Chandra Verma, Farid J. Ghadessy
Software Mentions: 3
Published: about 5 years ago

10.1002/mgg3.1503

Identification of common differentially expressed genes in Turner (45,X) and Klinefelter (47,XXY) syndromes using bioinformatics analysis
Cited by: 5
Author(s): María Carolina Manotas, Juan M. Calderón, Liliana López‐Kleine, Fernando Suárez‐Obando, Olga Moreno, Alejandra Rojas
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0000242

Epigenetic Activation of a Subset of mRNAs by eIF4E Explains Its Effects on Cell Proliferation
Cited by: 203
Author(s): Yaël Mamane, Emmanuel Petroulakis, Yvan Martineau, Takaaki Sato, Ola Larsson, Vinagolu K. Rajasekhar, Nahum Sonenberg
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pone.0002737

Type I Interferon: Potential Therapeutic Target for Psoriasis?
Cited by: 253
Author(s): Yihong Yao, Laura K. Richman, Chris Morehouse, Melissa de los Reyes, Brandon W. Higgs, Anmarie Boutrin, Barbara White, Anthony J. Coyle, James G. Krueger, Peter A. Kiener, Bahija Jallal
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pone.0037108

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation
Cited by: 10
Author(s): Jamie Bates, Julia Salzman, Damon May, Patty B. Garcia, Gregory J. Hogan, Martin W. McIntosh, Mark S. Schlissel, Pat Brown
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0095347

Identification of Gene Expression Changes from Colitis to CRC in the Mouse CAC Model
Cited by: 14
Author(s): Xin Li, Yuyan Gao, Ming Yang, Qi Zhao, Guangyu Wang, Yan Yang, Yue Yang, Hui Liu, Yanqiao Zhang
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0204100

Biologically anchored knowledge expansion approach uncovers KLF4 as a novel insulin signaling regulator
Cited by: 3
Author(s): Annamalai Muthiah, Morgan S. Angulo, Natalie N. Walker, Susanna R. Keller, Jae K. Lee
Software Mentions: 3
Published: almost 6 years ago

10.15252/emmm.201607084

<scp>CDK</scp>4 phosphorylation status and a linked gene expression profile predict sensitivity to palbociclib
Cited by: 62
Author(s): Eric Raspé, Katia Coulonval, Jaime Miguel Gomes Pita, Sabine Paternot, Françoise Rothé, Laure Twyffels, Sylvain Brohée, Ligia Craciun, Denis Larsimont, Véronique Kruys, Flavienne Sandras, Isabelle Salmon, Steven Van Laere, Martine Piccart, Michail Ignatiadis, Christos Sotiriou, Pierre P. Roger
Software Mentions: 3
Published: over 7 years ago

10.1038/srep27623

Multiplex giant magnetoresistive biosensor microarrays identify interferon-associated autoantibodies in systemic lupus erythematosus
Cited by: 31
Author(s): J. Lee, D. James Haddon, Hannah Wand, J. M. Price, Vivian K. Diep, Drew A. Hall, Michelle Petri, Emily C. Baechler, Imelda Balboni, Paul J. Utz, Shan X. Wang
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.103184

Plasma proteomic profiling of young and old mice reveals cadherin-13 prevents age-related bone loss
Cited by: 14
Author(s): Yong Ryoul Yang, Mohammad Humayun Kabir, Jin Hee Park, Jae-Il Park, Jae Sook Kang, Shinyeong Ju, Yeo Jin Shin, Seung Min Lee, Jaemin Lee, Seokho Kim, Kwang-Pyo Lee, Soo Young Lee, Cheolju Lee, Kideok D. Kwon
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-017-1810-x

Robust gene selection methods using weighting schemes for microarray data analysis
Cited by: 14
Author(s): Seok Kang, Jongwoo Song
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0074712

A Degenerative Retinal Process in HIV-Associated Non-Infectious Retinopathy
Cited by: 25
Author(s): Igor Kozák, Roman Šášik, William R. Freeman, Leslee Sprague, María Laura Gomez, Lingyun Cheng, Sharif El-Emam, Francesca Mojana, Dirk-Uwe Bartsch, Jenny Bosten, Radha Ayyagari, Gary Hardiman
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0149285

CD10-Equipped Melanoma Cells Acquire Highly Potent Tumorigenic Activity: A Plausible Explanation of Their Significance for a Poor Prognosis
Cited by: 8
Author(s): Junna Oba, Takeshi Nakahara, Akiko Hashimoto-Hachiya, Min Liu, Takeru Abe, Akihito Hagihara, Takehiko Yokomizo, Masutaka Furue
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.11726

