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1

Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning

Coudray, Nicolas, Ocampo, Paolo Santiago, Sakellaropoulos, Theodore, Narula, Navneet, Snuderl, Matija, Fenyö, David, Moreira, Andre L., Razavian, Narges, Tsirigos, Aristotelis

Journal:

Nature Medicine

Year:

2018

Language:

english

File:

PDF, 1.47 MB

english, 2018

2

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

Trimarchi, Thomas, Bilal, Erhan, Ntziachristos, Panagiotis, Fabbri, Giulia, Dalla-Favera, Riccardo, Tsirigos, Aristotelis, Aifantis, Iannis

Journal:

Year:

2014

Language:

english

File:

PDF, 3.34 MB

english, 2014

3

[IEEE 2001 MILCOM Proceedings Communications for Network-Centric Operations: Creating the Information Force - McLean, VA, USA (28-31 Oct. 2001)] 2001 MILCOM Proceedings Communications for Network-Centric Operations: Creating the Information Force (Cat. No.01CH37277) - Multipath routing in mobile ad hoc networks or how to route in the presence of frequent topology changes

Tsirigos, A., Haas, Z.J.

Year:

2001

Language:

english

File:

PDF, 938 KB

english, 2001

4

Ketones and lactate increase cancer cell “stemness,” driving recurrence, metastasis and poor clinical outcome in breast cancer

Martinez-Outschoorn, Ubaldo E., Prisco, Marco, Ertel, Adam, Tsirigos, Aristotelis, Lin, Zhao, Pavlides, Stephanos, Wang, Chengwang, Flomenberg, Neal, Knudsen, Erik S., Howell, Anthony, Pestell, Richar

Journal:

Year:

2011

Language:

english

File:

PDF, 6.86 MB

english, 2011

5

Ketones and lactate “fuel” tumor growth and metastasis

Bonuccelli, Gloria, Tsirigos, Aristotelis, Whitaker-Menezes, Diana, Pavlides, Stephanos, Pestell, Richard G., Chiavarina, Barbara, Frank, Philippe G., Flomenberg, Neal, Howell, Anthony, Martinez-Outsc

Journal:

Year:

2010

Language:

english

File:

PDF, 1.14 MB

english, 2010

6

Semi-supervised learning of Hidden Markov Models for biological sequence analysis

Tamposis, Ioannis A, Tsirigos, Konstantinos D, Theodoropoulou, Margarita C, Kontou, Panagiota I, Bagos, Pantelis G, Hancock, John

Journal:

Year:

2018

Language:

english

File:

PDF, 1.11 MB

english, 2018

7

SignalP 5.0 improves signal peptide predictions using deep neural networks

Almagro Armenteros, José Juan, Tsirigos, Konstantinos D., Sønderby, Casper Kaae, Petersen, Thomas Nordahl, Winther, Ole, Brunak, Søren, von Heijne, Gunnar, Nielsen, Henrik

Journal:

Nature Biotechnology

Year:

2019

Language:

english

File:

PDF, 1.40 MB

english, 2019

8

Accurate phylogenetic classification of variable-length DNA fragments

McHardy, Alice Carolyn, Martín, Héctor García, Tsirigos, Aristotelis, Hugenholtz, Philip, Rigoutsos, Isidore

Journal:

Year:

2006

Language:

english

File:

PDF, 324 KB

english, 2006

9

A conserved activation element in BMP signaling during Drosophila development

Weiss, Alexander, Charbonnier, Enrica, Ellertsdóttir, Elín, Tsirigos, Aristotelis, Wolf, Christian, Schuh, Reinhard, Pyrowolakis, George, Affolter, Markus

Journal:

Nature Structural and Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.47 MB

english, 2009

10

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia

Ntziachristos, Panagiotis, Tsirigos, Aristotelis, Vlierberghe, Pieter Van, Nedjic, Jelena, Trimarchi, Thomas, Flaherty, Maria Sol, Ferres-Marco, Dolors, da Ros, Vanina, Tang, Zuojian, Siegle, Jasmin

Journal:

Nature Medicine

Year:

2012

Language:

english

File:

PDF, 16.76 MB

english, 2012

11

A guideline to proteome-wide α-helical membrane protein topology predictions

Konstantinos D. Tsirigos, Aron Hennerdal, Lukas Käll, Arne Elofsson

Journal:

Year:

2012

Language:

english

File:

PDF, 921 KB

english, 2012

12

OMiR: Identification of associations between OMIM diseases and microRNAs

Simona Rossi, Aristotelis Tsirigos, Antonio Amoroso, Nicoletta Mascellani, Isidore Rigoutsos, George A. Calin, Stefano Volinia

Journal:

Year:

2011

Language:

english

File:

PDF, 301 KB

english, 2011

13

Multipath routing in the presence of frequent topological changes

Tsirigos, A., Haas, Z.J.

