The shakeup at Lenta.ru last year came as the government was pushing through a slew of new laws to strengthen its control over the Internet, which President Vladimir Putin has described as a "CIA project."
Some of the laws, including those giving the government broad leeway to block websites and blogs, have proven possible to get around.
"Putin and his people are sure that all things are constructed like a hierarchy, but the Internet is a net and everyone can participate in the process," said Irina Borogan, who co-authored a new book about the Russian Internet called "The Red Web."
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Other measures may prove more formidable, including a law that came into force on Sept. 1 obliging companies to keep servers containing information on Russian citizens on Russian soil. Russian Internet companies also have been asked to provide information on users of social networks and online money-transfer services.
For years, it had been the televised image of Russia that counted for the Kremlin, since television is where most Russians get their news. Independent TV stations were taken under control or pushed off the air, but cyberspace was left alone.
This began to change after the Arab Spring revolutions toppled governments across the Middle East and anger at election fraud in Russia led to a wave of unprecedented protests against President Vladimir Putin in 2011-2012.
Then came the Ukraine crisis of early 2014, when pro-Western protests drove out the Russia-friendly president and Russia responded by quickly annexing Ukraine's Crimean Peninsula.
Timchenko was fired in March 2014, after running an interview with the leader of the Ukrainian far-right group Right Sector. Most of her staff walked out with her, and some of them have joined her at a new media project-in-exile called Meduza.
The site is based in Latvia because, Timchenko says, new Russian Internet legislation makes it impossible to predict when a media organization could come under pressure.
"It's a difficult situation because none of these laws are needed - all the laws that have been brought into force in the last one and a half years. Because terror is not when they get everyone all at once, but when they can get anyone at any moment for any reason," Timchenko said in an interview with The Associated Press.
In 2014, Putin signed a bill allowing authorities to ban any online content deemed "extremist." Critics of the law have said it is so loosely worded it is difficult to tell what content is actually deemed extremist and therefore is open to abuse by authorities simply seeking to ban content they don't like.
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Another restrictive law passed in 2014 requires bloggers with more than 3,000 followers to register as media organizations.
Several opposition websites accused of extremism have been blocked altogether, including that of former world chess champion Garry Kasparov, a harsh critic of Putin now in exile.
The blog of opposition leader and anti-corruption campaigner Alexei Navalny also has been blocked, but his supporters have found ways to fight back.
"When the law came into force and Alexei Navalny's blog was blocked for the first time, we decided to get around the ban legally by creating various mirror sites of the blog," said Ruslan Leviev, an active blogger and opposition activist who has also monitored the conflict in Ukraine and Russia's military presence in Syria.
Leviev believes the government's attempts to control the Internet are failing. He describes the new measures as "fragile and faulty, and often having completely the opposite effect."
When Roskomnadzor, the federal agency that regulates the Internet, blocks an opposition website, it rises sharply in popularity because it has been blocked, Leviev said.
When the military conflict broke out in eastern Ukraine in April 2014, Russia deployed a new method to influence the flow of information on the Internet. In what has been dubbed a "hybrid war," new websites and social media accounts were set up to flood the Internet with information, blurring the lines between reality and fiction.
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"Everyone was surprised how quickly the Kremlin changed tactics with this conflict," said Andrei Soldatov, the other co-author of "The Red Web," who has studied the Internet and the Russian security services for more than a decade.
"When Russia has faced problems with its neighbors in the past, different tactics were used: DDOS (distributed denial of service) attacks against Estonia, Georgia, Lithuania, and so on," he said. "Everyone expected something similar in Ukraine, but it never happened. Instead we got these attacks of trolls."
Also in April 2014, Pavel Durov, the founder of Vkontakte, Russia's most popular social network, was forced out after he refused to cooperate with Russian authorities when they demanded information on Ukrainian protesters.
The change of management at Vkontakte, which has 240 million registered users from across the Russian-speaking world, was seen as reminiscent of the earlier taming of Russia's national television channels and Timchenko's Lenta.ru.
Yet despite the crackdown, users continued to post material that was undesirable for the Kremlin: Russian soldiers posted accounts of the fighting in eastern Ukraine that contradicted Kremlin denials that troops had been sent to support the separatists, and relatives wrote posts about funerals of Russian servicemen who had died fighting there.
The information was shared by other users and ended up being widely covered in the international media.
An information war may be on, but the porous nature of the Internet makes it nearly impossible to impose a complete ban, Soldatov said.
It is too early yet to say if he is right. The Kremlin's campaign to restrict the Internet continues apace.
Apple and Booking.com are among those who have rented servers in Russia to comply with the law that went into force on Sept. 1. Twitter and Facebook, both favorite tools of the Russian opposition, have yet to say whether they will comply.
However, Roskomnadzor, the Internet regulator, said it would have no problem blocking these services if they proved to be problematic for Russia.