A three-gene signature for prognosis in patients with MGMT promoter-methylated glioblastoma
Cited by: 37
Author(s): Wen Wang, Lu Zhang, Zheng Wang, Fan Yang, Haoyuan Wang, Tingyu Liang, Fan Wu, Qing Lan, Jiangfei Wang, Jizong Zhao
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0094325

Genes Influenced by the Non-Muscle Isoform of Myosin Light Chain Kinase Impact Human Cancer Prognosis
Cited by: 17
Author(s): Tong Zhou, Ting Wang, Joe G.N. Garcia
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0015573

Discovery and Preclinical Validation of Salivary Transcriptomic and Proteomic Biomarkers for the Non-Invasive Detection of Breast Cancer
Cited by: 222
Author(s): Lei Zhang, Hua Xiao, Scott Karlan, Hui Zhou, Jenny Gross, David Elashoff, David Akin, Xinmin Yan, David Chia, Beth Y. Karlan, David T. Wong
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1001231

Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells
Cited by: 79
Author(s): Karsten Jürchott, Ralf‐Jürgen Kuban, Till Krech, Nils Blüthgen, Ulrike Stein, Wolfgang Walther, Christian Friese, Szymon M. Kiełbasa, Ute Ungethüm, Per Lund, Thomas Knösel, Wolfgang Kemmner, Markus Morkel, Johannes Fritzmann, Peter M. Schlag, Walter Birchmeier, Tammo Krueger, Silke Sperling, Christine Sers, Hans-Dieter Royer, Hanspeter Herzel, Reinhold Schäfer
Software Mentions: 2
Published: almost 14 years ago

10.1016/j.molonc.2014.10.012

A DNA methylation‐based definition of biologically distinct breast cancer subtypes
Cited by: 144
Author(s): Olafur A. Stefansson, Sebastián Morán, Antonio Gómez, Sergi Sayols, Carlos Arribas-Jorba, Juan Sandoval, Hólmfríður Hilmarsdóttir, Elínborg J Ólafsdóttir, Laufey Tryggvadóttír, Jón G. Jonasson, Jórunn E. Eyfjörd, Manel Esteller
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12935-018-0603-2

Expression profile analysis of antisense long non-coding RNA identifies WDFY3-AS2 as a prognostic biomarker in diffuse glioma
Cited by: 30
Author(s): Fan Wu, Zheng Zhao, Rui‐Chao Chai, Yuqing Liu, Kuanyu Wang, Zhiliang Wang, Guanzhang Li, Ruoyu Huang, Haiyan Jiang, Kenan Zhang
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.12624

LncRNA profile study reveals four-lncRNA signature associated with the prognosis of patients with anaplastic gliomas
Cited by: 57
Author(s): Wen Wang, Fan Yang, Lu Zhang, Jing Chen, Zheng Zhao, Haoyuan Wang, Fan Wu, Tingyu Liang, Xiaoyan Yan, Jiye Li, Qing Lan, Jiangfei Wang, Jizong Zhao
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2020.586688

Systematic Analysis of Competing Endogenous RNA Networks in Diffuse Large B-Cell Lymphoma and Hodgkin’s Lymphoma
Cited by: 6
Author(s): Jisoo Kang, Ping Yao, Qiang Tang, Ying Wang, Yuwei Zhou, Jian Huang
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13068-017-0720-5

Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries
Cited by: 24
Author(s): Barindra Sana, Burton K. Chia, Sarada Raghavan, R. Balamurugan, Niranjan Nagarajan, Jayasree Seayad, Farid J. Ghadessy
Software Mentions: 2
Published: over 7 years ago

10.1155/2013/267375

Identification of Lung-Cancer-Related Genes with the Shortest Path Approach in a Protein-Protein Interaction Network
Cited by: 23
Author(s): Biqing Li, Jin You, Chen Lei, Jian Zhang, Ning Zhang, Haipeng Li, Tao Huang, Xiangyin Kong, Yu-Dong Cai
Software Mentions: 2
Published: over 11 years ago

10.1186/1755-8794-1-51

Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease
Cited by: 15
Author(s): Jessica D. Tenenbaum, Michael G. Walker, Paul J. Utz, Atul J. Butte
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12916-015-0292-9

Improved survival among colon cancer patients with increased differentially expressed pathways
Cited by: 17
Author(s): Martha L. Slattery, Jennifer S. Herrick, Lila E. Mullany, Jason Gertz, Roger K. Wolff
Software Mentions: 2
Published: over 9 years ago