Journal:

IEEE Communications Magazine

Year:

2001

Language:

english

File:

PDF, 874 KB

english, 2001

14

Mitochondria “fuel” breast cancer metabolism: Fifteen markers of mitochondrial biogenesis label epithelial cancer cells, but are excluded from adjacent stromal cells

Sotgia, Federica, Whitaker-Menezes, Diana, Martinez-Outschoorn, Ubaldo E., Salem, Ahmed F., Tsirigos, Aristotelis, Lamb, Rebecca, Sneddon, Sharon, Hulit, James, Howell, Anthony, Lisanti, Michael P.

Journal:

Year:

2012

Language:

english

File:

PDF, 4.35 MB

english, 2012

15

The autophagic tumor stroma model of cancer

Pavlides, Stephanos, Tsirigos, Aristotelis, Migneco, Gemma, Whitaker-Menezes, Diana, Chiavarina, Barbara, Flomenberg, Neal, Frank, Philippe G., Casimiro, Mathew C., Wang, Chenguang, Pestell, Richard G

Journal:

Year:

2010

Language:

english

File:

PDF, 2.25 MB

english, 2010

16

GenomicTools: a computational platform for developing high-throughput analytics in genomics

Tsirigos, A., Haiminen, N., Bilal, E., Utro, F.

Journal:

Year:

2012

Language:

english

File:

PDF, 100 KB

english, 2012

17

Dynamic changes in the human methylome during differentiation

Laurent, L., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C. T., Low, H. M., Kin Sung, K. W., Rigoutsos, I., Loring, J., Wei, C.-L.

Journal:

Genome Research

Year:

2010

Language:

english

File:

PDF, 1.62 MB

english, 2010

18

The milk protein α-casein functions as a tumor suppressor via activation of STAT1 signaling, effectively preventing breast cancer tumor growth and metastasis

Bonuccelli, Gloria, Castello-Cros, Remedios, Capozza, Franco, Martinez-Outschoorn, Ubaldo E., Lin, Zhao, Tsirigos, Aristotelis, Xuanmao, Jiao, Whitaker-Menezes, Diana, Howell, Anthony, Lisanti, Michae

Journal:

Year:

2012

Language:

english

File:

PDF, 2.76 MB

english, 2012

19

A new computational method for the detection of horizontal gene transfer events

Journal:

Nucleic Acids Research

Year:

2005

Language:

english

File:

PDF, 4.66 MB

english, 2005

20

Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model

Bagos, Pantelis G., Tsirigos, Konstantinos D., Liakopoulos, Theodore D., Hamodrakas, Stavros J.

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 1.70 MB

english, 2008

21

Large Tilts in Transmembrane Helices Can Be Induced during Tertiary Structure Formation

Virkki, Minttu, Boekel, Carolina, Illergård, Kristoffer, Peters, Christoph, Shu, Nanjiang, Tsirigos, Konstantinos D., Elofsson, Arne, von Heijne, Gunnar, Nilsson, IngMarie

Journal:

Journal of Molecular Biology

Year:

2014

Language:

english

File:

PDF, 2.61 MB

english, 2014

22

Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia

Ntziachristos, Panagiotis, Tsirigos, Aristotelis, Welstead, G. Grant, Trimarchi, Thomas, Bakogianni, Sofia, Xu, Luyao, Loizou, Evangelia, Holmfeldt, Linda, Strikoudis, Alexandros, King, Bryan, Mullend

Journal:

Year:

2014

Language:

english

File:

PDF, 5.03 MB

english, 2014

23

Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers

Witkiewicz, Agnieszka K., Kline, Jessica, Queenan, Maria, Brody, Jonathan R., Tsirigos, Aristotelis, Bilal, Erhan, Pavlides, Stephanos, Ertel, Adam, Sotgia, Federica, Lisanti, Michael P

Journal:

Year:

2011

Language:

english

File:

PDF, 6.11 MB

english, 2011

24

SOX2 is a cancer-specific regulator of tumour initiating potential in cutaneous squamous cell carcinoma

Siegle, Jasmin M., Basin, Alice, Sastre-Perona, Ana, Yonekubo, Yoshiya, Brown, Jessie, Sennett, Rachel, Rendl, Michael, Tsirigos, Aristotelis, Carucci, John A., Schober, Markus

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.65 MB

english, 2014

25

Analysis of Multipath Routing—Part I: The Effect on the Packet Delivery Ratio

Tsirigos, A., Haas, Z.J.