10.1186/s12979-017-0091-6

Transcriptomic evidence of a para-inflammatory state in the middle aged lumbar spinal cord
Cited by: 8
Author(s): William Galbavy, Yong Lu, Martin Kaczocha, Michelino Puopolo, Lixin Liu, Mario J. Rebecchi
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-1227-8

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential
Cited by: 33
Author(s): Joshua D. Welch, Jeanette Baran-Gale, Charles M. Perou, Praveen Sethupathy, Jan F. Prins
Software Mentions: 2
Published: over 9 years ago

10.1038/srep18475

Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases
Cited by: 42
Author(s): Anna Lundmark, Haleh Davanian, Tove Båge, Gunnar Johannsen, Catalin Koro, Joakim Lundeberg, Tülay Yucel‐Lindberg
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-11-483

Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types
Cited by: 14
Author(s): Noor Dawany, Aydın Tözeren
Software Mentions: 2
Published: almost 14 years ago

10.1038/s41598-018-23168-x

Identification of p38 MAPK as a novel therapeutic target for Friedreich’s ataxia
Cited by: 9
Author(s): M. Grazia Cotticelli, Shujuan J. Xia, Avinash Kaur, Daniel W. Lin, Yongping Wang, Eric Ruff, John W. Tobias, Robert B. Wilson
Software Mentions: 2
Published: over 6 years ago

10.1186/2213-0802-1-12

MicroRNAs implicated in dysregulation of gene expression following human lung transplantation
Cited by: 21
Author(s): Wei Zhang, Tong Zhou, Shwu‐Fan Ma, Roberto F. Machado, Sangeeta Bhorade, Joe G.N. Garcia
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2407-11-332

Serum estradiol levels associated with specific gene expression patterns in normal breast tissue and in breast carcinomas
Cited by: 35
Author(s): Vilde Drageset Haakensen, Trine Bjøro, Torben Lüders, Margit Riis, Ida K. Bukholm, Vessela N. Kristensen, Melissa A. Troester, Marit M. Homen, Giske Ursin, Anne Lise Børresen-Dale, Åslaug Helland
Software Mentions: 2
Published: about 13 years ago

10.1186/s12859-017-1712-y

Early response index: a statistic to discover potential early stage disease biomarkers
Cited by: 6
Author(s): Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael, Thomas G. Forsthuber, Jianqiu Michelle Zhang
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0113765

Proteomic Analysis of Highly Prevalent Amyloid A Amyloidosis Endemic to Endangered Island Foxes
Cited by: 15
Author(s): Patricia M. Gaffney, Denise M. Imai, Deana L. Clifford, Majid Ghassemian, Roman Šášik, Aaron N. Chang, Timothy OʼBrien, Judith A. Coppinger, Margarita Trejo, Eliezer Masliah, Linda Munson, Christina J. Sigurdson
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0011310

The Gene Expression Profile in the Synovium as a Predictor of the Clinical Response to Infliximab Treatment in Rheumatoid Arthritis
Cited by: 84
Author(s): Johan Lindberg, Carla A. Wijbrandts, Lisa G. M. van Baarsen, Gustavo A. Nader, Lars Klareskog, Anca I. Catrina, Rogier M. Thurlings, Margriet J. Vervoordeldonk, Joakim Lundeberg, Paul P. Tak
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0055522

Low SP1 Expression Differentially Affects Intestinal-Type Compared with Diffuse-Type Gastric Adenocarcinoma
Cited by: 18
Author(s): Hun Seok Lee, Cheol-Keun Park, Ensel Oh, Özgür Cem Erkín, Hun Soon Jung, Mi-Hyun Cho, Mi Kwon, Seoung Wan Chae, Seok-Hyung Kim, Lihui Wei, Min-Jeong Park, Su-Yeon Lee, Hyun-Kwon Yang, Lei Jia, Yoon–La Choi, Young Kee Shin
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0099121

Modulation of Chromatin Remodelling Induced by the Freshwater Cyanotoxin Cylindrospermopsin in Human Intestinal Caco-2 Cells
Cited by: 13
Author(s): Antoine Huguet, Aurélie Hatton, Romain Villot, Hélène Quenault, Yannick Blanchard, Valérie Fessard
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.7604