Journal:

IEEE Transactions on Wireless Communications

Year:

2004

Language:

english

File:

PDF, 317 KB

english, 2004

26

Analysis of Multipath Routing, Part 2: Mitigation of the Effects of Frequently Changing Network Topologies

Tsirigos, A., Haas, Z.J.

Journal:

IEEE Transactions on Wireless Communications

Year:

2004

Language:

english

File:

PDF, 613 KB

english, 2004

27

Combinatorial Modulation of Signaling Pathways Reveals Cell-Type-Specific Requirements for Highly Efficient and Synchronous iPSC Reprogramming

Vidal, Simon E., Amlani, Bhishma, Chen, Taotao, Tsirigos, Aristotelis, Stadtfeld, Matthias

Journal:

Stem Cell Reports

Year:

2014

Language:

english

File:

PDF, 2.13 MB

english, 2014

28

Loss of stromal caveolin-1 leads to oxidative stress, mimics hypoxia and drives inflammation in the tumor microenvironment, conferring the “reverse Warburg effect”: A transcriptional informatics analysis with validation

Pavlides, Stephanos, Tsirigos, Aristotelis, Vera, Iset, Flomenberg, Neal, Frank, Philippe G., Casimiro, Mathew C., Wang, Chenguang, Fortina, Paolo, Addya, Sankar, Pestell, Richard G., Martinez-Outscho

Journal:

Year:

2010

Language:

english

File:

PDF, 6.16 MB

english, 2010

29

PREDICTION OF CELL WALL SORTING SIGNALS IN GRAM-POSITIVE BACTERIA WITH A HIDDEN MARKOV MODEL: APPLICATION TO COMPLETE GENOMES

LITOU, ZOI I., BAGOS, PANTELIS G., TSIRIGOS, KONSTANTINOS D., LIAKOPOULOS, THEODORE D., HAMODRAKAS, STAVROS J.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2008

Language:

english

File:

PDF, 782 KB

english, 2008

30

Is cancer a metabolic rebellion against host aging? In the quest for immortality, tumor cells try to save themselves by boosting mitochondrial metabolism

Ertel, Adam, Tsirigos, Aristotelis, Whitaker-Menezes, Diana, Birbe, Ruth, Pavlides, Stephanos, Martinez-Outschoorn, Ubaldo E., Pestell, Richard G., Howell, Anthony, Sotgia, Federica, Lisanti, Michael

Journal:

Year:

2012

Language:

english

File:

PDF, 3.77 MB

english, 2012

31

Anterior-posterior positional information in the absence of a strong Bicoid gradient

Ochoa-Espinosa, A., Yu, D., Tsirigos, A., Struffi, P., Small, S.

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 1.22 MB

english, 2009

32

Glycolytic cancer associated fibroblasts promote breast cancer tumor growth, without a measurable increase in angiogenesis: Evidence for stromal-epithelial metabolic coupling

Migneco, Gemma, Whitaker-Menezes, Diana, Chiavarina, Barbara, Castello-Cros, Remedios, Pavlides, Stephanos, Pestell, Richard G., Fatatis, Alessandro, Flomenberg, Neal, Tsirigos, Aristotelis, Howell, A

Journal:

Year:

2010

Language:

english

File:

PDF, 2.05 MB

english, 2010

33

ExTopoDB: a database of experimentally derived topological models of transmembrane proteins

Tsaousis, G. N., Tsirigos, K. D., Andrianou, X. D., Liakopoulos, T. D., Bagos, P. G., Hamodrakas, S. J.

Journal:

Year:

2010

Language:

english

File:

PDF, 124 KB

english, 2010

34

Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes

Rigoutsos, I., Huynh, T., Miranda, K., Tsirigos, A., McHardy, A., Platt, D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2006

Language:

english

File:

PDF, 3.26 MB

english, 2006

35

Understanding the "lethal" drivers of tumor-stroma co-evolution

Lisanti, Michael P., Martinez-Outschoorn, Ubaldo E., Chiavarina, Barbara, Pavlides, Stephanos, Whitaker-Menezes, Diana, Tsirigos, Aristotelis, Witkiewicz, Agnieszka K., Lin, Zhao, Balliet, Renee M., H

Journal:

Cancer Biology & Therapy

Year:

2010

Language:

english

File:

PDF, 1.43 MB

english, 2010

36

CXCL12-Producing Vascular Endothelial Niches Control Acute T Cell Leukemia Maintenance

Pitt, Lauren A., Tikhonova, Anastasia N., Hu, Hai, Trimarchi, Thomas, King, Bryan, Gong, Yixiao, Sanchez-Martin, Marta, Tsirigos, Aris, Littman, Dan R., Ferrando, Adolfo A., Morrison, Sean J., Fooksma

Journal:

Year:

2015

Language:

english

File:

PDF, 6.22 MB

english, 2015

37

OMPdb: a database of -barrel outer membrane proteins from Gram-negative bacteria

Tsirigos, K. D., Bagos, P. G., Hamodrakas, S. J.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 2.30 MB

english, 2011

38

Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes

Tsirigos, Aristotelis, Rigoutsos, Isidore, Stormo, Gary D.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 390 KB

english, 2009

39

Combined prediction of Tat and Sec signal peptides with hidden Markov models

Bagos, P. G., Nikolaou, E. P., Liakopoulos, T. D., Tsirigos, K. D.

Journal:

Year:

2010

Language:

english

File:

PDF, 223 KB

english, 2010

40

The autophagic tumor stroma model of cancer or “battery-operated tumor growth”

Martinez-Outschoorn, Ubaldo E., Whitaker-Menezes, Diana, Pavlides, Stephanos, Chiavarina, Barbara, Bonuccelli, Gloria, Trimmer, Casey, Tsirigos, Aristotelis, Migneco, Gemma, Witkiewicz, Agnieszka K.,

Journal:

Year:

2010

Language:

english

File:

PDF, 2.09 MB

english, 2010

41

Prediction of signal peptides in archaea

Bagos, P.G., Tsirigos, K.D., Plessas, S.K., Liakopoulos, T.D., Hamodrakas, S.J.

Journal:

Protein Engineering Design and Selection

Year:

2008

Language:

english

File:

PDF, 368 KB

english, 2008

42

Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ

Whitaker-Menezes, Diana, Martinez-Outschoorn, Ubaldo E., Flomenberg, Neal, Birbe, Ruth, Witkiewicz, Agnieszka K., Howell, Anthony, Pavlides, Stephanos, Tsirigos, Aristotelis, Ertel, Adam, Pestell, Ric

Journal:

Year:

2011

Language:

english

File:

PDF, 8.40 MB

english, 2011

43

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

J. Mullenders, B. Aranda-orgilles, P. Lhoumaud, M. Keller, J. Pae, K. Wang, C. Kayembe, P. P. Rocha, R. Raviram, Y. Gong, P. K. Premsrirut, A. Tsirigos, R. Bonneau, J. A. Skok, L. Cimmino, D. Hoehn, I

Year:

2015

Language:

english

File:

PDF, 4.36 MB

english, 2015

44

Improved topology prediction using the terminal hydrophobic helices rule.

Peters, Christoph, Tsirigos, Konstantinos D., Shu, Nanjiang, Elofsson, Arne

Journal:

Year:

2015

Language:

english

File:

PDF, 237 KB

english, 2015

45

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes

Journal:

Nucleic Acids Research

Year:

2005

Language:

english

File:

PDF, 5.15 MB

english, 2005

46

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs

Tsirigos, A., Rigoutsos, I.

Journal:

Nucleic Acids Research

Year:

2008

Language:

english

File:

PDF, 4.00 MB

english, 2008

47

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

Tsirigos, Konstantinos D., Peters, Christoph, Shu, Nanjiang, Käll, Lukas, Elofsson, Arne

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 763 KB

english, 2015

48

RNASEQ IDENTIFIES DIFFERENTIAL EXPRESSION OF PLATELET TRANSCRIPTS IN SUBJECTS WITH PERIPHERAL ARTERY DISEASE

Montenont, Emilie, Lhakhan, Tenzin, Newman, Jonathan D., Bissoon, Edna, Cambria, Matthew, Rubin, Maya, Suarez, Yajaira, Heguy, Adriana, Tsirigos, Aristotelis, Berger, Jeffrey S.

Journal:

Journal of the American College of Cardiology

Year:

2016

Language:

english

File:

PDF, 378 KB

english, 2016

49

[IEEE 2016 Annual Conference on Information Science and Systems (CISS) - Princeton, NJ, USA (2016.3.16-2016.3.18)] 2016 Annual Conference on Information Science and Systems (CISS) - Detecting community structures in Hi-C genomic data

Cabreros, Irineo, Abbe, Emmanuel, Tsirigos, Aristotelis

Year:

2016

Language:

english

File:

PDF, 539 KB

english, 2016

50

Technical Basis for EPAʼs Proposed Regulation on the Cleanup of Sites Contaminated with Radioactivity

Wolbarst, A. B., Mauro, J., Anigstein, R., Back, D., Bartlett, J. W., Beres, D., Chan, D., Clark, M. E., Doehnert, M., Durman, E., Hay, S., Hull, H. B., Lailas, N., MacKinney, J., Ralston, L., Tsirigo

Journal:

Year:

1996

Language:

english

File:

PDF, 572 KB

english, 1996

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