Gene expression analyses of primary melanomas reveal CTHRC1 as an important player in melanoma progression
Cited by: 31
Author(s): Johanna Eriksson, Vadim Le Joncour, Pirjo Nummela, Tiina Jahkola, Susanna Virolainen, Pirjo Laakkonen, Olli Saksela, Erkki Hölttä
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0082309

Vitamin D Receptor, an Important Transcription Factor Associated with Aldosterone-Producing Adenoma
Cited by: 12
Author(s): Caifeng Bi, Bo Li, Lili Du, Lishan Wang, Yingqi Zhang, Cheng Zhang, Aixia Zhai
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0223024

Acute sprint exercise transcriptome in human skeletal muscle
Cited by: 31
Author(s): Håkan Rundqvist, Andreas Montelius, Ted Österlund, Barbara Norman, Mona Esbjörnsson, Eva Jansson
Software Mentions: 1
Published: almost 5 years ago

10.7150/ijms.35269

MicroRNA-425-5p Expression Affects BRAF/RAS/MAPK Pathways In Colorectal Cancers
Cited by: 28
Author(s): Andrea Angius, Giovanna Pira, Antonio Mario Scanu, Paolo Uva, Giovanni Sotgiu, Laura Saderi, Alessandra Manca, Caterina Serra, Elena Uleri, Claudia Piu, Maurizio Caocci, Gabriele Ibba, Angelo Zinellu, Maria Rosaria Cesaraccio, Francesca Sanges, Maria Rosaria Muroni, Antonina Dolei, Paolo Cossu-Rocca, Maria Rosaria De Miglio
Software Mentions: 1
Published: over 5 years ago

10.1038/srep06107

Expression of Nicotinamide Phosphoribosyltransferase-Influenced Genes Predicts Recurrence-Free Survival in Lung and Breast Cancers
Cited by: 22
Author(s): Tong Zhou, Ting Wang, Joe G.N. Garcia
Software Mentions: 1
Published: about 10 years ago

10.1093/infdis/jiy727

Identifying the Components of Acidosis in Patients With Severe Plasmodium falciparum Malaria Using Metabolomics
Cited by: 32
Author(s): Stije J. Leopold, Aniruddha Ghose, Erik Allman, Hugh Kingston, Amir Hossain, Asok Kumar Dutta, Katherine Plewes, Kesinee Chotivanich, Nicholas P. J. Day, Joel Tärning, Markus Winterberg, Nicholas J. White, Manuel Llinás, Arjen M. Dondorp
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-10-126

Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array
Cited by: 48
Author(s): Xingyi Hang, Peiyao Li, Zhifeng Li, Wubin Qu, Ying Yu, Hualing Li, Zhiyong Shen, Hao Zheng, Yan Gao, Yonghong Wu, Minghua Deng, Zhixian Sun, Chenggang Zhang
Software Mentions: 1
Published: over 15 years ago

10.18632/oncotarget.13112

Pubertal and adult windows of susceptibility to a high animal fat diet in <i>Trp53-null</i> mammary tumorigenesis
Cited by: 20
Author(s): Yuanchang Zhu, Mark D. Aupperlee, Yong Zhao, Ying Tan, Erin L. Kirk, Xuezheng Sun, Melissa A. Troester, Richard C. Schwartz, Sandra Z. Haslam
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep16889

Nuclear factor, erythroid 2-like 2-associated molecular signature predicts lung cancer survival
Cited by: 37
Author(s): Zhi‐Gang Qian, Tong Zhou, Christopher I. Gurguis, Xiaoyan Xu, Qing Wen, Jingzhu Lv, Fang Fang, Louise Hecker, Anne E. Cress, Viswanathan Natarajan, Jeffrey R. Jacobson, Donna D. Zhang, Joe G.N. Garcia, Ting Wang
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0096577

The Long Non-Coding HOTAIR Is Modulated by Cyclic Stretch and WNT/β-CATENIN in Human Aortic Valve Cells and Is a Novel Repressor of Calcification Genes
Cited by: 99
Author(s): Katrina Carrion, Jeffrey Dyo, Vishal Patel, Roman Šášik, Salah A. Mohamed, Gary Hardiman, Vishal Nigam
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0120361

The Identification of Specific Methylation Patterns across Different Cancers
Cited by: 47
Author(s): Chunlong Zhang, Hongyan Zhao, Jie Li, Hongbo Liu, Fang Wang, Yanjun Wei, Jianzhong Su, Dongwei Zhang, Tiefu Liu, Yan Zhang
Software Mentions: 1
Published: over 9 years ago

Projects: cran: samr

Papers Mentioning samr 114